Starting phenix.real_space_refine on Tue Nov 19 04:51:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st0_40753/11_2024/8st0_40753_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st0_40753/11_2024/8st0_40753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st0_40753/11_2024/8st0_40753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st0_40753/11_2024/8st0_40753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st0_40753/11_2024/8st0_40753_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8st0_40753/11_2024/8st0_40753_trim.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians S 138 5.16 5 Na 1 4.78 5 C 16766 2.51 5 N 4245 2.21 5 O 4881 1.98 5 H 25323 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 51354 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 6403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6403 Classifications: {'peptide': 393} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 6197 Classifications: {'peptide': 384} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 362} Chain breaks: 1 Chain: "C" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 6197 Classifications: {'peptide': 384} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 362} Chain breaks: 1 Chain: "D" Number of atoms: 6403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6403 Classifications: {'peptide': 393} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 373} Chain breaks: 1 Chain: "E" Number of atoms: 6197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 6197 Classifications: {'peptide': 384} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 362} Chain breaks: 1 Chain: "F" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "G" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3267 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "H" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "I" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3267 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "J" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3325 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "K" Number of atoms: 3267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3267 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 202} Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {'ACH': 1, 'NAG': 1, 'OCT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'ACH': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 24.58, per 1000 atoms: 0.48 Number of scatterers: 51354 At special positions: 0 Unit cell: (168.324, 211.484, 153.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 138 16.00 Na 1 11.00 O 4881 8.00 N 4245 7.00 C 16766 6.00 H 25323 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.04 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS E 130 " - pdb=" SG CYS E 144 " distance=2.05 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 202 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 147 " - pdb=" SG CYS I 202 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 93 " distance=2.03 Simple disulfide: pdb=" SG CYS J 139 " - pdb=" SG CYS J 199 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 147 " - pdb=" SG CYS K 202 " 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 L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 701 " - " ASN A 148 " " NAG D 701 " - " ASN D 148 " " NAG L 1 " - " ASN B 143 " " NAG M 1 " - " ASN C 143 " " NAG N 1 " - " ASN E 143 " Time building additional restraints: 13.05 Conformation dependent library (CDL) restraints added in 3.9 seconds 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6176 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 49 sheets defined 30.0% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.86 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 Processing helix chain 'A' and resid 75 through 80 removed outlier: 4.239A pdb=" N GLU A 80 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 217 through 224 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 234 through 235 No H-bonds generated for 'chain 'A' and resid 234 through 235' Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.737A pdb=" N GLY A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 268 Processing helix chain 'A' and resid 278 through 306 Processing helix chain 'A' and resid 315 through 330 removed outlier: 5.839A pdb=" N VAL A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 539 through 592 Processing helix chain 'A' and resid 593 through 599 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 70 through 75 removed outlier: 4.073A pdb=" N ASP B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 209 through 226 removed outlier: 4.426A pdb=" N ILE B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Proline residue: B 219 - end of helix removed outlier: 3.722A pdb=" N LEU B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 4.572A pdb=" N VAL B 230 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 262 Processing helix chain 'B' and resid 270 through 298 Processing helix chain 'B' and resid 307 through 322 removed outlier: 3.531A pdb=" N GLU B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N LEU B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Proline residue: B 319 - end of helix Processing helix chain 'B' and resid 397 through 448 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 209 through 226 removed outlier: 4.711A pdb=" N ILE C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Proline residue: C 219 - end of helix removed outlier: 3.634A pdb=" N LEU C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 4.763A pdb=" N VAL C 230 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.585A pdb=" N GLY C 238 " --> pdb=" O SER C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 262 Processing helix chain 'C' and resid 270 through 298 Processing helix chain 'C' and resid 307 through 322 removed outlier: 3.627A pdb=" N GLU C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Proline residue: C 319 - end of helix Processing helix chain 'C' and resid 397 through 448 Processing helix chain 'D' and resid 6 through 19 Processing helix chain 'D' and resid 75 through 79 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 217 through 234 removed outlier: 4.600A pdb=" N ILE D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.711A pdb=" N LEU D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 removed outlier: 4.571A pdb=" N VAL D 238 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 246 removed outlier: 3.539A pdb=" N CYS D 245 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 246 " --> pdb=" O SER D 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 242 through 246' Processing helix chain 'D' and resid 247 through 268 Processing helix chain 'D' and resid 278 through 306 Processing helix chain 'D' and resid 315 through 330 removed outlier: 5.763A pdb=" N VAL D 326 " --> pdb=" O PHE D 322 " (cutoff:3.500A) Proline residue: D 327 - end of helix Processing helix chain 'D' and resid 539 through 591 Processing helix chain 'D' and resid 593 