Starting phenix.real_space_refine on Thu Sep 18 16:10:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7umm_26605/09_2025/7umm_26605_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7umm_26605/09_2025/7umm_26605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7umm_26605/09_2025/7umm_26605_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7umm_26605/09_2025/7umm_26605_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7umm_26605/09_2025/7umm_26605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7umm_26605/09_2025/7umm_26605.map" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 69 5.16 5 C 11442 2.51 5 N 3090 2.21 5 O 3546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18147 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2707 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 19, 'TRANS': 321} Chain breaks: 1 Chain: "H" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1614 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 201} Chain: "L" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1672 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, I, J, M, N, E, F Time building chain proxies: 3.03, per 1000 atoms: 0.17 Number of scatterers: 18147 At special positions: 0 Unit cell: (147.675, 136.125, 155.1, 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 69 16.00 O 3546 8.00 N 3090 7.00 C 11442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 98 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 310 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 601 " - " ASN A 62 " " NAG A 602 " - " ASN A 133 " " NAG B 601 " - " ASN B 62 " " NAG B 602 " - " ASN B 133 " " NAG C 601 " - " ASN C 62 " " NAG C 602 " - " ASN C 133 " " NAG D 1 " - " ASN A 95 " " NAG E 1 " - " ASN B 95 " " NAG F 1 " - " ASN C 95 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 641.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4290 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 63 sheets defined 14.5% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 64 through 71 Processing helix chain 'A' and resid 105 through 115 removed outlier: 4.074A pdb=" N SER A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 4.185A pdb=" N TRP A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 200 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 408 through 442 Processing helix chain 'B' and resid 64 through 71 Processing helix chain 'B' and resid 105 through 115 removed outlier: 4.074A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 removed outlier: 4.184A pdb=" N TRP B 131 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 200 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 408 through 442 Processing helix chain 'C' and resid 64 through 71 Processing helix chain 'C' and resid 105 through 115 removed outlier: 4.075A pdb=" N SER C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 4.184A pdb=" N TRP C 131 " --> pdb=" O LYS C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 408 through 442 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 158 through 160 No H-bonds generated for 'chain 'H' and resid 158 through 160' Processing helix chain 'H' and resid 203 through 206 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 158 through 160 No H-bonds generated for 'chain 'I' and resid 158 through 160' Processing helix chain 'I' and resid 203 through 206 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 158 through 160 No H-bonds generated for 'chain 'J' and resid 158 through 160' Processing helix chain 'J' and resid 203 through 206 Processing helix chain 'L' and resid 83 through 87 Processing helix chain 'L' and resid 125 through 131 removed outlier: 3.708A pdb=" N LEU L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 192 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 125 through 131 removed outlier: 3.708A pdb=" N LEU M 129 " --> pdb=" O SER M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 192 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 125 through 131 removed outlier: 3.709A pdb=" N LEU N 129 " --> pdb=" O SER N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.153A pdb=" N LEU A 51 " --> pdb=" O ALA A 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.387A pdb=" N LEU A 58 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER A 118 " --> pdb=" O SER A 265 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 183 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER A 118 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 145 removed outlier: 4.416A pdb=" N CYS A 143 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 150 " --> pdb=" O CYS A 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA8, first strand: chain 'A' and resid 292 through 293 removed outlier: 3.511A pdb=" N CYS A 286 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AB1, first strand: chain 'B' and resid 37 through 39 Processing sheet with id=AB2, first strand: chain 'B' and resid 51 through 52 removed outlier: 6.153A pdb=" N LEU B 51 " --> pdb=" O ALA B 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 59 removed outlier: 6.388A pdb=" N LEU B 58 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER B 118 " --> pdb=" O SER B 265 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU B 183 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER B 118 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 140 through 145 removed outlier: 4.416A pdb=" N CYS B 143 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER B 150 " --> pdb=" O CYS B 143 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AB8, first strand: chain 'B' and resid 292 through 293 removed outlier: 3.511A pdb=" N CYS B 286 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 299 