Starting phenix.real_space_refine on Tue Sep 24 18:50:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/09_2024/7add_11724.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/09_2024/7add_11724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/09_2024/7add_11724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/09_2024/7add_11724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/09_2024/7add_11724.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7add_11724/09_2024/7add_11724.cif" } resolution = 4.3 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= 0.003 sd= 0.017 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 98 5.49 5 Mg 6 5.21 5 S 223 5.16 5 Be 5 3.05 5 C 32023 2.51 5 N 9121 2.21 5 O 10117 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 51610 Number of models: 1 Model: "" Number of chains: 21 Chain: "a" Number of atoms: 3280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3280 Classifications: {'peptide': 417} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 398} Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3852 Classifications: {'peptide': 495} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 480} Chain: "U" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1825 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Chain: "V" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2504 Classifications: {'peptide': 321} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 303} Chain: "W" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "X" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'PCIS': 2, 'PTRANS': 54, 'TRANS': 1283} Chain: "Y" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1358, 10545 Classifications: {'peptide': 1358} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1302} Chain: "K" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 538 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain breaks: 1 Chain: "L" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 704 Classifications: {'DNA': 35} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 34} Chain breaks: 1 Chain: "R" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 590 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 22} Chain breaks: 1 Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "c" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 36 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "b" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39504 SG CYS Y 70 54.748 119.874 118.065 1.00187.89 S ATOM 39518 SG CYS Y 72 54.953 116.532 119.073 1.00178.12 S ATOM 39626 SG CYS Y 85 52.811 118.016 121.591 1.00190.63 S ATOM 45338 SG CYS Y 814 69.868 185.845 119.810 1.00113.47 S ATOM 45903 SG CYS Y 888 72.009 181.687 119.875 1.00100.48 S ATOM 45954 SG CYS Y 895 68.988 181.850 118.048 1.00102.60 S ATOM 45975 SG CYS Y 898 72.521 184.573 117.833 1.00 95.45 S Restraints were copied for chains: b, c, d, e, f Time building chain proxies: 20.77, per 1000 atoms: 0.40 Number of scatterers: 51610 At special positions: 0 Unit cell: (162.44, 228.16, 194.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 223 16.00 P 98 15.00 Mg 6 11.99 F 15 9.00 O 10117 8.00 N 9121 7.00 C 32023 6.00 Be 5 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.52 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y1502 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 70 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 85 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 72 " pdb=" ZN Y1503 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 888 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 898 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 895 " pdb="ZN ZN Y1503 " - pdb=" SG CYS Y 814 " Number of angles added : 6 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11746 Finding SS restraints... Secondary structure from input PDB file: 234 helices and 63 sheets defined 41.6% alpha, 16.7% beta 28 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 13.79 Creating SS restraints... Processing helix chain 'f' and resid 3 through 8 Processing helix chain 'f' and resid 10 through 21 Processing helix chain 'f' and resid 30 through 45 Processing helix chain 'f' and resid 82 through 90 removed outlier: 3.798A pdb=" N ILE f 86 " --> pdb=" O SER f 82 " (cutoff:3.500A) Processing helix chain 'f' and resid 125 through 129 removed outlier: 3.701A pdb=" N ARG f 128 " --> pdb=" O GLU f 125 " (cutoff:3.500A) Processing helix chain 'f' and resid 155 through 166 removed outlier: 4.036A pdb=" N ALA f 159 " --> pdb=" O GLU f 155 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU f 162 " --> pdb=" O THR f 158 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 199 Processing helix chain 'f' and resid 212 through 220 removed outlier: 3.539A pdb=" N VAL f 216 " --> pdb=" O ARG f 212 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 256 removed outlier: 3.705A pdb=" N HIS f 239 " --> pdb=" O PRO f 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 278 Processing helix chain 'f' and resid 291 through 293 No H-bonds generated for 'chain 'f' and resid 291 through 293' Processing helix chain 'f' and resid 294 through 303 Processing helix chain 'f' and resid 325 through 337 removed outlier: 4.683A pdb=" N GLY f 337 " --> pdb=" O GLU f 333 " (cutoff:3.500A) Processing helix chain 'f' and resid 346 through 351 Processing helix chain 'f' and resid 367 through 372 removed outlier: 3.807A pdb=" N THR f 372 " --> pdb=" O GLU f 369 " (cutoff:3.500A) Processing helix chain 'f' and resid 373 through 388 Processing helix chain 'f' and resid 392 through 405 Processing helix chain 'f' and resid 408 through 417 removed outlier: 3.510A pdb=" N LYS f 417 " --> pdb=" O PHE f 413 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 8 Processing helix chain 'a' and resid 10 through 21 Processing helix chain 'a' and resid 30 through 45 Processing helix chain 'a' and resid 82 through 90 removed outlier: 3.797A pdb=" N ILE a 86 " --> pdb=" O SER a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 129 removed outlier: 3.700A pdb=" N ARG a 128 " --> pdb=" O GLU a 125 " (cutoff:3.500A) Processing helix chain 'a' and resid 155 through 166 removed outlier: 4.036A pdb=" N ALA a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU a 162 " --> pdb=" O THR a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 199 Processing helix chain 'a' and resid 212 through 220 removed outlier: 3.539A pdb=" N VAL a 216 " --> pdb=" O ARG a 212 " (cutoff:3.500A) Processing helix chain 'a' and resid 235 through 256 removed outlier: 3.705A pdb=" N HIS a 239 " --> pdb=" O PRO a 235 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 278 Processing helix chain 'a' and resid 291 through 293 No H-bonds generated for 'chain 'a' and resid 291 through 293' Processing