through 599 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 70 through 75 removed outlier: 4.240A pdb=" N ASP E 75 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 209 through 226 removed outlier: 4.758A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Proline residue: E 219 - end of helix removed outlier: 3.617A pdb=" N LEU E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 233 removed outlier: 4.381A pdb=" N VAL E 230 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 238 removed outlier: 3.565A pdb=" N GLY E 238 " --> pdb=" O SER E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 262 Processing helix chain 'E' and resid 270 through 298 Processing helix chain 'E' and resid 307 through 315 Processing helix chain 'E' and resid 316 through 322 removed outlier: 3.573A pdb=" N ALA E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 447 Processing helix chain 'F' and resid 84 through 88 Processing helix chain 'F' and resid 126 through 133 removed outlier: 3.511A pdb=" N LEU F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'G' and resid 193 through 198 removed outlier: 4.096A pdb=" N SER G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 188 through 194 removed outlier: 4.093A pdb=" N ARG H 193 " --> pdb=" O ASP H 189 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS H 194 " --> pdb=" O GLU H 190 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 33 removed outlier: 3.532A pdb=" N TYR I 33 " --> pdb=" O PHE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 removed outlier: 3.577A pdb=" N ARG I 66 " --> pdb=" O GLU I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 63 through 66' Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'I' and resid 163 through 165 No H-bonds generated for 'chain 'I' and resid 163 through 165' Processing helix chain 'J' and resid 84 through 88 removed outlier: 3.977A pdb=" N LEU J 88 " --> pdb=" O ALA J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 187 through 192 Processing helix chain 'K' and resid 29 through 33 removed outlier: 3.502A pdb=" N SER K 32 " --> pdb=" O THR K 29 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR K 33 " --> pdb=" O PHE K 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 29 through 33' Processing helix chain 'K' and resid 63 through 66 removed outlier: 3.605A pdb=" N ARG K 66 " --> pdb=" O GLU K 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 63 through 66' Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'K' and resid 207 through 210 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 88 removed outlier: 4.078A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 removed outlier: 4.078A pdb=" N ARG A 122 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET A 56 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP A 49 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR A 58 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N HIS A 68 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 37 " --> pdb=" O HIS A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 99 removed outlier: 4.503A pdb=" N SER A 155 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR A 204 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASP A 206 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR A 192 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N THR A 208 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA A 210 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 188 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 212 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 83 removed outlier: 4.139A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 79 through 83 removed outlier: 4.139A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN B 55 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU B 42 " --> pdb=" O ASN B 55 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N TRP B 57 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA B 40 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N THR B 59 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N SER B 38 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLU B 61 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N MET B 36 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N GLU B 63 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N GLN B 34 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N TYR B 65 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 13.872A pdb=" N THR B 32 " --> pdb=" O TYR B 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.081A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE B 204 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 5.081A pdb=" N SER B 150 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL B 197 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 83 removed outlier: 4.082A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 79 through 83 removed outlier: 4.082A pdb=" N SER C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASN C 55 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU C 42 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N TRP C 57 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ALA C 40 " --> pdb=" O TRP C 57 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR C 59 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER C 38 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLU C 61 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N MET C 36 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N GLU C 63 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N GLN C 34 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.292A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE C 204 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 5.292A pdb=" N SER C 150 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL C 197 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.730A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY D 121 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 84 through 88 removed outlier: 3.730A pdb=" N ARG D 122 " --> pdb=" O PHE D 118 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY D 121 " --> pdb=" O ASP D 69 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET D 56 " --> pdb=" O ASP D 49 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASP D 49 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR D 58 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU D 47 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASN D 60 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N HIS D 68 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU D 37 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.481A pdb=" N SER D 155 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR D 204 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR D 194 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASP D 206 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR D 192 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR D 208 " --> pdb=" O