through 300 Processing sheet with id=AC1, first strand: chain 'C' and resid 37 through 39 Processing sheet with id=AC2, first strand: chain 'C' and resid 51 through 52 removed outlier: 6.154A pdb=" N LEU C 51 " --> pdb=" O ALA C 284 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.388A pdb=" N LEU C 58 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER C 118 " --> pdb=" O SER C 265 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 183 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 116 through 122 removed outlier: 3.566A pdb=" N SER C 118 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 140 through 145 removed outlier: 4.416A pdb=" N CYS C 143 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER C 150 " --> pdb=" O CYS C 143 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 171 through 173 Processing sheet with id=AC8, first strand: chain 'C' and resid 292 through 293 removed outlier: 3.512A pdb=" N CYS C 286 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 299 through 300 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.576A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.697A pdb=" N ILE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR H 178 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR H 178 " --> pdb=" O ASP H 146 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 153 through 156 removed outlier: 4.073A pdb=" N TYR H 196 " --> pdb=" O VAL H 213 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.577A pdb=" N ILE I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.696A pdb=" N ILE I 110 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR I 178 " --> pdb=" O ASP I 146 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR I 178 " --> pdb=" O ASP I 146 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 153 through 156 removed outlier: 4.072A pdb=" N TYR I 196 " --> pdb=" O VAL I 213 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.576A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.696A pdb=" N ILE J 110 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR J 178 " --> pdb=" O ASP J 146 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 128 through 132 removed outlier: 5.639A pdb=" N TYR J 178 " --> pdb=" O ASP J 146 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 153 through 156 removed outlier: 4.073A pdb=" N TYR J 196 " --> pdb=" O VAL J 213 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.111A pdb=" N LEU L 11 " --> pdb=" O GLU L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AF4, first strand: chain 'L' and resid 57 through 58 removed outlier: 6.708A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR L 53 " --> pdb=" O ILE L 37 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE L 37 " --> pdb=" O TYR L 53 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER L 135 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU L 185 " --> pdb=" O SER L 135 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL L 137 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU L 183 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU L 139 " --> pdb=" O SER L 181 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N SER L 181 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN L 141 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU L 179 " --> pdb=" O ASN L 141 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.146A pdb=" N TRP L 152 " --> pdb=" O GLN L 159 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AF8, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.110A pdb=" N LEU M 11 " --> pdb=" O GLU M 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'M' and resid 30 through 31 Processing sheet with id=AG1, first strand: chain 'M' and resid 57 through 58 removed outlier: 6.707A pdb=" N TRP M 39 " --> pdb=" O LEU M 51 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR M 53 " --> pdb=" O ILE M 37 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE M 37 " --> pdb=" O TYR M 53 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER M 135 " --> pdb=" O LEU M 185 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU M 185 " --> pdb=" O SER M 135 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL M 137 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU M 183 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU M 139 " --> pdb=" O SER M 181 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N SER M 181 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ASN M 141 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU M 179 " --> pdb=" O ASN M 141 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 157 through 159 removed outlier: 4.145A pdb=" N TRP M 152 " --> pdb=" O GLN M 159 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG5, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.111A pdb=" N LEU N 11 " --> pdb=" O GLU N 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'N' and resid 30 through 31 Processing sheet with id=AG7, first strand: chain 'N' and resid 57 through 58 removed outlier: 6.708A pdb=" N TRP N 39 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TYR N 53 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE N 37 " --> pdb=" O TYR N 53 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'N' and resid 118 through 122 removed outlier: 5.101A pdb=" N SER N 135 " --> pdb=" O LEU N 185 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU N 185 " --> pdb=" O SER N 135 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL N 137 " --> pdb=" O LEU N 183 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU N 183 " --> pdb=" O VAL N 137 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU N 139 " --> pdb=" O SER N 181 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N SER N 181 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN N 141 " --> pdb=" O LEU N 179 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU N 179 " --> pdb=" O ASN N 141 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 157 through 159 removed outlier: 4.146A pdb=" N TRP N 152 " --> pdb=" O GLN N 159 " (cutoff:3.500A) 741 hydrogen bonds defined for protein. 