helix chain 'a' and resid 294 through 303 Processing helix chain 'a' and resid 325 through 337 removed outlier: 4.683A pdb=" N GLY a 337 " --> pdb=" O GLU a 333 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 351 Processing helix chain 'a' and resid 367 through 372 removed outlier: 3.807A pdb=" N THR a 372 " --> pdb=" O GLU a 369 " (cutoff:3.500A) Processing helix chain 'a' and resid 373 through 388 Processing helix chain 'a' and resid 392 through 405 Processing helix chain 'a' and resid 408 through 417 removed outlier: 3.510A pdb=" N LYS a 417 " --> pdb=" O PHE a 413 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 8 Processing helix chain 'b' and resid 10 through 21 Processing helix chain 'b' and resid 30 through 45 Processing helix chain 'b' and resid 82 through 90 removed outlier: 3.798A pdb=" N ILE b 86 " --> pdb=" O SER b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 129 removed outlier: 3.700A pdb=" N ARG b 128 " --> pdb=" O GLU b 125 " (cutoff:3.500A) Processing helix chain 'b' and resid 155 through 166 removed outlier: 4.036A pdb=" N ALA b 159 " --> pdb=" O GLU b 155 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU b 162 " --> pdb=" O THR b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 183 through 199 Processing helix chain 'b' and resid 212 through 220 removed outlier: 3.539A pdb=" N VAL b 216 " --> pdb=" O ARG b 212 " (cutoff:3.500A) Processing helix chain 'b' and resid 235 through 256 removed outlier: 3.705A pdb=" N HIS b 239 " --> pdb=" O PRO b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 266 through 278 Processing helix chain 'b' and resid 291 through 293 No H-bonds generated for 'chain 'b' and resid 291 through 293' Processing helix chain 'b' and resid 294 through 303 Processing helix chain 'b' and resid 325 through 337 removed outlier: 4.683A pdb=" N GLY b 337 " --> pdb=" O GLU b 333 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 351 Processing helix chain 'b' and resid 367 through 372 removed outlier: 3.806A pdb=" N THR b 372 " --> pdb=" O GLU b 369 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 388 Processing helix chain 'b' and resid 392 through 405 Processing helix chain 'b' and resid 408 through 417 removed outlier: 3.510A pdb=" N LYS b 417 " --> pdb=" O PHE b 413 " (cutoff:3.500A) Processing helix chain 'c' and resid 3 through 8 Processing helix chain 'c' and resid 10 through 21 Processing helix chain 'c' and resid 30 through 45 Processing helix chain 'c' and resid 82 through 90 removed outlier: 3.797A pdb=" N ILE c 86 " --> pdb=" O SER c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 125 through 129 removed outlier: 3.701A pdb=" N ARG c 128 " --> pdb=" O GLU c 125 " (cutoff:3.500A) Processing helix chain 'c' and resid 155 through 166 removed outlier: 4.036A pdb=" N ALA c 159 " --> pdb=" O GLU c 155 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU c 162 " --> pdb=" O THR c 158 " (cutoff:3.500A) Processing helix chain 'c' and resid 183 through 199 Processing helix chain 'c' and resid 212 through 220 removed outlier: 3.539A pdb=" N VAL c 216 " --> pdb=" O ARG c 212 " (cutoff:3.500A) Processing helix chain 'c' and resid 235 through 256 removed outlier: 3.705A pdb=" N HIS c 239 " --> pdb=" O PRO c 235 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 Processing helix chain 'c' and resid 291 through 293 No H-bonds generated for 'chain 'c' and resid 291 through 293' Processing helix chain 'c' and resid 294 through 303 Processing helix chain 'c' and resid 325 through 337 removed outlier: 4.682A pdb=" N GLY c 337 " --> pdb=" O GLU c 333 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 351 Processing helix chain 'c' and resid 367 through 372 removed outlier: 3.807A pdb=" N THR c 372 " --> pdb=" O GLU c 369 " (cutoff:3.500A) Processing helix chain 'c' and resid 373 through 388 Processing helix chain 'c' and resid 392 through 405 Processing helix chain 'c' and resid 408 through 417 removed outlier: 3.510A pdb=" N LYS c 417 " --> pdb=" O PHE c 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 8 Processing helix chain 'd' and resid 10 through 21 Processing helix chain 'd' and resid 30 through 45 Processing helix chain 'd' and resid 82 through 90 removed outlier: 3.797A pdb=" N ILE d 86 " --> pdb=" O SER d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 125 through 129 removed outlier: 3.700A pdb=" N ARG d 128 " --> pdb=" O GLU d 125 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 166 removed outlier: 4.036A pdb=" N ALA d 159 " --> pdb=" O GLU d 155 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU d 162 " --> pdb=" O THR d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 199 Processing helix chain 'd' and resid 212 through 220 removed outlier: 3.539A pdb=" N VAL d 216 " --> pdb=" O ARG d 212 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 256 removed outlier: 3.705A pdb=" N HIS d 239 " --> pdb=" O PRO d 235 " (cutoff:3.500A) Processing helix chain 'd' and resid 266 through 278 Processing helix chain 'd' and resid 291 through 293 No H-bonds generated for 'chain 'd' and resid 291 through 293' Processing helix chain 'd' and resid 294 through 303 Processing helix chain 'd' and resid 325 through 337 removed outlier: 4.683A pdb=" N GLY d 337 " --> pdb=" O GLU d 333 " (cutoff:3.500A) Processing helix chain 'd' and resid 346 through 351 Processing helix chain 'd' and resid 367 through 372 removed outlier: 3.807A pdb=" N THR d 372 " --> pdb=" O GLU d 369 " (cutoff:3.500A) Processing helix chain 'd' and resid 373 through 388 Processing helix chain 'd' and resid 392 through 405 Processing helix chain 'd' and resid 408 through 417 removed outlier: 3.511A pdb=" N LYS d 417 " --> pdb=" O PHE d 413 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 8 Processing helix chain 'e' and resid 10 through 21 Processing helix chain 'e' and resid 30 through 45 Processing helix chain 'e' and resid 82 through 90 removed outlier: 3.797A pdb=" N ILE e 86 " --> pdb=" O SER e 82 " (cutoff:3.500A) Processing helix chain 'e' and resid 125 through 129 removed outlier: 3.701A pdb=" N ARG e 128 " --> pdb=" O GLU e 125 " (cutoff:3.500A) Processing helix chain 'e' and resid 155 through 166 removed outlier: 4.036A pdb=" N ALA e 159 " --> pdb=" O GLU e 155 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU e 162 " --> pdb=" O THR e 158 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 199 Processing helix chain 'e' and resid 212 through 220 removed outlier: 3.539A pdb=" N VAL e 216 " --> pdb=" O ARG e 212 " (cutoff:3.500A) Processing helix chain 'e' and resid 235 through 256 removed outlier: 3.706A pdb=" N HIS e 239 " --> pdb=" O PRO e 235 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 278 Processing helix chain 'e' and resid 291 through 293 No H-bonds generated for 