GLY D 190 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY D 190 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA D 210 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA D 188 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL D 212 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 79 through 83 removed outlier: 4.089A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY E 116 " --> pdb=" O ASP E 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 83 removed outlier: 4.089A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY E 116 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASN E 55 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU E 42 " --> pdb=" O ASN E 55 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N TRP E 57 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA E 40 " --> pdb=" O TRP E 57 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N THR E 59 " --> pdb=" O SER E 38 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER E 38 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLU E 61 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N MET E 36 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N GLU E 63 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N GLN E 34 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N TYR E 65 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 13.754A pdb=" N THR E 32 " --> pdb=" O TYR E 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.235A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE E 204 " --> pdb=" O VAL E 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 92 through 94 removed outlier: 5.235A pdb=" N SER E 150 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL E 197 " --> pdb=" O SER E 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 50 through 54 removed outlier: 6.415A pdb=" N TRP F 40 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N TYR F 54 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU F 38 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY F 89 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.626A pdb=" N ASN F 142 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS F 139 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER F 182 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 153 through 155 removed outlier: 4.291A pdb=" N TRP F 153 " --> pdb=" O ARG F 160 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 197 through 201 removed outlier: 3.748A pdb=" N LYS F 212 " --> pdb=" O CYS F 199 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 4 through 7 removed outlier: 4.028A pdb=" N THR G 79 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.504A pdb=" N MET G 13 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS G 39 " --> pdb=" O ARG G 48 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG G 48 " --> pdb=" O LYS G 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.504A pdb=" N MET G 13 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TYR G 109 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 127 through 130 removed outlier: 3.514A pdb=" N GLY G 151 " --> pdb=" O TYR G 182 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR G 182 " --> pdb=" O GLY G 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.525A pdb=" N VAL G 204 " --> pdb=" O VAL G 213 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.132A pdb=" N LEU H 11 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY H 89 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU H 42 " --> pdb=" O LEU H 51 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU H 51 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.563A pdb=" N VAL H 138 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER H 182 " --> pdb=" O CYS H 139 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER H 179 " --> pdb=" O THR H 169 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 158 through 159 removed outlier: 3.529A pdb=" N LYS H 154 " --> pdb=" O THR H 198 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.518A pdb=" N VAL I 19 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR I 79 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.360A pdb=" N ILE I 35 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU I 51 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 127 through 131 removed outlier: 3.747A pdb=" N LEU I 148 " --> pdb=" O TYR I 129 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY I 146 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR I 182 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL I 143 " --> pdb=" O VAL I 190 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 127 through 131 removed outlier: 3.747A pdb=" N LEU I 148 " --> pdb=" O TYR I 129 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY I 146 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR I 182 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER I 187 " --> pdb=" O HIS I 171 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 158 through 161 removed outlier: 4.292A pdb=" N CYS I 202 " --> pdb=" O LYS I 215 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS I 215 " --> pdb=" O CYS I 202 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.046A pdb=" N LEU J 11 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL J 90 " --> pdb=" O GLN J 43 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU J 38 " --> pdb=" O TYR J 54 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR J 54 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP J 40 " --> pdb=" O LEU J 52 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 119 through 120 removed outlier: 3.521A pdb=" N SER J 182 " --> pdb=" O CYS J 139 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR J 178 " --> pdb=" O ASN J 143 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 119 through 120 removed outlier: 3.521A pdb=" N SER J 182 " --> pdb=" O CYS J 139 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR J 178 " --> pdb=" O ASN J 143 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER J 179 " --> pdb=" O THR J 169 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 149 through 152 removed outlier: 3.599A pdb=" N LYS J 152 " --> pdb=" O GLU J 200 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 154 through 155 Processing sheet with id=AE8, first strand: chain 'J' and resid 196 through 198 Processing sheet with id=AE9, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.691A pdb=" N VAL K 19 " --> pdb=" O LEU K 84 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.396A pdb=" N ILE K 35 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU K 51 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP K 37 " --> pdb=" O ILE K 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 127 through 130 removed outlier: 3.543A pdb=" N CYS K 147 " --> pdb=" O SER K 186 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR K 182 " --> pdb=" O GLY K 151 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER K 187 " --> pdb=" O HIS K 171 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 142 through 144 Processing sheet with id=AF4, first strand: chain 'K' and resid 158 through 160 removed outlier: 3.983A pdb=" N CYS K 202 " --> pdb=" O LYS K 215 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS K 215 " --> pdb=" O CYS K 202 " (cutoff:3.500A) 1273 hydrogen bonds defined for protein. 