1854 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: 2.96 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5529 1.33 - 1.45: 3746 1.45 - 1.57: 9223 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 18588 Sorted by residual: bond pdb=" C ILE B 55 " pdb=" N ALA B 56 " ideal model delta sigma weight residual 1.331 1.251 0.080 2.07e-02 2.33e+03 1.48e+01 bond pdb=" C ILE A 55 " pdb=" N ALA A 56 " ideal model delta sigma weight residual 1.331 1.251 0.080 2.07e-02 2.33e+03 1.48e+01 bond pdb=" C ILE C 55 " pdb=" N ALA C 56 " ideal model delta sigma weight residual 1.331 1.252 0.079 2.07e-02 2.33e+03 1.47e+01 bond pdb=" C MET B 411 " pdb=" O MET B 411 " ideal model delta sigma weight residual 1.236 1.282 -0.046 1.21e-02 6.83e+03 1.43e+01 bond pdb=" C MET A 411 " pdb=" O MET A 411 " ideal model delta sigma weight residual 1.236 1.282 -0.046 1.21e-02 6.83e+03 1.42e+01 ... (remaining 18583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 24929 2.64 - 5.27: 334 5.27 - 7.91: 18 7.91 - 10.55: 0 10.55 - 13.19: 3 Bond angle restraints: 25284 Sorted by residual: angle pdb=" CB MET I 81 " pdb=" CG MET I 81 " pdb=" SD MET I 81 " ideal model delta sigma weight residual 112.70 125.89 -13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CB MET J 81 " pdb=" CG MET J 81 " pdb=" SD MET J 81 " ideal model delta sigma weight residual 112.70 125.88 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CB MET H 81 " pdb=" CG MET H 81 " pdb=" SD MET H 81 " ideal model delta sigma weight residual 112.70 125.87 -13.17 3.00e+00 1.11e-01 1.93e+01 angle pdb=" N ARG N 215 " pdb=" CA ARG N 215 " pdb=" C ARG N 215 " ideal model delta sigma weight residual 109.96 114.87 -4.91 1.49e+00 4.50e-01 1.09e+01 angle pdb=" N ARG L 215 " pdb=" CA ARG L 215 " pdb=" C ARG L 215 " ideal model delta sigma weight residual 109.96 114.84 -4.88 1.49e+00 4.50e-01 1.07e+01 ... (remaining 25279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 10350 18.03 - 36.07: 720 36.07 - 54.10: 126 54.10 - 72.14: 27 72.14 - 90.17: 15 Dihedral angle restraints: 11238 sinusoidal: 4533 harmonic: 6705 Sorted by residual: dihedral pdb=" CA MET B 279 " pdb=" C MET B 279 " pdb=" N ASP B 280 " pdb=" CA ASP B 280 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA MET C 279 " pdb=" C MET C 279 " pdb=" N ASP C 280 " pdb=" CA ASP C 280 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA MET A 279 " pdb=" C MET A 279 " pdb=" N ASP A 280 " pdb=" CA ASP A 280 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 11235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2624 0.101 - 0.202: 199 0.202 - 0.303: 0 0.303 - 0.404: 3 0.404 - 0.505: 3 Chirality restraints: 2829 Sorted by residual: chirality pdb=" CG LEU C 240 " pdb=" CB LEU C 240 " pdb=" CD1 LEU C 240 " pdb=" CD2 LEU C 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.08 -0.51 2.00e-01 2.50e+01 6.38e+00 chirality pdb=" CG LEU A 240 " pdb=" CB LEU A 240 " pdb=" CD1 LEU A 240 " pdb=" CD2 LEU A 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" CG LEU B 240 " pdb=" CB LEU B 240 " pdb=" CD1 LEU B 240 " pdb=" CD2 LEU B 240 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 2826 not shown) Planarity restraints: 3258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 165 " 0.037 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO C 166 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 166 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 166 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 165 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 166 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 166 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 166 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 165 " 0.037 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO B 166 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " 0.030 5.00e-02 4.00e+02 ... (remaining 3255 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 297 2.60 - 3.17: 17111 3.17 - 3.75: 27881 3.75 - 4.32: 41611 4.32 - 4.90: 68454 Nonbonded interactions: 155354 Sorted by model distance: nonbonded pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS H 142 " pdb=" SG CYS H 198 " model vdw 2.034 3.760 nonbonded pdb=" SG CYS J 142 " pdb=" SG CYS J 198 " model vdw 2.034 3.760 ... (remaining 155349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.240 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 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 : 0.014 0.131 18612 Z= 0.582 Angle : 0.841 13.185 25344 Z= 0.450 Chirality : 0.058 0.505 2829 Planarity : 0.005 0.055 3249 Dihedral : 13.077 90.173 6912 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.45 % Allowed : 0.30 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.16), residues: 2298 helix: -2.41 (0.27), residues: 216 sheet: -0.63 (0.18), residues: 810 loop : -1.59 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 24 TYR 0.018 0.002 TYR I 95 PHE 0.027 0.002 PHE A 119 TRP 0.033 0.002 TRP I 50 HIS 0.017 0.002 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.01390 (18588) covalent geometry : angle 0.82443 (25284) SS BOND : bond 0.00336 ( 12) SS BOND : angle 0.68321 ( 24) hydrogen bonds : bond 0.15966 ( 660) hydrogen bonds : angle 9.28832 ( 1854) link_BETA1-4 : bond 0.01184 ( 3) link_BETA1-4 : angle 6.54844 ( 9) link_NAG-ASN : bond 0.00999 ( 9) link_NAG-ASN : angle 3.50868 