'chain 'e' and resid 291 through 293' Processing helix chain 'e' and resid 294 through 303 Processing helix chain 'e' and resid 325 through 337 removed outlier: 4.683A pdb=" N GLY e 337 " --> pdb=" O GLU e 333 " (cutoff:3.500A) Processing helix chain 'e' and resid 346 through 351 Processing helix chain 'e' and resid 367 through 372 removed outlier: 3.806A pdb=" N THR e 372 " --> pdb=" O GLU e 369 " (cutoff:3.500A) Processing helix chain 'e' and resid 373 through 388 Processing helix chain 'e' and resid 392 through 405 Processing helix chain 'e' and resid 408 through 417 removed outlier: 3.511A pdb=" N LYS e 417 " --> pdb=" O PHE e 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 19 through 39 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 103 through 131 Processing helix chain 'A' and resid 201 through 213 removed outlier: 3.829A pdb=" N LEU A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 279 through 288 removed outlier: 3.623A pdb=" N MET A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 333 removed outlier: 4.025A pdb=" N ALA A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 425 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 441 through 452 removed outlier: 3.853A pdb=" N GLY A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.589A pdb=" N LEU A 459 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'U' and resid 34 through 50 removed outlier: 3.653A pdb=" N THR U 38 " --> pdb=" O GLY U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 88 Processing helix chain 'U' and resid 113 through 115 No H-bonds generated for 'chain 'U' and resid 113 through 115' Processing helix chain 'U' and resid 212 through 229 Processing helix chain 'U' and resid 230 through 232 No H-bonds generated for 'chain 'U' and resid 230 through 232' Processing helix chain 'V' and resid 18 through 21 Processing helix chain 'V' and resid 34 through 49 removed outlier: 3.769A pdb=" N THR V 38 " --> pdb=" O GLY V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 87 removed outlier: 3.729A pdb=" N GLY V 87 " --> pdb=" O LEU V 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 113 through 115 No H-bonds generated for 'chain 'V' and resid 113 through 115' Processing helix chain 'V' and resid 154 through 165 removed outlier: 3.718A pdb=" N ARG V 158 " --> pdb=" O PRO V 154 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU V 165 " --> pdb=" O SER V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 212 through 229 Processing helix chain 'V' and resid 230 through 232 No H-bonds generated for 'chain 'V' and resid 230 through 232' Processing helix chain 'V' and resid 250 through 255 removed outlier: 3.803A pdb=" N LEU V 254 " --> pdb=" O ASP V 250 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG V 255 " --> pdb=" O PRO V 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 250 through 255' Processing helix chain 'V' and resid 256 through 260 Processing helix chain 'V' and resid 263 through 272 Processing helix chain 'V' and resid 277 through 282 Processing helix chain 'V' and resid 285 through 289 Processing helix chain 'V' and resid 296 through 309 removed outlier: 3.706A pdb=" N LEU V 300 " --> pdb=" O GLY V 296 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU V 307 " --> pdb=" O ILE V 303 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA V 308 " --> pdb=" O LYS V 304 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 11 Processing helix chain 'W' and resid 16 through 32 Processing helix chain 'W' and resid 45 through 57 removed outlier: 3.578A pdb=" N GLY W 57 " --> pdb=" O GLU W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 80 Processing helix chain 'X' and resid 4 through 10 removed outlier: 3.643A pdb=" N ARG X 10 " --> pdb=" O THR X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 37 Processing helix chain 'X' and resid 42 through 46 removed outlier: 3.934A pdb=" N GLY X 45 " --> pdb=" O ASP X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 55 Processing helix chain 'X' and resid 81 through 89 Processing helix chain 'X' and resid 205 through 212 removed outlier: 4.234A pdb=" N ILE X 209 " --> pdb=" O PRO X 205 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 225 Processing helix chain 'X' and resid 270 through 281 removed outlier: 3.616A pdb=" N ASP X 280 " --> pdb=" O GLN X 276 " (cutoff:3.500A) Processing helix chain 'X' and resid 288 through 293 removed outlier: 4.132A pdb=" N ILE X 292 " --> pdb=" O PRO X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 329 removed outlier: 3.861A pdb=" N GLY X 329 " --> pdb=" O LEU X 325 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 353 removed outlier: 3.624A pdb=" N THR X 350 " --> pdb=" O TYR X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 358 through 371 Processing helix chain 'X' and resid 379 through 390 removed outlier: 4.035A pdb=" N SER X 383 " --> pdb=" O GLU X 379 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE X 389 " --> pdb=" O PHE X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 409 Processing helix chain 'X' and resid 421 through 438 Processing helix chain 'X' and resid 455 through 480 removed outlier: 3.655A pdb=" N MET X 459 " --> pdb=" O SER X 455 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG X 470 " --> pdb=" O VAL X 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 497 through 508 Processing helix chain 'X' and resid 519 through 528 Processing helix chain 'X' and resid 539 through 543 Processing helix chain 'X' and resid 544 through 549 removed outlier: 3.650A pdb=" N ARG X 548 " --> pdb=" O GLY X 544 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP X 549 " --> pdb=" O PHE X 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 544 through 549' Processing helix chain 'X' and resid 551 through 555 removed outlier: 3.528A pdb=" N TYR X 555 " --> pdb=" O PRO X 552 " (cutoff:3.500A) Processing helix chain 'X' and resid 664 through 668 removed outlier: 3.774A pdb=" N LEU X 667 " --> pdb=" O GLY X 664 " (cutoff:3.500A) Processing helix chain 'X' and resid 675 through 687 removed outlier: 3.622A pdb=" N ARG X 687 " --> pdb=" O ALA X 683 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 712 removed outlier: 3.527A pdb=" N ALA X 709 " --> pdb=" O GLU X 705 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL X 710 " --> pdb=" O ARG X 706 " (cutoff:3.500A) Processing helix chain 'X' and resid 820 through 825 Processing helix chain 'X' and resid 858 through 863 Processing helix chain 'X' and resid 896 through 904 removed outlier: 3.784A pdb=" N ALA X 904 " --> pdb=" O LYS X 900 " (cutoff:3.500A) Processing helix chain 'X' and resid 942 through 980 Processing helix chain 'X' and resid 982 through 990 Processing helix chain 'X' and resid 992 through 996 removed outlier: 3.801A pdb=" N ASP X 995 " --> pdb=" O LEU X 992 " (cutoff:3.500A) Processing helix chain 'X' and resid 1003 through 1038 removed outlier: 5.280A pdb=" N ASN X1009 " --> pdb=" O GLU X1005 " (cutoff:3.500A) Processing helix chain 'X' and resid 1081 through 1085 Processing helix chain 'X' and resid 1101 through 1106 removed outlier: 4.388A pdb=" N SER X1105 " --> pdb=" O LEU X1101 " (cutoff:3.500A) Processing helix chain 'X' and resid 1109 through 1133 Processing helix chain 'X' and resid 1137 through 1150 Processing helix chain 'X' and resid 1167 through 1177 removed outlier: 3.569A pdb=" N ARG X1171 " --> pdb=" O GLU X1167 " (cutoff:3.500A) Processing helix chain 'X' and resid 1191 through 1202 removed outlier: 3.580A pdb=" N ILE X1195 " --> pdb=" O LYS X1191 " (cutoff:3.500A) Processing helix chain 'X' and resid 1271 through 1281 Processing helix chain 'X' and resid 1283 through 1292 Processing helix chain 'X' and resid 1297 through 1309 Processing helix chain 'X' and resid 1320 through 1333 Processing helix chain 'Y' and resid 26 through 33 Processing helix chain 'Y' and resid 94 through 100 removed outlier: 3.546A pdb=" N VAL Y 97 " --> pdb=" O GLN Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 128 Processing helix chain 'Y' and resid 131 through 140 Processing helix chain 'Y' and resid 161 through 167 Processing helix chain 'Y' and resid 181 through 191 removed outlier: 3.770A pdb=" N SER Y 191 " --> pdb=" O ALA Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 208 Processing helix chain 'Y' and resid 211 through 230 removed outlier: 3.502A pdb=" N ALA Y 226 " --> pdb=" O LYS Y 222 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE Y 227 " --> pdb=" O LEU Y 223 " (cutoff:3.500A) Processing helix chain 'Y' and resid 233 through 236 Processing helix chain 'Y' and resid 246 through 250 removed outlier: 3.516A pdb=" N LEU Y 249 " --> pdb=" O PRO Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 263 through 283 removed outlier: 3.559A pdb=" N ASP Y 267 " --> pdb=" O SER Y 263 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 308 removed outlier: 3.625A pdb=" N VAL Y 292 " --> pdb=" O PRO Y 288 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG Y 293 " --> pdb=" O ASP Y 289 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 332 Processing helix chain 'Y' and resid 336 through 341 Processing helix chain 'Y' and resid 370 through 377 Processing helix chain 'Y' and resid 377 through 388 Processing helix chain 'Y' and resid 393 through 404 Processing helix chain 'Y' and resid 408 through 416 Processing helix chain 'Y' and resid 430 through 432 No H-bonds generated for 'chain 'Y' and resid 430 through 432' Processing helix chain 'Y' and resid 453 through 458 removed outlier: 3.635A pdb=" N TYR Y 457 " --> pdb=" O VAL Y 453 " (cutoff:3.500A) Processing helix chain 'Y' and resid 473 through 483 Processing helix chain 'Y' and resid 503 through 515 Processing helix chain 'Y' and resid 529 through 539 Processing helix chain 'Y' and resid 574 through 580 Processing helix chain 'Y' and resid 597 through 613 Processing helix chain 'Y' and resid 614 through 636 removed outlier: 4.470A pdb=" N ILE Y 619 " --> pdb=" O LYS Y 615 " (cutoff:3.500A) Processing helix chain 'Y' and resid 649 through 670 Processing helix chain 'Y' and resid 674 through 702 removed outlier: 3.838A pdb=" N ASP Y 684 " --> pdb=" O ASN Y 680 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE Y 685 " --> pdb=" O LYS Y 681 " (cutoff:3.500A) Processing helix chain 'Y' and resid 720 through 728 removed outlier: 3.643A pdb=" N SER Y 728 " --> pdb=" O MET Y 724 " (cutoff:3.500A) Processing helix chain 'Y' and resid 733 through 742 Processing helix chain 'Y' and resid 768 through 804 removed outlier: 3.978A pdb=" N LYS Y 781 " --> pdb=" O HIS Y 777 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY Y 782 " --> pdb=" O GLY Y 778 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR Y 786 " --> pdb=" O GLY Y 782 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA Y 787 " --> pdb=" O LEU Y 783 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ASN Y 792 " --> pdb=" O LEU Y 788 " (cutoff:3.500A) Processing helix chain 'Y' and resid 835 through 840 Processing helix chain 'Y' and resid 865 through 875 Processing helix chain 'Y' and resid 896 through 900 Processing helix chain 'Y' and resid 914 through 925 removed outlier: 3.956A pdb=" N ILE Y 918 " --> pdb=" O ALA Y 914 " (cutoff:3.500A) Processing helix chain 'Y' and resid 926 through 930 Processing helix chain 'Y' and resid 1068 through 1073 removed outlier: 4.009A pdb=" N ASP Y1073 " --> pdb=" O ALA Y1069 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1137 through 1147 Processing helix chain 'Y' and resid 1216 through 1225 Processing helix chain 'Y' and resid 1225 through 1245 removed outlier: 4.084A pdb=" N VAL Y1229 " --> pdb=" O GLY Y1225 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN Y1244 " --> pdb=" O VAL Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1249 through 1261 removed outlier: 4.453A pdb=" N ILE Y1253 " --> pdb=" O ASN Y1249 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU Y1261 " --> pdb=" O VAL Y1257 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1281 through 1294 removed outlier: 4.151A pdb=" N GLU Y1291 " --> pdb=" O ILE Y1287 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU Y1292 " --> pdb=" O ALA Y1288 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA Y1294 " --> pdb=" O ARG Y1290 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1308 through 1313 removed outlier: 3.838A pdb=" N SER Y1313 " --> pdb=" O ILE Y1309 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1318 through 1324 removed outlier: 3.958A pdb=" N ALA Y1322 " --> pdb=" O SER Y1318 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1327 through 1339 Processing helix chain 'Y' and resid 1347 through 1353 removed outlier: 3.769A pdb=" N VAL Y1353 " --> pdb=" O GLU Y1349 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1360 through 1373 removed outlier: 4.434A pdb=" N ALA Y1364 " --> pdb=" O GLY Y1360 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR Y1365 " --> pdb=" O THR Y1361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'f' and resid 49 through 57 removed outlier: 3.705A pdb=" N ILE f 79 " --> pdb=" O LEU f 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU f 113 " --> pdb=" O TYR f 80 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA f 112 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS f 100 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL f 116 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER f 98 " --> pdb=" O VAL f 116 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU f 118 " --> pdb=" O THR f 96 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR f 96 " --> pdb=" O