3528 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: 22.06 Time building geometry restraints manager: 15.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 25292 1.02 - 1.23: 89 1.23 - 1.43: 11254 1.43 - 1.63: 15183 1.63 - 1.84: 210 Bond restraints: 52028 Sorted by residual: bond pdb=" NE ARG E 81 " pdb=" HE ARG E 81 " ideal model delta sigma weight residual 0.860 0.971 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C1 BMA L 3 " pdb=" C2 BMA L 3 " ideal model delta sigma weight residual 1.519 1.555 -0.036 2.00e-02 2.50e+03 3.27e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N THR D 157 " pdb=" CA THR D 157 " ideal model delta sigma weight residual 1.458 1.478 -0.020 1.22e-02 6.72e+03 2.78e+00 bond pdb=" N ASP J 1 " pdb=" CA ASP J 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.74e+00 ... (remaining 52023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.89: 93840 4.89 - 9.77: 18 9.77 - 14.66: 3 14.66 - 19.55: 0 19.55 - 24.43: 9 Bond angle restraints: 93870 Sorted by residual: angle pdb=" CB LEU K 53 " pdb=" CG LEU K 53 " pdb=" HG LEU K 53 " ideal model delta sigma weight residual 109.00 84.57 24.43 3.00e+00 1.11e-01 6.63e+01 angle pdb=" CB LEU I 53 " pdb=" CG LEU I 53 " pdb=" HG LEU I 53 " ideal model delta sigma weight residual 109.00 84.64 24.36 3.00e+00 1.11e-01 6.59e+01 angle pdb=" CB LEU G 53 " pdb=" CG LEU G 53 " pdb=" HG LEU G 53 " ideal model delta sigma weight residual 109.00 84.81 24.19 3.00e+00 1.11e-01 6.50e+01 angle pdb=" CD1 LEU I 53 " pdb=" CG LEU I 53 " pdb=" HG LEU I 53 " ideal model delta sigma weight residual 108.00 84.37 23.63 3.00e+00 1.11e-01 6.21e+01 angle pdb=" CD1 LEU K 53 " pdb=" CG LEU K 53 " pdb=" HG LEU K 53 " ideal model delta sigma weight residual 108.00 84.45 23.55 3.00e+00 1.11e-01 6.16e+01 ... (remaining 93865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.92: 23379 21.92 - 43.85: 1229 43.85 - 65.77: 238 65.77 - 87.70: 58 87.70 - 109.62: 15 Dihedral angle restraints: 24919 sinusoidal: 13429 harmonic: 11490 Sorted by residual: dihedral pdb=" CB CYS J 23 " pdb=" SG CYS J 23 " pdb=" SG CYS J 93 " pdb=" CB CYS J 93 " ideal model delta sinusoidal sigma weight residual 93.00 169.80 -76.80 1 1.00e+01 1.00e-02 7.41e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 93 " pdb=" CB CYS F 93 " ideal model delta sinusoidal sigma weight residual 93.00 162.76 -69.76 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS B 130 " pdb=" SG CYS B 130 " pdb=" SG CYS B 144 " pdb=" CB CYS B 144 " ideal model delta sinusoidal sigma weight residual 93.00 36.85 56.15 1 1.00e+01 1.00e-02 4.25e+01 ... (remaining 24916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.343: 4185 0.343 - 0.687: 0 0.687 - 1.030: 0 1.030 - 1.373: 0 1.373 - 1.716: 3 Chirality restraints: 4188 Sorted by residual: chirality pdb=" CG LEU G 53 " pdb=" CB LEU G 53 " pdb=" CD1 LEU G 53 " pdb=" CD2 LEU G 53 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.37e+01 chirality pdb=" CG LEU I 53 " pdb=" CB LEU I 53 " pdb=" CD1 LEU I 53 " pdb=" CD2 LEU I 53 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.14e+01 chirality pdb=" CG LEU K 53 " pdb=" CB LEU K 53 " pdb=" CD1 LEU K 53 " pdb=" CD2 LEU K 53 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.14e+01 ... (remaining 4185 not shown) Planarity restraints: 7546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 13 " 0.058 5.00e-02 4.00e+02 8.64e-02 1.19e+01 pdb=" N PRO C 14 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 14 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 14 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 216 " 0.215 9.50e-02 1.11e+02 7.23e-02 6.73e+00 pdb=" NE ARG J 216 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG J 216 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG J 216 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG J 216 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG J 216 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG J 216 " -0.008 2.00e-02 2.50e+03 pdb="HH21 ARG J 216 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG J 216 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE G 173 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO G 174 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 174 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 174 " 0.031 5.00e-02 4.00e+02 ... (remaining 7543 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.90: 176 1.90 - 2.58: 51307 2.58 - 3.25: 152214 3.25 - 3.93: 201530 3.93 - 4.60: 314100 Nonbonded interactions: 719327 Sorted by model distance: nonbonded pdb=" O MET C 431 " pdb=" OD1 ASP C 434 " model vdw 1.229 2.800 nonbonded pdb=" HG1 THR B 3 " pdb=" OD2 ASP B 75 " model vdw 1.516 2.450 nonbonded pdb=" O LYS H 55 " pdb=" H ASN H 58 " model vdw 1.531 2.450 nonbonded pdb=" O LYS J 55 " pdb=" H ASN J 58 " model vdw 1.568 2.450 nonbonded pdb=" OE1 GLU I 63 " pdb="HH12 ARG I 66 " model vdw 1.599 2.450 ... (remaining 719322 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 599 or resid 701 through 702)) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'C' selection = (chain 'E' and resid 1 through 449) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 3.910 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: 1.790 Check model and map are aligned: 0.360 Set scattering table: 0.440 Process input model: 102.850 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.004 0.057 26705 Z= 0.257 Angle : 0.578 10.282 36400 Z= 0.303 Chirality : 0.064 1.716 4188 Planarity : 0.004 0.097 4523 Dihedral : 14.839 109.620 9781 Min Nonbonded Distance : 1.229 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.15), residues: 3214 helix: 2.74 (0.18), residues: 768 sheet: -0.09 (0.16), residues: 999 loop : -0.57 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 195 HIS 0.005 0.001 HIS C 297 PHE 0.019 0.002 PHE C 254 TYR 0.013 0.001 TYR E 95 ARG 0.014 0.001 ARG J 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 4.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 24 ARG cc_start: 0.6492 (mtp-110) cc_final: 0.6126 (mtp85) REVERT: G 19 VAL cc_start: 0.5146 (t) cc_final: 0.4930 (t) REVERT: G 47 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6978 (mt-10) REVERT: H 39 GLU cc_start: 0.7463 (mt-10) cc_final: 0.7209 (mt-10) REVERT: H 47 GLN cc_start: 0.7585 (mt0) cc_final: 0.7245 (mt0) REVERT: H 115 ASP cc_start: 0.4615 (p0) cc_final: 0.4307 (p0) REVERT: I 184 LEU cc_start: 0.5385 (tt) cc_final: 0.5143 (tm) REVERT: J 24 ARG cc_start: 0.5492 (ptp-110) cc_final: 0.5266 (mmm160) REVERT: J 79 LYS cc_start: 0.5943 (mttm) cc_final: 0.5632 (mttm) REVERT: K 6 GLN cc_start: 0.7567 (tp40) cc_final: 0.7148 (tp40) REVERT: K 96 TYR cc_start: 0.8416 (m-80) cc_final: 0.8121 (m-80) outliers start: 0 outliers final: 1 residues processed: 320 average time/residue: 2.9270 time to fit residues: 1092.0486 Evaluate side-chains 267 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 4.