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 284 time to evaluate : 0.742 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: A 50 CYS cc_start: 0.6385 (m) cc_final: 0.6066 (m) REVERT: A 411 MET cc_start: 0.7604 (mmt) cc_final: 0.6951 (mmt) REVERT: B 50 CYS cc_start: 0.6435 (m) cc_final: 0.6156 (m) REVERT: B 424 ASP cc_start: 0.7349 (m-30) cc_final: 0.7146 (m-30) REVERT: C 50 CYS cc_start: 0.6400 (m) cc_final: 0.6123 (m) REVERT: C 411 MET cc_start: 0.7646 (mmt) cc_final: 0.6861 (mmt) REVERT: C 424 ASP cc_start: 0.7360 (m-30) cc_final: 0.7142 (m-30) REVERT: I 156 TRP cc_start: 0.8475 (m100) cc_final: 0.8038 (m100) REVERT: J 156 TRP cc_start: 0.8519 (m100) cc_final: 0.8312 (m100) REVERT: M 149 LYS cc_start: 0.7731 (tttp) cc_final: 0.7427 (mmmt) outliers start: 9 outliers final: 3 residues processed: 287 average time/residue: 0.1346 time to fit residues: 58.5142 Evaluate side-chains 205 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 202 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain C residue 62 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN B 59 GLN C 287 GLN H 166 HIS H 201 ASN J 65 GLN J 166 HIS L 193 HIS ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 151 GLN M 193 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.116274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.086935 restraints weight = 32177.997| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.43 r_work: 0.2924 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18612 Z= 0.188 Angle : 0.681 8.559 25344 Z= 0.347 Chirality : 0.049 0.244 2829 Planarity : 0.005 0.037 3249 Dihedral : 6.575 51.191 2763 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.95 % Allowed : 8.18 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.17), residues: 2298 helix: 0.36 (0.33), residues: 225 sheet: -0.21 (0.18), residues: 825 loop : -1.04 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 259 TYR 0.020 0.002 TYR N 144 PHE 0.016 0.002 PHE C 119 TRP 0.022 0.002 TRP I 50 HIS 0.007 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00416 (18588) covalent geometry : angle 0.66641 (25284) SS BOND : bond 0.00316 ( 12) SS BOND : angle 0.65773 ( 24) hydrogen bonds : bond 0.03865 ( 660) hydrogen bonds : angle 6.71039 ( 1854) link_BETA1-4 : bond 0.01867 ( 3) link_BETA1-4 : angle 4.87225 ( 9) link_NAG-ASN : bond 0.00458 ( 9) link_NAG-ASN : angle 3.24773 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 CYS cc_start: 0.7927 (m) cc_final: 0.7485 (m) REVERT: A 440 ARG cc_start: 0.6553 (ttp80) cc_final: 0.6280 (mmp-170) REVERT: B 50 CYS cc_start: 0.7941 (m) cc_final: 0.7504 (m) REVERT: C 50 CYS cc_start: 0.7678 (m) cc_final: 0.7260 (m) REVERT: C 420 ASP cc_start: 0.7565 (t0) cc_final: 0.7344 (t0) REVERT: C 440 ARG cc_start: 0.6611 (ttp80) cc_final: 0.6311 (mmp-170) REVERT: H 62 GLN cc_start: 0.8343 (tp40) cc_final: 0.8080 (tt0) REVERT: H 147 TYR cc_start: 0.8247 (p90) cc_final: 0.8030 (p90) REVERT: H 156 TRP cc_start: 0.8633 (m100) cc_final: 0.7990 (m100) REVERT: I 87 ARG cc_start: 0.8321 (mtm110) cc_final: 0.8081 (mtm-85) REVERT: I 125 LYS cc_start: 0.8067 (tmtt) cc_final: 0.7462 (tmtt) REVERT: I 156 TRP cc_start: 0.8587 (m100) cc_final: 0.7930 (m100) REVERT: J 147 TYR cc_start: 0.8213 (p90) cc_final: 0.8003 (p90) REVERT: M 149 LYS cc_start: 0.7783 (tttp) cc_final: 0.7471 (mmmt) outliers start: 19 outliers final: 14 residues processed: 271 average time/residue: 0.1586 time to fit residues: 63.7396 Evaluate side-chains 206 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain N residue 183 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 217 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 155 optimal weight: 0.1980 chunk 165 optimal weight: 6.9990 chunk 191 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** B 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN ** L 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.082837 restraints weight = 32976.779| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.57 r_work: 0.2834 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 18612 Z= 0.291 Angle : 0.717 8.834 25344 Z= 0.359 Chirality : 0.049 0.229 2829 Planarity : 0.005 0.043 3249 Dihedral : 6.602 51.102 2763 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.86 % Allowed : 9.59 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.17), residues: 2298 helix: 0.83 (0.34), residues: 222 sheet: -0.01 (0.18), residues: 789 loop : -1.11 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 18 TYR 0.015 0.002 TYR N 144 PHE 0.015 0.002 PHE A 119 TRP 0.024 0.002 TRP I 50 HIS 0.005 0.001 HIS B 303 Details of bonding type rmsd covalent geometry : bond 0.00670 (18588) covalent geometry : angle 0.69721 (25284) SS BOND : bond 0.00468 ( 12) SS BOND : angle 2.48178 ( 24) hydrogen bonds : bond 0.03766 ( 660) hydrogen bonds : angle 6.41626 ( 1854) link_BETA1-4 : bond 0.01153 ( 3) link_BETA1-4 : angle 4.73668 ( 9) link_NAG-ASN : bond 0.00657 ( 9) link_NAG-ASN : angle 3.71187 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.741 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: A 411 MET cc_start: 0.8592 (mmt) cc_final: 0.8016 (mmt) REVERT: B 50 CYS cc_start: 0.7512 (m) cc_final: 0.7140 (m) REVERT: B 316 SER cc_start: 0.7522 (t) cc_final: 0.7175 (p) REVERT: B 411 MET cc_start: 0.8251 (mmt) cc_final: 0.7659 (mpp) REVERT: C 268 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7504 (p90) REVERT: H 147 TYR cc_start: 0.8242 (p90) cc_final: 0.8015 (p90) REVERT: H 156 TRP cc_start: 0.8668 (m100) cc_final: 0.8032 (m100) REVERT: J 147 TYR cc_start: 0.8157 (p90) cc_final: 0.7907 (p90) REVERT: M 149 LYS cc_start: 0.7895 (tttp) cc_final: 0.7494 (mmmt) outliers start: 37 outliers final: 23 residues processed: 235 average