GLU f 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'f' and resid 138 through 139 removed outlier: 3.551A pdb=" N ILE f 261 " --> pdb=" O VAL f 203 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU f 204 " --> pdb=" O GLU f 226 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL f 228 " --> pdb=" O LEU f 204 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL f 206 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER f 230 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU f 208 " --> pdb=" O SER f 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'f' and resid 138 through 139 removed outlier: 6.574A pdb=" N GLY f 174 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ALA f 319 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE f 176 " --> pdb=" O ALA f 319 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N GLU f 342 " --> pdb=" O ASN f 361 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN f 361 " --> pdb=" O GLU f 342 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS f 344 " --> pdb=" O ASP f 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 49 through 57 removed outlier: 3.704A pdb=" N ILE a 79 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU a 113 " --> pdb=" O TYR a 80 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA a 112 " --> pdb=" O ARG a 102 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS a 100 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL a 116 " --> pdb=" O SER a 98 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER a 98 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU a 118 " --> pdb=" O THR a 96 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR a 96 " --> pdb=" O GLU a 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 138 through 139 removed outlier: 3.551A pdb=" N ILE a 261 " --> pdb=" O VAL a 203 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU a 204 " --> pdb=" O GLU a 226 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL a 228 " --> pdb=" O LEU a 204 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL a 206 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER a 230 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU a 208 " --> pdb=" O SER a 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 138 through 139 removed outlier: 6.574A pdb=" N GLY a 174 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA a 319 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE a 176 " --> pdb=" O ALA a 319 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N GLU a 342 " --> pdb=" O ASN a 361 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN a 361 " --> pdb=" O GLU a 342 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS a 344 " --> pdb=" O ASP a 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 49 through 57 removed outlier: 3.705A pdb=" N ILE b 79 " --> pdb=" O LEU b 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU b 113 " --> pdb=" O TYR b 80 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA b 112 " --> pdb=" O ARG b 102 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS b 100 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL b 116 " --> pdb=" O SER b 98 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER b 98 " --> pdb=" O VAL b 116 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU b 118 " --> pdb=" O THR b 96 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR b 96 " --> pdb=" O GLU b 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 138 through 139 removed outlier: 3.552A pdb=" N ILE b 261 " --> pdb=" O VAL b 203 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU b 204 " --> pdb=" O GLU b 226 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL b 228 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL b 206 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER b 230 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU b 208 " --> pdb=" O SER b 230 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 138 through 139 removed outlier: 6.574A pdb=" N GLY b 174 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ALA b 319 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE b 176 " --> pdb=" O ALA b 319 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N GLU b 342 " --> pdb=" O ASN b 361 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN b 361 " --> pdb=" O GLU b 342 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS b 344 " --> pdb=" O ASP b 359 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 49 through 57 removed outlier: 3.706A pdb=" N ILE c 79 " --> pdb=" O LEU c 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU c 113 " --> pdb=" O TYR c 80 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA c 112 " --> pdb=" O ARG c 102 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS c 100 " --> pdb=" O LEU c 114 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL c 116 " --> pdb=" O SER c 98 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER c 98 " --> pdb=" O VAL c 116 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU c 118 " --> pdb=" O THR c 96 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR c 96 " --> pdb=" O GLU c 118 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 138 through 139 removed outlier: 3.552A pdb=" N ILE c 261 " --> pdb=" O VAL c 203 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU c 204 " --> pdb=" O GLU c 226 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL c 228 " --> pdb=" O LEU c 204 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL c 206 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N SER c 230 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU c 208 " --> pdb=" O SER c 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 138 through 139 removed outlier: 6.574A pdb=" N GLY c 174 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA c 319 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE c 176 " --> pdb=" O ALA c 319 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N GLU c 342 " --> pdb=" O ASN c 361 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASN c 361 " --> pdb=" O GLU c 342 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS c 344 " --> pdb=" O ASP c 359 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'd' and resid 49 through 57 removed outlier: 3.705A pdb=" N ILE d 79 " --> pdb=" O LEU d 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU d 113 " --> pdb=" O TYR d 80 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA d 112 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LYS d 100 " --> pdb=" O LEU d 114 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL d 116 " --> pdb=" O SER d 98 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N SER d 98 " --> pdb=" O VAL d 116 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU d 