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 582 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 chunk 133 optimal weight: 0.0000 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 0.0970 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN G 6 GLN H 43 GLN I 60 ASN K 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26705 Z= 0.181 Angle : 0.555 10.783 36400 Z= 0.291 Chirality : 0.063 1.709 4188 Planarity : 0.004 0.051 4523 Dihedral : 6.824 66.742 3744 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.19 % Allowed : 6.80 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3214 helix: 2.93 (0.18), residues: 763 sheet: -0.09 (0.16), residues: 1027 loop : -0.62 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 317 HIS 0.004 0.001 HIS H 194 PHE 0.012 0.001 PHE C 254 TYR 0.011 0.001 TYR C 428 ARG 0.004 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: C 36 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8004 (tmm) REVERT: C 189 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7781 (mt-10) REVERT: C 442 VAL cc_start: 0.7960 (OUTLIER) cc_final: 0.7662 (t) REVERT: D 171 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7174 (mtt90) REVERT: D 320 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6378 (ptt-90) REVERT: E 95 TYR cc_start: 0.8266 (OUTLIER) cc_final: 0.7688 (m-10) REVERT: E 249 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8240 (tp) REVERT: F 24 ARG cc_start: 0.6386 (mtp-110) cc_final: 0.6010 (mtp85) REVERT: F 180 MET cc_start: 0.5924 (ttt) cc_final: 0.5450 (ttt) REVERT: G 47 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7035 (mt-10) REVERT: H 39 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7590 (mt-10) REVERT: H 47 GLN cc_start: 0.7582 (mt0) cc_final: 0.7201 (mt0) REVERT: H 59 ARG cc_start: 0.7047 (ttp-110) cc_final: 0.6454 (ttt-90) REVERT: H 65 ASP cc_start: 0.5327 (t70) cc_final: 0.4954 (t0) REVERT: H 180 MET cc_start: 0.5141 (tpp) cc_final: 0.4852 (tpp) REVERT: I 107 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7823 (ttp) REVERT: J 79 LYS cc_start: 0.5911 (mttm) cc_final: 0.5593 (mttm) REVERT: K 4 GLN cc_start: 0.8009 (tt0) cc_final: 0.7388 (tt0) REVERT: K 6 GLN cc_start: 0.7676 (tp40) cc_final: 0.7240 (tp40) REVERT: K 13 MET cc_start: 0.5993 (mmm) cc_final: 0.5662 (mmm) REVERT: K 125 PRO cc_start: 0.5657 (Cg_exo) cc_final: 0.5434 (Cg_endo) REVERT: K 176 VAL cc_start: 0.4727 (t) cc_final: 0.4468 (m) outliers start: 35 outliers final: 15 residues processed: 303 average time/residue: 2.7157 time to fit residues: 968.4010 Evaluate side-chains 291 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 268 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 320 ARG Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain J residue 27 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 289 optimal weight: 6.9990 chunk 312 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 286 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 6 GLN H 43 GLN H 217 ASN I 60 ASN K 4 GLN K 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26705 Z= 0.209 Angle : 0.544 10.664 36400 Z= 0.283 Chirality : 0.063 1.705 4188 Planarity : 0.004 0.051 4523 Dihedral : 5.316 35.815 3744 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.26 % Allowed : 7.85 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3214 helix: 2.87 (0.18), residues: 769 sheet: -0.15 (0.16), residues: 1017 loop : -0.68 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 317 HIS 0.004 0.001 HIS C 297 PHE 0.017 0.001 PHE C 254 TYR 0.011 0.001 TYR A 547 ARG 0.004 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 264 time to evaluate : 3.929 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: B 214 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8193 (mp) REVERT: C 36 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8045 (tmm) REVERT: C 442 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7684 (t) REVERT: D 171 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7174 (mtt90) REVERT: E 16 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7522 (ppt170) REVERT: E 95 TYR cc_start: 0.8361 (OUTLIER) cc_final: 0.7692 (m-10) REVERT: E 249 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8290 (tp) REVERT: F 180 MET cc_start: 0.5661 (ttt) cc_final: 0.5076 (ttt) REVERT: G 47 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7025 (mt-10) REVERT: H 39 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7639 (mt-10) REVERT: H 47 GLN cc_start: 0.7607 (mt0) cc_final: 0.7236 (mt0) REVERT: H 59 ARG cc_start: 0.7055 (ttp-110) cc_final: 0.6498 (ttt-90) REVERT: H 180 MET cc_start: 0.5037 (tpp) cc_final: 0.4794 (tpp) REVERT: I 63 GLU cc_start: 0.7374 (tt0) cc_final: 0.7025 (tt0) REVERT: I 107 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7837 (ttp) REVERT: J 54 TYR cc_start: 0.7410 (p90) cc_final: 0.7117 (p90) REVERT: J 79 LYS cc_start: 0.5889 (mttm) cc_final: 0.5588 (mttm) REVERT: K 78 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7495 (mtpt) REVERT: K 176 VAL cc_start: 0.4814 (t) cc_final: 0.4462 (m) outliers start: 37 outliers final: 18 residues processed: 283 average time/residue: 2.8145 time to fit residues: 940.0892 Evaluate side-chains 283 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 257 time to evaluate : 3.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain J residue 27 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 290 optimal weight: 7.9990 chunk 307 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 275 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 50 GLN F 43 GLN G 6 GLN K 4 GLN K 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 26705 Z= 0.362 Angle : 0.640 11.340 36400 Z= 0.338 Chirality : 0.065 1.714 4188 Planarity : 0.005 0.051 4523 Dihedral : 5.415 44.938 3742 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.56 % Allowed : 8.67 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3214 helix: 2.29 (0.18), residues: 782 sheet: -0.24 (0.16), residues: 997 loop : -0.86 (0.16), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 596 HIS 0.006 0.001 HIS C 297 PHE 0.029 0.002 PHE C 254 TYR 0.022 0.002 TYR I 105 ARG 0.007 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 4.