time/residue: 0.1626 time to fit residues: 56.5738 Evaluate side-chains 217 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 22 CYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 199 ASN Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain M residue 151 GLN Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 103 optimal weight: 0.4980 chunk 156 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN ** B 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN J 65 GLN L 170 GLN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.115481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.085639 restraints weight = 32509.256| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.51 r_work: 0.2893 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18612 Z= 0.138 Angle : 0.604 7.093 25344 Z= 0.306 Chirality : 0.045 0.249 2829 Planarity : 0.004 0.044 3249 Dihedral : 6.106 47.179 2763 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.76 % Allowed : 11.90 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.17), residues: 2298 helix: 1.13 (0.35), residues: 222 sheet: 0.10 (0.18), residues: 789 loop : -0.94 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 18 TYR 0.014 0.001 TYR N 144 PHE 0.014 0.001 PHE A 119 TRP 0.019 0.001 TRP I 156 HIS 0.004 0.001 HIS N 202 Details of bonding type rmsd covalent geometry : bond 0.00312 (18588) covalent geometry : angle 0.58644 (25284) SS BOND : bond 0.00383 ( 12) SS BOND : angle 2.41381 ( 24) hydrogen bonds : bond 0.03306 ( 660) hydrogen bonds : angle 6.07928 ( 1854) link_BETA1-4 : bond 0.01062 ( 3) link_BETA1-4 : angle 4.35839 ( 9) link_NAG-ASN : bond 0.00414 ( 9) link_NAG-ASN : angle 3.04409 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.749 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: A 411 MET cc_start: 0.8426 (mmt) cc_final: 0.8015 (mmt) REVERT: B 316 SER cc_start: 0.7537 (t) cc_final: 0.7222 (p) REVERT: B 411 MET cc_start: 0.8132 (mmt) cc_final: 0.7663 (mpp) REVERT: C 316 SER cc_start: 0.7358 (t) cc_final: 0.7096 (p) REVERT: H 62 GLN cc_start: 0.8206 (tp40) cc_final: 0.7879 (tt0) REVERT: H 156 TRP cc_start: 0.8629 (m100) cc_final: 0.8046 (m100) REVERT: I 81 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8661 (ttp) REVERT: I 87 ARG cc_start: 0.8228 (mtm110) cc_final: 0.7994 (mtm-85) REVERT: I 96 CYS cc_start: 0.7993 (p) cc_final: 0.7419 (p) REVERT: J 23 LYS cc_start: 0.8304 (tttm) cc_final: 0.7744 (ttpp) REVERT: J 147 TYR cc_start: 0.8136 (p90) cc_final: 0.7864 (p90) REVERT: L 11 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8299 (mm) REVERT: M 149 LYS cc_start: 0.7870 (tttp) cc_final: 0.7511 (mmmt) REVERT: M 151 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6598 (tt0) REVERT: N 11 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8225 (mm) outliers start: 35 outliers final: 19 residues processed: 267 average time/residue: 0.1478 time to fit residues: 59.7171 Evaluate side-chains 229 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain M residue 151 GLN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 ASN ** B 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN J 65 GLN L 57 ASN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.084467 restraints weight = 32323.734| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.52 r_work: 0.2872 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18612 Z= 0.183 Angle : 0.613 7.216 25344 Z= 0.308 Chirality : 0.046 0.242 2829 Planarity : 0.005 0.046 3249 Dihedral : 6.045 47.802 2763 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.91 % Allowed : 13.40 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.17), residues: 2298 helix: 1.22 (0.35), residues: 222 sheet: 0.17 (0.18), residues: 789 loop : -0.91 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 87 TYR 0.017 0.002 TYR N 144 PHE 0.013 0.002 PHE A 119 TRP 0.017 0.001 TRP I 50 HIS 0.012 0.001 HIS L 202 Details of bonding type rmsd covalent geometry : bond 0.00420 (18588) covalent geometry : angle 0.59424 (25284) SS BOND : bond 0.00253 ( 12) SS BOND : angle 2.27597 ( 24) hydrogen bonds : bond 0.03209 ( 660) hydrogen bonds : angle 5.95229 ( 1854) link_BETA1-4 : bond 0.01552 ( 3) link_BETA1-4 : angle 4.60855 ( 9) link_NAG-ASN : bond 0.00485 ( 9) link_NAG-ASN : angle 3.19267 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.797 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: A 411 MET cc_start: 0.8460 (mmt) cc_final: 0.8024 (mmt) REVERT: C 440 ARG cc_start: 0.6629 (ttp80) cc_final: 0.6285 (mmp-170) REVERT: H 156 TRP cc_start: 0.8664 (m100) cc_final: 0.8224 (m100) REVERT: H 211 LYS cc_start: 0.8376 (tppp) cc_final: 0.8121 (ttmm) REVERT: I 81 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8698 (ttp) REVERT: I 87 ARG cc_start: 0.8219 (mtm110) cc_final: 0.7985 (mtm-85) REVERT: J 23 LYS cc_start: 0.8480 (tttm) cc_final: 0.7915 (ttpp) REVERT: J 147 TYR cc_start: 0.8150 (p90) cc_final: 0.7884 (p90) REVERT: L 11 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8284 (mm) REVERT: L 24 ARG cc_start: 0.7732 (ttm170) cc_final: 0.7198 (ttp80) REVERT: L 199 GLU cc_start: 0.7953 (pt0) cc_final: 0.7178 (pt0) REVERT: M 149 LYS cc_start: 0.7871 (tttp) cc_final: 0.7488 (mmmt) REVERT: N 11 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8231 (mm) REVERT: N 147 GLU cc_start: 0.7821 (mp0) cc_final: 0.7503 (mp0) REVERT: N 199 GLU cc_start: 0.7774 (pt0) cc_final: 0.7006 (pt0) outliers start: 38 outliers final: 24 residues processed: 258 average time/residue: 0.1608 time to fit residues: 61.4601 Evaluate side-chains 243 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 268 PHE Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 199 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 171 VAL Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 