118 " --> pdb=" O THR d 96 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR d 96 " --> pdb=" O GLU d 118 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 138 through 139 removed outlier: 3.553A pdb=" N ILE d 261 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU d 204 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL d 228 " --> pdb=" O LEU d 204 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL d 206 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER d 230 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU d 208 " --> pdb=" O SER d 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'd' and resid 138 through 139 removed outlier: 6.574A pdb=" N GLY d 174 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA d 319 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE d 176 " --> pdb=" O ALA d 319 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N GLU d 342 " --> pdb=" O ASN d 361 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN d 361 " --> pdb=" O GLU d 342 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS d 344 " --> pdb=" O ASP d 359 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'e' and resid 49 through 57 removed outlier: 3.705A pdb=" N ILE e 79 " --> pdb=" O LEU e 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU e 113 " --> pdb=" O TYR e 80 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA e 112 " --> pdb=" O ARG e 102 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS e 100 " --> pdb=" O LEU e 114 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL e 116 " --> pdb=" O SER e 98 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER e 98 " --> pdb=" O VAL e 116 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU e 118 " --> pdb=" O THR e 96 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR e 96 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'e' and resid 138 through 139 removed outlier: 3.552A pdb=" N ILE e 261 " --> pdb=" O VAL e 203 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU e 204 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL e 228 " --> pdb=" O LEU e 204 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL e 206 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N SER e 230 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU e 208 " --> pdb=" O SER e 230 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'e' and resid 138 through 139 removed outlier: 6.574A pdb=" N GLY e 174 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA e 319 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE e 176 " --> pdb=" O ALA e 319 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N GLU e 342 " --> pdb=" O ASN e 361 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N ASN e 361 " --> pdb=" O GLU e 342 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS e 344 " --> pdb=" O ASP e 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 137 through 145 removed outlier: 6.702A pdb=" N SER A 151 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL A 145 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASN A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 195 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU A 163 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N PHE A 196 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 223 through 229 Processing sheet with id=AC3, first strand: chain 'A' and resid 297 through 299 Processing sheet with id=AC4, first strand: chain 'U' and resid 12 through 13 removed outlier: 3.551A pdb=" N GLU U 29 " --> pdb=" O ARG U 12 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LYS U 25 " --> pdb=" O MET U 205 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N MET U 205 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR U 27 " --> pdb=" O ILE U 203 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE U 203 " --> pdb=" O THR U 27 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLU U 29 " --> pdb=" O LEU U 201 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU U 201 " --> pdb=" O GLU U 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 52 through 53 Processing sheet with id=AC6, first strand: chain 'U' and resid 97 through 105 removed outlier: 6.153A pdb=" N GLN U 147 " --> pdb=" O VAL U 56 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N VAL U 56 " --> pdb=" O GLN U 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 90 through 92 Processing sheet with id=AC8, first strand: chain 'U' and resid 108 through 111 Processing sheet with id=AC9, first strand: chain 'V' and resid 16 through 17 Processing sheet with id=AD1, first strand: chain 'V' and resid 97 through 101 removed outlier: 6.177A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 90 through 92 Processing sheet with id=AD3, first strand: chain 'V' and resid 110 through 111 Processing sheet with id=AD4, first strand: chain 'X' and resid 13 through 14 removed outlier: 6.581A pdb=" N LYS X 13 " --> pdb=" O ALA X1183 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 59 through 60 removed outlier: 3.557A pdb=" N ILE X 59 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS X 99 " --> pdb=" O VAL X 71 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR X 73 " --> pdb=" O ARG X 97 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG X 97 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU X 75 " --> pdb=" O PRO X 95 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ALA X 94 " --> pdb=" O GLU X 126 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU X 126 " --> pdb=" O ALA X 94 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU X 96 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE X 104 " --> pdb=" O ASP X 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASP X 116 " --> pdb=" O ILE X 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 136 through 137 Processing sheet with id=AD7, first strand: chain 'X' and resid 451 through 454 removed outlier: 3.505A pdb=" N SER X 147 " --> pdb=" O ARG X 529 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 154 through 160 removed outlier: 6.381A pdb=" N TYR X 172 " --> pdb=" O PHE X 188 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE X 188 " --> pdb=" O TYR X 172 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 228 through 231 Processing sheet with id=AE1, first strand: chain 'X' and resid 239 through 240 removed outlier: 4.276A pdb=" N MET X 239 " --> pdb=" O ILE X 285 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE X 285 " --> pdb=" O MET X 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'X' and resid 255 through 257 removed outlier: 6.446A pdb=" N ALA X 257 " --> pdb=" O VAL X 261 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL X 261 " --> pdb=" O ALA X 257 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 