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: B 214 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8323 (mp) REVERT: C 36 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8201 (tmm) REVERT: C 442 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7766 (t) REVERT: D 104 ASP cc_start: 0.6920 (t0) cc_final: 0.6362 (m-30) REVERT: D 171 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7238 (mtt90) REVERT: D 573 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8297 (t0) REVERT: E 16 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7727 (ppt170) REVERT: E 95 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7648 (m-10) REVERT: E 249 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8354 (tp) REVERT: F 24 ARG cc_start: 0.6438 (mtp-110) cc_final: 0.5988 (mtp85) REVERT: F 111 ILE cc_start: 0.6046 (pt) cc_final: 0.5634 (pp) REVERT: F 180 MET cc_start: 0.5733 (ttt) cc_final: 0.5118 (ttt) REVERT: G 47 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7025 (mt-10) REVERT: H 39 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7434 (mt-10) REVERT: H 47 GLN cc_start: 0.7556 (mt0) cc_final: 0.7175 (mt0) REVERT: H 59 ARG cc_start: 0.7096 (ttp-110) cc_final: 0.6504 (ttt-90) REVERT: H 180 MET cc_start: 0.5060 (tpp) cc_final: 0.4807 (tpp) REVERT: I 63 GLU cc_start: 0.7372 (tt0) cc_final: 0.7050 (tt0) REVERT: I 107 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7966 (ttp) REVERT: J 54 TYR cc_start: 0.7459 (p90) cc_final: 0.7157 (p90) REVERT: J 168 TRP cc_start: 0.4554 (m-90) cc_final: 0.4132 (m-90) REVERT: K 41 ARG cc_start: 0.4853 (ptt90) cc_final: 0.4473 (mtm180) REVERT: K 47 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: K 63 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6136 (mm-30) REVERT: K 176 VAL cc_start: 0.4822 (t) cc_final: 0.4474 (m) outliers start: 46 outliers final: 15 residues processed: 291 average time/residue: 2.9691 time to fit residues: 1007.4671 Evaluate side-chains 288 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 261 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 GLU Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 63 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 228 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 212 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 156 optimal weight: 0.1980 chunk 275 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 43 GLN G 83 GLN K 4 GLN K 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26705 Z= 0.166 Angle : 0.528 10.493 36400 Z= 0.274 Chirality : 0.062 1.699 4188 Planarity : 0.004 0.045 4523 Dihedral : 4.880 32.606 3742 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.16 % Allowed : 9.59 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3214 helix: 2.81 (0.18), residues: 769 sheet: -0.23 (0.16), residues: 1018 loop : -0.79 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 596 HIS 0.003 0.001 HIS E 412 PHE 0.011 0.001 PHE C 254 TYR 0.012 0.001 TYR A 547 ARG 0.004 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 4.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8243 (mp) REVERT: C 36 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8055 (tmm) REVERT: C 442 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7709 (t) REVERT: D 104 ASP cc_start: 0.6846 (t0) cc_final: 0.6317 (m-30) REVERT: D 171 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7166 (mtt90) REVERT: E 16 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7624 (ppt170) REVERT: E 95 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7747 (m-10) REVERT: E 249 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8306 (tp) REVERT: E 317 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7314 (ttpt) REVERT: F 24 ARG cc_start: 0.6438 (mtp-110) cc_final: 0.5992 (mtp85) REVERT: F 180 MET cc_start: 0.5317 (ttt) cc_final: 0.4738 (ttt) REVERT: G 47 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6940 (mp0) REVERT: G 122 LYS cc_start: 0.4962 (tppt) cc_final: 0.4286 (tmmm) REVERT: H 39 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7446 (mt-10) REVERT: H 59 ARG cc_start: 0.7055 (ttp-110) cc_final: 0.6443 (ttt-90) REVERT: H 65 ASP cc_start: 0.5203 (t0) cc_final: 0.4832 (t0) REVERT: H 180 MET cc_start: 0.5089 (tpp) cc_final: 0.4812 (tpp) REVERT: I 63 GLU cc_start: 0.7380 (tt0) cc_final: 0.7049 (tt0) REVERT: I 107 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7778 (ttp) REVERT: I 148 LEU cc_start: 0.5013 (mp) cc_final: 0.4717 (tt) REVERT: K 13 MET cc_start: 0.5842 (mmm) cc_final: 0.5479 (mmm) REVERT: K 41 ARG cc_start: 0.4755 (ptt90) cc_final: 0.4394 (mmm-85) REVERT: K 47 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: K 63 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6157 (mm-30) REVERT: K 176 VAL cc_start: 0.4802 (t) cc_final: 0.4447 (m) outliers start: 34 outliers final: 15 residues processed: 282 average time/residue: 2.8714 time to fit residues: 949.1007 Evaluate side-chains 283 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 258 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain F residue 142 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 63 GLU Chi-restraints excluded: chain K residue 107 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 60 optimal weight: 0.3980 chunk 180 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 307 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 142 optimal weight: 0.0010 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 GLN K 4 GLN K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26705 Z= 0.177 Angle : 0.521 10.565 36400 Z= 0.270 Chirality : 0.062 1.689 4188 Planarity : 0.004 0.051 4523 Dihedral : 4.709 31.214 3742 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.29 % Allowed : 9.96 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3214 helix: 2.94 (0.18), residues: 769 sheet: -0.19 (0.16), residues: 1018 loop : -0.76 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 317 HIS 0.003 0.001 HIS E 297 PHE 0.016 0.001 PHE C 254 TYR 0.013 0.001 TYR G 105 ARG 0.007 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 262 time to evaluate : 4.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8221 (mp) REVERT: C 36 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8047 (tmm) REVERT: C 442 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7691 (t) REVERT: D 104 ASP cc_start: 0.6868 (t0) cc_final: 0.6339 (m-30) REVERT: D 171 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7188 (mtt90) REVERT: E 16 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7610 (ppt170) REVERT: E 95 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7760 (m-10) REVERT: E 249 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8301 (tp) REVERT: E 317 LYS cc_start: 0.7783 (mtpt) cc_final: 0.7309 (ttpt) REVERT: F 24 ARG cc_start: 0.6461 (mtp-110) cc_final: 0.6009 (mtp85) REVERT: F 180 MET cc_start: 0.5352 (ttt) cc_final: 0.4773 (ttt) REVERT: G 47 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6986 (mp0) REVERT: G 83 GLN cc_start: 0.7167 (OUTLIER) cc_final: 0.6928 (tp-100) REVERT: G 122 LYS cc_start: 0.4958 (tppt) cc_final: 0.4320 (tmmm) REVERT: H 39 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7424 (mt-10) REVERT: H 59 ARG cc_start: 0.7111 (ttp-110) cc_final: 0.6535 (ttt-90) REVERT: H 180 MET cc_start: 0.5021 (tpp) cc_final: 0.4730 (tpp) REVERT: I 63 GLU cc_start: 0.7377 (tt0) cc_final: 0.7044 (tt0) REVERT: I 107 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7704 (ttp) REVERT: J 87 ASP cc_start: 0.3242 (m-30) cc_final: 0.2946 (m-30) REVERT: K 11 GLU cc_start: 0.6075 (mm-30) cc_final: 0.5590 (mm-30) REVERT: K 13 MET cc_start: 0.5842 (mmm) cc_final: 0.5308 (mmm) REVERT: K 41 ARG cc_start: 0.4765 (ptt90) cc_final: 0.4410 (mmm-85) REVERT: K 47 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6627 (mp0) REVERT: K 63 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6161 (mm-30) REVERT: K 176 VAL cc_start: 0.4787 (t) cc_final: 0.4427 (m) outliers start: 38 outliers final: 16 residues processed: 280 average time/residue: 2.8754 time to fit residues: 943.5673 Evaluate side-chains 281 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 3.