151 GLN Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 183 LEU Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 108 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 130 optimal weight: 9.9990 chunk 202 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 415 ASN I 6 GLN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086000 restraints weight = 32141.358| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.40 r_work: 0.2912 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18612 Z= 0.131 Angle : 0.572 7.159 25344 Z= 0.289 Chirality : 0.044 0.250 2829 Planarity : 0.004 0.045 3249 Dihedral : 5.728 45.525 2759 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.81 % Allowed : 14.46 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.18), residues: 2298 helix: 1.38 (0.36), residues: 222 sheet: 0.31 (0.18), residues: 789 loop : -0.77 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 18 TYR 0.015 0.001 TYR N 144 PHE 0.013 0.001 PHE A 119 TRP 0.021 0.001 TRP M 152 HIS 0.009 0.001 HIS L 202 Details of bonding type rmsd covalent geometry : bond 0.00297 (18588) covalent geometry : angle 0.55557 (25284) SS BOND : bond 0.00262 ( 12) SS BOND : angle 1.99771 ( 24) hydrogen bonds : bond 0.03020 ( 660) hydrogen bonds : angle 5.72198 ( 1854) link_BETA1-4 : bond 0.01663 ( 3) link_BETA1-4 : angle 4.49540 ( 9) link_NAG-ASN : bond 0.00420 ( 9) link_NAG-ASN : angle 2.77608 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 242 time to evaluate : 0.758 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: A 316 SER cc_start: 0.7490 (t) cc_final: 0.7198 (p) REVERT: A 411 MET cc_start: 0.8516 (mmt) cc_final: 0.8192 (mmt) REVERT: C 268 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7507 (p90) REVERT: H 62 GLN cc_start: 0.8417 (tp40) cc_final: 0.8056 (tt0) REVERT: H 156 TRP cc_start: 0.8628 (m100) cc_final: 0.8051 (m100) REVERT: H 211 LYS cc_start: 0.8307 (tppp) cc_final: 0.8032 (ttmm) REVERT: I 81 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8804 (ttp) REVERT: I 87 ARG cc_start: 0.8232 (mtm110) cc_final: 0.8018 (mtm-85) REVERT: J 23 LYS cc_start: 0.8535 (tttm) cc_final: 0.8222 (ttmm) REVERT: J 147 TYR cc_start: 0.8266 (p90) cc_final: 0.7980 (p90) REVERT: L 4 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8629 (mmt) REVERT: L 11 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8466 (mm) REVERT: L 24 ARG cc_start: 0.7881 (ttm170) cc_final: 0.7331 (ttp80) REVERT: L 85 GLU cc_start: 0.8355 (pt0) cc_final: 0.7737 (pm20) REVERT: M 149 LYS cc_start: 0.7820 (tttp) cc_final: 0.7490 (mmmt) REVERT: N 11 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8280 (mm) REVERT: N 147 GLU cc_start: 0.7913 (mp0) cc_final: 0.7579 (mp0) REVERT: N 189 ASP cc_start: 0.7659 (t0) cc_final: 0.7417 (t0) outliers start: 36 outliers final: 20 residues processed: 265 average time/residue: 0.1526 time to fit residues: 59.7104 Evaluate side-chains 243 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 200 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 195 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN M 42 GLN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.115467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.085331 restraints weight = 32622.446| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.44 r_work: 0.2895 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18612 Z= 0.158 Angle : 0.586 7.348 25344 Z= 0.293 Chirality : 0.045 0.242 2829 Planarity : 0.004 0.046 3249 Dihedral : 5.711 45.926 2759 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.86 % Allowed : 15.01 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.18), residues: 2298 helix: 1.39 (0.36), residues: 222 sheet: 0.33 (0.18), residues: 795 loop : -0.64 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 18 TYR 0.016 0.001 TYR N 144 PHE 0.013 0.001 PHE N 120 TRP 0.022 0.001 TRP M 152 HIS 0.011 0.001 HIS M 202 Details of bonding type rmsd covalent geometry : bond 0.00363 (18588) covalent geometry : angle 0.56907 (25284) SS BOND : bond 0.00272 ( 12) SS BOND : angle 1.91790 ( 24) hydrogen bonds : bond 0.02990 ( 660) hydrogen bonds : angle 5.64011 ( 1854) link_BETA1-4 : bond 0.01542 ( 3) link_BETA1-4 : angle 4.50312 ( 9) link_NAG-ASN : bond 0.00434 ( 9) link_NAG-ASN : angle 2.91695 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 0.768 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: A 316 SER cc_start: 0.7491 (t) cc_final: 0.7188 (p) REVERT: A 411 MET cc_start: 0.8503 (mmt) cc_final: 0.8179 (mmt) REVERT: C 226 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7706 (mttt) REVERT: C 268 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7545 (p90) REVERT: H 156 TRP cc_start: 0.8667 (m100) cc_final: 0.8064 (m100) REVERT: H 211 LYS cc_start: 0.8310 (tppp) cc_final: 0.8062 (ttmm) REVERT: I 23 LYS cc_start: 0.8741 (tttp) cc_final: 0.8276 (ttpp) REVERT: I 87 ARG cc_start: 0.8245 (mtm110) cc_final: 0.8043 (mtm-85) REVERT: J 23 LYS cc_start: 0.8571 (tttm) cc_final: 0.8281 (ttmm) REVERT: J 147 TYR cc_start: 0.8308 (p90) cc_final: 0.7972 (p90) REVERT: L 4 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8636 (mmt) REVERT: L 11 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8423 (mm) REVERT: L 18 ARG cc_start: 0.8097 (ttm110) cc_final: 0.7776 (ttm110) REVERT: L 24 ARG cc_start: 0.7895 (ttm170) cc_final: 0.7489 (ttp80) REVERT: M 149 LYS cc_start: 0.7489 (tttp) cc_final: 0.7149 (mmmt) REVERT: M 205 LEU cc_start: 0.5583 (OUTLIER) cc_final: 0.5162 (mt) REVERT: N 11 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8247 (mm) REVERT: N 147 GLU cc_start: 0.7878 (mp0) cc_final: 0.7504 (mp0) REVERT: N 189 ASP cc_start: 0.7555 (t0) cc_final: 0.7332 (t0) REVERT: N 205 LEU cc_start: 0.5903 (OUTLIER) cc_final: 