296 through 297 removed outlier: 4.306A pdb=" N MET X 315 " --> pdb=" O VAL X 297 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 301 through 302 removed outlier: 4.030A pdb=" N CYS X 311 " --> pdb=" O TYR X 301 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 580 through 581 removed outlier: 5.584A pdb=" N GLU X 602 " --> pdb=" O LYS X 593 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 580 through 581 removed outlier: 3.554A pdb=" N ILE X 616 " --> pdb=" O ARG X 637 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 623 through 624 removed outlier: 3.986A pdb=" N HIS X 628 " --> pdb=" O ASP X 624 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 716 through 717 removed outlier: 6.834A pdb=" N ALA X 716 " --> pdb=" O LEU X 783 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 748 through 752 removed outlier: 6.463A pdb=" N LYS X 735 " --> pdb=" O VAL X 724 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL X 724 " --> pdb=" O LYS X 735 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 798 through 804 removed outlier: 8.761A pdb=" N ILE X1096 " --> pdb=" O ASN X 799 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG X 801 " --> pdb=" O ILE X1096 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU X1098 " --> pdb=" O ARG X 801 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA X 803 " --> pdb=" O LEU X1098 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE X 816 " --> pdb=" O SER X1077 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE X1079 " --> pdb=" O ILE X 816 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N VAL X 818 " --> pdb=" O ILE X1079 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 830 through 841 removed outlier: 6.484A pdb=" N THR X 830 " --> pdb=" O LYS X1057 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS X1057 " --> pdb=" O THR X 830 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N HIS X 832 " --> pdb=" O ALA X1055 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA X1055 " --> pdb=" O HIS X 832 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN X 834 " --> pdb=" O TYR X1053 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR X1053 " --> pdb=" O GLN X 834 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU X 836 " --> pdb=" O LYS X1051 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS X1051 " --> pdb=" O LEU X 836 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N CYS X 838 " --> pdb=" O ILE X1049 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE X1049 " --> pdb=" O CYS X 838 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER X 840 " --> pdb=" O LEU X1047 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU X1047 " --> pdb=" O THR X 935 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N THR X 935 " --> pdb=" O LEU X1047 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE X1049 " --> pdb=" O VAL X 933 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL X 933 " --> pdb=" O ILE X1049 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS X1051 " --> pdb=" O VAL X 931 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL X 931 " --> pdb=" O LYS X1051 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR X1053 " --> pdb=" O ILE X 929 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 1087 through 1088 Processing sheet with id=AF4, first strand: chain 'X' and resid 1244 through 1246 removed outlier: 3.513A pdb=" N SER Y 350 " --> pdb=" O ARG X1246 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 1244 through 1246 removed outlier: 3.513A pdb=" N SER Y 350 " --> pdb=" O ARG X1246 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE Y 447 " --> pdb=" O ARG Y 352 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL Y 354 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU Y 449 " --> pdb=" O VAL Y 354 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR Y 356 " --> pdb=" O LEU Y 449 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 1269 through 1270 Processing sheet with id=AF7, first strand: chain 'X' and resid 1337 through 1338 Processing sheet with id=AF8, first strand: chain 'Y' and resid 34 through 37 removed outlier: 7.476A pdb=" N HIS Y 104 " --> pdb=" O PHE Y 35 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU Y 37 " --> pdb=" O HIS Y 104 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N GLU Y 106 " --> pdb=" O GLU Y 37 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU Y 107 " --> pdb=" O THR Y 240 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR Y 240 " --> pdb=" O LEU Y 107 " (cutoff:3.500A) removed outlier: 10.786A pdb=" N SER Y 109 " --> pdb=" O ILE Y 238 " (cutoff:3.500A) removed outlier: 10.320A pdb=" N ILE Y 238 " --> pdb=" O SER Y 109 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 159 through 160 removed outlier: 4.166A pdb=" N ASP Y 177 " --> pdb=" O ILE Y 147 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Y' and resid 547 through 557 Processing sheet with id=AG2, first strand: chain 'Y' and resid 809 through 811 Processing sheet with id=AG3, first strand: chain 'Y' and resid 819 through 822 Processing sheet with id=AG4, first strand: chain 'Y' and resid 957 through 961 removed outlier: 3.548A pdb=" N GLU Y 981 " --> pdb=" O SER Y 961 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU Y 993 " --> pdb=" O LEU Y 984 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 965 through 967 Processing sheet with id=AG6, first strand: chain 'Y' and resid 1098 through 1100 removed outlier: 4.357A pdb=" N LYS Y1079 " --> pdb=" O ARG Y1036 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG Y1036 " --> pdb=" O LYS Y1079 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL Y1035 " --> pdb=" O VAL Y1113 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL Y1113 " --> pdb=" O VAL Y1035 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 1059 through 1060 removed outlier: 3.790A pdb=" N ARG Y1123 " --> pdb=" O ILE Y1106 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 1162 through 1165 removed outlier: 3.749A pdb=" N GLU Y1188 " --> pdb=" O LEU Y1175 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 1264 through 1266 2128 hydrogen bonds defined for protein. 6015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 23.50 Time building geometry restraints manager: 11.