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 63 GLU Chi-restraints excluded: chain K residue 107 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 175 optimal weight: 0.3980 chunk 224 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 306 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 58 ASN K 4 GLN K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26705 Z= 0.223 Angle : 0.542 10.725 36400 Z= 0.282 Chirality : 0.063 1.701 4188 Planarity : 0.004 0.051 4523 Dihedral : 4.806 31.383 3742 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.39 % Allowed : 10.30 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3214 helix: 2.87 (0.18), residues: 769 sheet: -0.18 (0.16), residues: 1018 loop : -0.77 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 317 HIS 0.004 0.001 HIS E 297 PHE 0.018 0.001 PHE C 254 TYR 0.016 0.002 TYR G 105 ARG 0.005 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 4.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8267 (mp) REVERT: C 36 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8070 (tmm) REVERT: C 442 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7694 (t) REVERT: D 104 ASP cc_start: 0.6908 (t0) cc_final: 0.6361 (m-30) REVERT: D 171 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7211 (mtt90) REVERT: E 16 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7731 (ppt170) REVERT: E 95 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7712 (m-10) REVERT: E 249 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8319 (tp) REVERT: E 317 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7336 (ttpt) REVERT: F 24 ARG cc_start: 0.6439 (mtp-110) cc_final: 0.5995 (mtp85) REVERT: F 180 MET cc_start: 0.5360 (ttt) cc_final: 0.4898 (mtp) REVERT: H 39 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7421 (mt-10) REVERT: H 59 ARG cc_start: 0.7195 (ttp-110) cc_final: 0.6557 (ttt-90) REVERT: H 65 ASP cc_start: 0.5178 (t0) cc_final: 0.4823 (t0) REVERT: H 180 MET cc_start: 0.4999 (tpp) cc_final: 0.4709 (tpp) REVERT: I 63 GLU cc_start: 0.7376 (tt0) cc_final: 0.7039 (tt0) REVERT: I 107 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7834 (ttp) REVERT: J 87 ASP cc_start: 0.3117 (m-30) cc_final: 0.2782 (m-30) REVERT: K 13 MET cc_start: 0.5829 (mmm) cc_final: 0.5459 (mmm) REVERT: K 41 ARG cc_start: 0.4865 (ptt90) cc_final: 0.4458 (mmm-85) REVERT: K 47 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6641 (mp0) REVERT: K 176 VAL cc_start: 0.4784 (t) cc_final: 0.4418 (m) outliers start: 41 outliers final: 18 residues processed: 283 average time/residue: 3.0107 time to fit residues: 999.9903 Evaluate side-chains 283 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 131 LYS Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 4 GLN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 107 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 92 optimal weight: 0.0870 chunk 60 optimal weight: 0.0020 chunk 59 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 240 optimal weight: 4.9990 overall best weight: 0.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 GLN K 4 GLN K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26705 Z= 0.153 Angle : 0.509 10.451 36400 Z= 0.262 Chirality : 0.062 1.693 4188 Planarity : 0.004 0.056 4523 Dihedral : 4.597 31.345 3742 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.16 % Allowed : 10.71 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3214 helix: 3.03 (0.18), residues: 769 sheet: -0.16 (0.16), residues: 1018 loop : -0.73 (0.16), residues: 1427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 168 HIS 0.004 0.001 HIS G 206 PHE 0.013 0.001 PHE C 254 TYR 0.011 0.001 TYR E 275 ARG 0.009 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 255 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7965 (mtp-110) REVERT: B 214 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8214 (mp) REVERT: C 442 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7696 (t) REVERT: D 104 ASP cc_start: 0.6796 (t0) cc_final: 0.6271 (m-30) REVERT: D 171 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7157 (mtt90) REVERT: D 570 MET cc_start: 0.8805 (ttm) cc_final: 0.8553 (mtp) REVERT: E 16 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7601 (ppt170) REVERT: E 95 TYR cc_start: 0.8423 (OUTLIER) cc_final: 0.7744 (m-10) REVERT: E 249 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8287 (tp) REVERT: E 317 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7301 (ttpt) REVERT: F 24 ARG cc_start: 0.6429 (mtp-110) cc_final: 0.5980 (mtp85) REVERT: F 180 MET cc_start: 0.5362 (ttt) cc_final: 0.4826 (mtp) REVERT: H 39 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7398 (mt-10) REVERT: H 59 ARG cc_start: 0.7175 (ttp-110) cc_final: 0.6585 (ttt-90) REVERT: H 180 MET cc_start: 0.5036 (tpp) cc_final: 0.4744 (tpp) REVERT: I 63 GLU cc_start: 0.7375 (tt0) cc_final: 0.7060 (tt0) REVERT: I 107 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7849 (ttt) REVERT: J 87 ASP cc_start: 0.3126 (m-30) cc_final: 0.2784 (m-30) REVERT: K 13 MET cc_start: 0.5842 (mmm) cc_final: 0.5475 (mmm) REVERT: K 41 ARG cc_start: 0.4801 (ptt90) cc_final: 0.4459 (mmm-85) REVERT: K 47 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: K 63 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.6099 (mm-30) REVERT: K 176 VAL cc_start: 0.4788 (t) cc_final: 0.4416 (m) outliers start: 34 outliers final: 14 residues processed: 275 average time/residue: 2.8534 time to fit residues: 919.6701 Evaluate side-chains 272 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 3.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 169 HIS Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 63 GLU Chi-restraints excluded: chain K residue 107 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 8.9990 chunk 293 optimal weight: 9.9990 chunk 267 optimal weight: 10.0000 chunk 285 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 258 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 83 GLN K 4 GLN K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 26705 Z= 0.287 Angle : 0.584 10.995 36400 Z= 0.306 Chirality : 0.063 1.702 4188 Planarity : 0.005 0.048 4523 Dihedral : 5.001 31.381 3742 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.19 % Allowed : 10.91 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3214 helix: 2.71 (0.18), residues: 769 sheet: -0.15 (0.16), residues: 997 loop : -0.81 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 596 HIS 0.006 0.001 HIS E 297 PHE 0.024 0.002 PHE C 254 TYR 0.025 0.002 TYR G 105 ARG 0.006 0.001 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 3.