0.5670 (mt) outliers start: 37 outliers final: 22 residues processed: 262 average time/residue: 0.1597 time to fit residues: 61.8291 Evaluate side-chains 254 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 268 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 171 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 205 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 112 optimal weight: 0.0370 chunk 96 optimal weight: 0.0970 chunk 72 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN M 170 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.117863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.084650 restraints weight = 32626.969| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.33 r_work: 0.2971 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18612 Z= 0.104 Angle : 0.554 7.389 25344 Z= 0.279 Chirality : 0.044 0.247 2829 Planarity : 0.004 0.047 3249 Dihedral : 5.349 43.379 2757 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.56 % Allowed : 15.41 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.18), residues: 2298 helix: 1.57 (0.36), residues: 222 sheet: 0.58 (0.19), residues: 792 loop : -0.64 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 18 TYR 0.012 0.001 TYR N 144 PHE 0.014 0.001 PHE N 120 TRP 0.028 0.001 TRP M 152 HIS 0.010 0.001 HIS M 202 Details of bonding type rmsd covalent geometry : bond 0.00233 (18588) covalent geometry : angle 0.53978 (25284) SS BOND : bond 0.00196 ( 12) SS BOND : angle 1.72247 ( 24) hydrogen bonds : bond 0.02821 ( 660) hydrogen bonds : angle 5.40306 ( 1854) link_BETA1-4 : bond 0.01745 ( 3) link_BETA1-4 : angle 4.47243 ( 9) link_NAG-ASN : bond 0.00446 ( 9) link_NAG-ASN : angle 2.41151 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 249 time to evaluate : 0.752 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: A 226 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7621 (mttt) REVERT: A 316 SER cc_start: 0.7359 (t) cc_final: 0.7072 (p) REVERT: C 195 GLN cc_start: 0.8705 (tt0) cc_final: 0.8185 (tp40) REVERT: H 156 TRP cc_start: 0.8634 (m100) cc_final: 0.8003 (m100) REVERT: J 23 LYS cc_start: 0.8483 (tttm) cc_final: 0.8174 (ttmm) REVERT: J 62 GLN cc_start: 0.8298 (tp40) cc_final: 0.8054 (tt0) REVERT: J 115 THR cc_start: 0.9095 (m) cc_final: 0.8889 (p) REVERT: J 147 TYR cc_start: 0.8096 (p90) cc_final: 0.7830 (p90) REVERT: J 156 TRP cc_start: 0.8650 (m100) cc_final: 0.7843 (m100) REVERT: L 4 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8457 (mmt) REVERT: L 11 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8526 (mm) REVERT: L 24 ARG cc_start: 0.7803 (ttm170) cc_final: 0.7264 (ttp80) REVERT: M 149 LYS cc_start: 0.7473 (tttp) cc_final: 0.7087 (mmmt) REVERT: M 205 LEU cc_start: 0.5513 (OUTLIER) cc_final: 0.5089 (mt) REVERT: N 11 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8248 (mm) REVERT: N 147 GLU cc_start: 0.7951 (mp0) cc_final: 0.7560 (mp0) outliers start: 31 outliers final: 20 residues processed: 273 average time/residue: 0.1573 time to fit residues: 64.1142 Evaluate side-chains 247 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 206 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 163 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 64 optimal weight: 0.0270 chunk 72 optimal weight: 0.0870 chunk 165 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.9618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 59 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN M 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.117458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.087080 restraints weight = 32457.002| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.51 r_work: 0.2927 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18612 Z= 0.117 Angle : 0.559 8.552 25344 Z= 0.282 Chirality : 0.044 0.240 2829 Planarity : 0.004 0.048 3249 Dihedral : 5.305 44.115 2757 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.51 % Allowed : 15.66 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.18), residues: 2298 helix: 1.61 (0.36), residues: 222 sheet: 0.49 (0.18), residues: 828 loop : -0.53 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 18 TYR 0.014 0.001 TYR N 144 PHE 0.013 0.001 PHE N 120 TRP 0.034 0.001 TRP M 152 HIS 0.015 0.001 HIS M 202 Details of bonding type rmsd covalent geometry : bond 0.00266 (18588) covalent geometry : angle 0.54593 (25284) SS BOND : bond 0.00209 ( 12) SS BOND : angle 1.67073 ( 24) hydrogen bonds : bond 0.02781 ( 660) hydrogen bonds : angle 5.32152 ( 1854) link_BETA1-4 : bond 0.01589 ( 3) link_BETA1-4 : angle 4.41111 ( 9) link_NAG-ASN : bond 0.00431 ( 9) link_NAG-ASN : angle 2.40227 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.785 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: A 226 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7587 (mttt) REVERT: A 316 SER cc_start: 0.7340 (t) cc_final: 0.6989 (p) REVERT: B 226 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7504 (mttm) REVERT: C 226 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7578 (mttt) REVERT: H 115 THR cc_start: 0.9077 (m) cc_final: 0.8817 (p) REVERT: H 156 TRP cc_start: 0.8609 (m100) cc_final: 0.7971 (m100) REVERT: I 65 GLN cc_start: 0.8424 (tp-100) cc_final: 0.8158 (tp40) REVERT: J 23 LYS cc_start: 0.8419 (tttm) cc_final: 0.7917 (ttpp) REVERT: J 62 GLN cc_start: 0.8114 (tp40) cc_final: 0.7889 (tt0) REVERT: J 65 GLN cc_start: 0.8518 (tp-100) cc_final: 0.8222 (tp-100) REVERT: J 147 TYR cc_start: 0.8084 (p90) cc_final: 0.7805 (p90) REVERT: L 4 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8319 (mmt) REVERT: L 11 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8487 (mm) REVERT: L 24 ARG cc_start: 0.7666 (ttm170) cc_final: 0.7157 (ttp80) REVERT: M 149 LYS cc_start: 0.7418 (tttp) cc_final: 0.7033 (mmmt) REVERT: M 152 TRP cc_start: 0.6787 (m100) cc_final: 0.6559 (m100) REVERT: M 205 LEU cc_start: 0.5477 (OUTLIER) cc_final: 0.5037 (mt) REVERT: N 11 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8169 (mm) REVERT: N 147 GLU cc_start: 0.7944 (mp0) cc_final: 0.7551 (mp0) outliers start: 30 outliers final: 22 residues processed: 251 average time/residue: 0.1534 time to fit residues: 57.8206 Evaluate side-chains 247 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 1 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 204 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 189 optimal weight: 0.0170 chunk 114 optimal weight: 6.9990 overall best weight: 1.4220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN C 59 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.116776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086637 restraints weight = 32351.636| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.41 r_work: 0.2926 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18612 Z= 0.137 Angle : 0.578 11.520 25344 Z= 0.289 Chirality : 0.044 0.238 2829 Planarity : 0.004 0.048 3249 Dihedral : 5.352 44.541 2757 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.56 % Allowed : 15.71 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.18), residues: 2298 helix: 1.54 (0.36), residues: 222 sheet: 0.55 (0.18), residues: 822 loop : -0.52 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 18 TYR 0.015 0.001 TYR N 144 PHE 0.013 0.001 PHE N 120 TRP 0.031 0.001 TRP M 152 HIS 0.013 0.001 HIS M 202 Details of bonding type rmsd covalent geometry : bond 0.00316 (18588) covalent geometry : angle 0.56472 (25284) SS BOND : bond 0.00221 ( 12) SS BOND : angle 1.66951 ( 24) hydrogen bonds : bond 0.02809 ( 660) hydrogen bonds : angle 5.32926 ( 1854) link_BETA1-4 : bond 0.01580 ( 3) link_BETA1-4 : angle 4.45908 ( 9) link_NAG-ASN : bond 0.00456 ( 9) link_NAG-ASN : angle 2.43359 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4596 Ramachandran restraints generated. 2298 Oldfield, 0 Emsley, 2298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7721 (mttt) REVERT: A 316 SER cc_start: 0.7358 (t) cc_final: 0.7044 (p) REVERT: B 226 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7635 (mttm) REVERT: C 226 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7652 (mttt) REVERT: H 115 THR cc_start: 0.9164 (m) cc_final: 0.8921 (p) REVERT: H 156 TRP cc_start: 0.8619 (m100) cc_final: 0.7961 (m100) REVERT: I 65 GLN cc_start: 0.8613 (tp-100) cc_final: 0.8294 (tp-100) REVERT: I 199 ASN cc_start: 0.7202 (p0) cc_final: 0.6957 (p0) REVERT: J 23 LYS cc_start: 0.8540 (tttm) cc_final: 0.8043 (ttpp) REVERT: J 62 GLN cc_start: 0.8352 (tp40) cc_final: 0.8097 (tt0) REVERT: J 65 GLN cc_start: 0.8664 (tp-100) cc_final: 0.8372 (tp40) REVERT: J 147 TYR cc_start: 0.8171 (p90) cc_final: 0.7919 (p90) REVERT: L 4 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8519 (mmt) REVERT: L 11 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8483 (mm) REVERT: L 24 ARG cc_start: 0.7847 (ttm170) cc_final: 0.7312 (ttp80) REVERT: M 149 LYS cc_start: 0.7352 (tttp) cc_final: 0.7001 (mmmt) REVERT: M 205 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5246 (mt) REVERT: N 11 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8239 (mm) REVERT: N 147 GLU cc_start: 0.8034 (mp0) cc_final: 0.7676 (mp0) outliers start: 31 outliers final: 21 residues processed: 248 average time/residue: 0.1538 time to fit residues: 57.1553 Evaluate side-chains 249 residues out of total 1995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 226 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 226 LYS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 282 CYS Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain C residue 282 CYS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 198 CYS Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 185 THR Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 185 THR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 189 ASP Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain N residue 11 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 196 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 156 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 149 optimal weight: 0.0270 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 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 = 0.3621 r_free = 0.3621 target = 0.117503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.084046 restraints weight = 32633.525| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.34 r_work: 0.2963 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18612 Z= 0.120 Angle : 0.561 8.334 25344 Z= 0.282 Chirality : 0.044 0.236 2829 Planarity : 0.004 0.049 3249 Dihedral : 5.285 44.128 2757 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.56 % Allowed : 15.91 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.18), residues: 2298 helix: 1.57 (0.35), residues: 222 sheet: 0.53 (0.18), residues: 834 loop : -0.47 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 18 TYR 0.014 0.001 TYR N 144 PHE 0.013 0.001 PHE N 120 TRP 0.029 0.001 TRP M 152 HIS 0.012 0.001 HIS M 202 Details of bonding type rmsd covalent geometry : bond 0.00275 (18588) covalent geometry : angle 0.54740 (25284) SS BOND : bond 0.00195 ( 12) SS BOND : angle 1.62037 ( 24) hydrogen bonds : bond 0.02763 ( 660) hydrogen bonds : angle 5.27215 ( 1854) link_BETA1-4 : bond 0.01591 ( 3) link_BETA1-4 : angle 4.43430 ( 9) link_NAG-ASN : bond 0.00427 ( 9) link_NAG-ASN : angle 2.35128 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4800.90 seconds wall clock time: 83 minutes 28.27 seconds (5008.27 seconds total)