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8045 (mtp-110) REVERT: A 592 PHE cc_start: 0.5791 (OUTLIER) cc_final: 0.4926 (m-10) REVERT: B 214 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8294 (mp) REVERT: C 36 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8130 (tmm) REVERT: C 442 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7697 (t) REVERT: D 104 ASP cc_start: 0.6982 (t0) cc_final: 0.6408 (m-30) REVERT: D 171 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7222 (mtt90) REVERT: E 16 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7752 (ppt170) REVERT: E 95 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.7635 (m-10) REVERT: E 249 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8351 (tp) REVERT: E 317 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7346 (ttpt) REVERT: F 84 GLU cc_start: 0.5657 (OUTLIER) cc_final: 0.4461 (mp0) REVERT: F 180 MET cc_start: 0.5376 (ttt) cc_final: 0.4917 (mtp) REVERT: H 24 ARG cc_start: 0.5130 (mtp85) cc_final: 0.4838 (mtp85) REVERT: H 39 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7404 (mt-10) REVERT: H 59 ARG cc_start: 0.7203 (ttp-110) cc_final: 0.6557 (ttt-90) REVERT: H 65 ASP cc_start: 0.5162 (t0) cc_final: 0.4813 (t0) REVERT: H 180 MET cc_start: 0.4806 (tpp) cc_final: 0.4534 (tpp) REVERT: I 63 GLU cc_start: 0.7379 (tt0) cc_final: 0.7057 (tt0) REVERT: I 107 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7891 (ttp) REVERT: J 54 TYR cc_start: 0.7456 (p90) cc_final: 0.7192 (p90) REVERT: J 87 ASP cc_start: 0.3098 (m-30) cc_final: 0.2670 (m-30) REVERT: K 41 ARG cc_start: 0.4907 (ptt90) cc_final: 0.4646 (mtm180) REVERT: K 47 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: K 63 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.6083 (mm-30) REVERT: K 176 VAL cc_start: 0.4653 (t) cc_final: 0.4282 (m) outliers start: 35 outliers final: 17 residues processed: 280 average time/residue: 2.9327 time to fit residues: 966.0742 Evaluate side-chains 289 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 259 time to evaluate : 4.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 63 GLU Chi-restraints excluded: chain K residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 6.9990 chunk 302 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 252 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 4 GLN K 6 GLN K 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26705 Z= 0.275 Angle : 0.584 11.073 36400 Z= 0.306 Chirality : 0.063 1.707 4188 Planarity : 0.005 0.065 4523 Dihedral : 5.118 39.906 3742 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.19 % Allowed : 11.02 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.15), residues: 3214 helix: 2.62 (0.18), residues: 769 sheet: -0.18 (0.16), residues: 997 loop : -0.87 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 168 HIS 0.006 0.001 HIS G 206 PHE 0.019 0.002 PHE C 254 TYR 0.025 0.002 TYR G 105 ARG 0.013 0.001 ARG A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6428 Ramachandran restraints generated. 3214 Oldfield, 0 Emsley, 3214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 4.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8025 (mtp-110) REVERT: B 214 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8347 (mp) REVERT: C 36 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8073 (tmm) REVERT: C 442 VAL cc_start: 0.8052 (OUTLIER) cc_final: 0.7761 (t) REVERT: D 104 ASP cc_start: 0.6994 (t0) cc_final: 0.6433 (m-30) REVERT: D 171 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7190 (mtt90) REVERT: D 573 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8246 (t0) REVERT: E 16 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7762 (ppt170) REVERT: E 95 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7684 (m-10) REVERT: E 249 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8354 (tp) REVERT: E 317 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7345 (ttpt) REVERT: F 84 GLU cc_start: 0.5636 (OUTLIER) cc_final: 0.4429 (mp0) REVERT: F 111 ILE cc_start: 0.6377 (pt) cc_final: 0.5917 (pp) REVERT: F 180 MET cc_start: 0.5306 (ttt) cc_final: 0.4721 (mtp) REVERT: H 24 ARG cc_start: 0.5137 (mtp85) cc_final: 0.4826 (mtp85) REVERT: H 39 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7416 (mt-10) REVERT: H 59 ARG cc_start: 0.7219 (ttp-110) cc_final: 0.6627 (ttt-90) REVERT: H 180 MET cc_start: 0.4900 (tpp) cc_final: 0.4656 (tpp) REVERT: I 63 GLU cc_start: 0.7391 (tt0) cc_final: 0.7071 (tt0) REVERT: I 107 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7853 (ttp) REVERT: I 148 LEU cc_start: 0.4889 (mp) cc_final: 0.4670 (tt) REVERT: J 87 ASP cc_start: 0.2911 (m-30) cc_final: 0.2321 (m-30) REVERT: J 168 TRP cc_start: 0.4266 (m-90) cc_final: 0.3900 (m-90) REVERT: K 41 ARG cc_start: 0.4995 (ptt90) cc_final: 0.4694 (mtm180) REVERT: K 47 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: K 63 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.6074 (mm-30) REVERT: K 176 VAL cc_start: 0.4719 (t) cc_final: 0.4339 (m) outliers start: 35 outliers final: 17 residues processed: 281 average time/residue: 3.0435 time to fit residues: 1015.0418 Evaluate side-chains 287 residues out of total 2941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 257 time to evaluate : 3.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ARG Chi-restraints excluded: chain B residue 9 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 171 ASP Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 171 ARG Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 581 ILE Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 16 ARG Chi-restraints excluded: chain E residue 95 TYR Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 107 MET Chi-restraints excluded: chain K residue 47 GLU Chi-restraints excluded: chain K residue 63 GLU Chi-restraints excluded: chain K residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 0.0770 chunk 268 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 252 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 259 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 4 GLN K 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.168784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108695 restraints weight = 82659.593| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.95 r_work: 0.3066 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26705 Z= 0.178 Angle : 0.534 10.582 36400 Z= 0.276 Chirality : 0.062 1.692 4188 Planarity : 0.004 0.065 4523 Dihedral : 4.849 32.206 3742 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.99 % Allowed : 11.42 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 3214 helix: 2.87 (0.18), residues: 769 sheet: -0.14 (0.16), residues: 997 loop : -0.81 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 317 HIS 0.005 0.001 HIS G 206 PHE 0.014 0.001 PHE C 254 TYR 0.014 0.001 TYR G 105 ARG 0.012 0.000 ARG K 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17445.65 seconds wall clock time: 303 minutes 53.99 seconds (18233.99 seconds total)