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16779 1.34 - 1.45: 6153 1.45 - 1.57: 29006 1.57 - 1.69: 186 1.69 - 1.81: 408 Bond restraints: 52532 Sorted by residual: bond pdb=" F2 BEF a1002 " pdb="BE BEF a1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" F2 BEF c 504 " pdb="BE BEF c 504 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" F2 BEF c 503 " pdb="BE BEF c 503 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" F2 BEF b1002 " pdb="BE BEF b1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF e1002 " pdb="BE BEF e1002 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 52527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 71224 5.15 - 10.30: 56 10.30 - 15.45: 12 15.45 - 20.60: 0 20.60 - 25.75: 2 Bond angle restraints: 71294 Sorted by residual: angle pdb=" O3' DC L 20 " pdb=" P DC L 21 " pdb=" OP2 DC L 21 " ideal model delta sigma weight residual 108.00 82.25 25.75 3.00e+00 1.11e-01 7.37e+01 angle pdb=" O3' DC L 20 " pdb=" P DC L 21 " pdb=" OP1 DC L 21 " ideal model delta sigma weight residual 108.00 84.32 23.68 3.00e+00 1.11e-01 6.23e+01 angle pdb=" CB LYS e 326 " pdb=" CG LYS e 326 " pdb=" CD LYS e 326 " ideal model delta sigma weight residual 111.30 122.88 -11.58 2.30e+00 1.89e-01 2.54e+01 angle pdb=" CB LYS b 326 " pdb=" CG LYS b 326 " pdb=" CD LYS b 326 " ideal model delta sigma weight residual 111.30 122.88 -11.58 2.30e+00 1.89e-01 2.54e+01 angle pdb=" CB LYS c 326 " pdb=" CG LYS c 326 " pdb=" CD LYS c 326 " ideal model delta sigma weight residual 111.30 122.87 -11.57 2.30e+00 1.89e-01 2.53e+01 ... (remaining 71289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 31381 35.23 - 70.46: 827 70.46 - 105.68: 63 105.68 - 140.91: 5 140.91 - 176.14: 7 Dihedral angle restraints: 32283 sinusoidal: 14085 harmonic: 18198 Sorted by residual: dihedral pdb=" O4' U R 24 " pdb=" C1' U R 24 " pdb=" N1 U R 24 " pdb=" C2 U R 24 " ideal model delta sinusoidal sigma weight residual 232.00 62.28 169.72 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" O1B ADP b1000 " pdb=" O3A ADP b1000 " pdb=" PB ADP b1000 " pdb=" PA ADP b1000 " ideal model delta sinusoidal sigma weight residual -60.00 102.99 -163.00 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP c 501 " pdb=" O5' ADP c 501 " pdb=" PA ADP c 501 " pdb=" O2A ADP c 501 " ideal model delta sinusoidal sigma weight residual 300.00 153.86 146.14 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 32280 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.401: 8159 0.401 - 0.802: 0 0.802 - 1.203: 0 1.203 - 1.604: 0 1.604 - 2.005: 1 Chirality restraints: 8160 Sorted by residual: chirality pdb=" P DC L 21 " pdb=" OP1 DC L 21 " pdb=" OP2 DC L 21 " pdb=" O5' DC L 21 " both_signs ideal model delta sigma weight residual True 2.35 0.34 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" P DC K -14 " pdb=" OP1 DC K -14 " pdb=" OP2 DC K -14 " pdb=" O5' DC K -14 " both_signs ideal model delta sigma weight residual True 2.35 -2.54 -0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CA ILE A 97 " pdb=" N ILE A 97 " pdb=" C ILE A 97 " pdb=" CB ILE A 97 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 8157 not shown) Planarity restraints: 9006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG L 2 " -0.026 2.00e-02 2.50e+03 1.26e-02 4.74e+00 pdb=" N9 DG L 2 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG L 2 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG L 2 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG L 2 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DG L 2 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG L 2 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG L 2 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG L 2 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG L 2 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU Y 658 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C GLU Y 658 " -0.033 2.00e-02 2.50e+03 pdb=" O GLU Y 658 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA Y 659 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU U 29 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO U 30 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO U 30 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO U 30 " 0.022 5.00e-02 4.00e+02 ... (remaining 9003 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 619 2.57 - 3.16: 42597 3.16 - 3.74: 83530 3.74 - 4.32: 110807 4.32 - 4.90: 177666 Nonbonded interactions: 415219 Sorted by model distance: nonbonded pdb="MG MG c 502 " pdb=" F3 BEF c 503 " model vdw 1.993 2.120 nonbonded pdb=" O1B ADP c 501 " pdb="MG MG c 502 " model vdw 2.008 2.170 nonbonded pdb=" O1B ADP d1000 " pdb="MG MG d1001 " model vdw 2.021 2.170 nonbonded pdb=" O2B ADP b1000 " pdb="MG MG b1001 " model vdw 2.034 2.170 nonbonded pdb=" F3 BEF c 504 " pdb="MG MG d1001 " model vdw 2.046 2.120 ... (remaining 415214 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 1 through 417) selection = (chain 'b' and resid 1 through 417) selection = (chain 'c' and resid 1 through 417) selection = (chain 'd' and resid 1 through 417) selection = (chain 'e' and resid 1 through 417) selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.050 Extract box with map and model: 1.400 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 106.880 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 52532 Z= 0.161 Angle : 0.583 25.746 71294 Z= 0.311 Chirality : 0.046 2.005 8160 Planarity : 0.003 0.042 9006 Dihedral : 15.539 176.142 20537 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.23 % Favored : 95.75 % Rotamer: Outliers : 3.45 % Allowed : 6.16 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.09), residues: 6306 helix: -1.25 (0.10), residues: 2388 sheet: -1.55 (0.15), residues: 803 loop : -2.57 (0.10), residues: 3115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 321 HIS 0.005 0.001 HIS c 42 PHE 0.009 0.001 PHE d 301 TYR 0.010 0.001 TYR U 177 ARG 0.002 0.000 ARG c 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 379 time to evaluate : 4.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 117 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8478 (p0) REVERT: a 341 MET cc_start: 0.7891 (tpt) cc_final: 0.7195 (tpt) REVERT: b 71 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8463 (p) REVERT: d 137 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.6945 (t) REVERT: e 71 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8613 (p) REVERT: A 339 MET cc_start: 0.8552 (mmt) cc_final: 0.8076 (pmm) REVERT: W 52 ARG cc_start: 0.9315 (ttp-170) cc_final: 0.9089 (ptm160) REVERT: W 60 ASN cc_start: 0.8856 (m-40) cc_final: 0.8473 (m-40) REVERT: W 79 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7683 (pt0) REVERT: X 107 ARG cc_start: 0.6336 (mmt180) cc_final: 0.5443 (mmm160) REVERT: Y 1145 PHE cc_start: 0.7415 (m-80) cc_final: 0.7163 (m-80) REVERT: Y 1189 MET cc_start: 0.8022 (tmm) cc_final: 0.7788 (tpp) outliers start: 186 outliers final: 48 residues processed: 546 average time/residue: 0.5639 time to fit residues: 499.2200 Evaluate side-chains 310 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 258 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 534 optimal weight: 9.9990 chunk 479 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 323 optimal weight: 50.0000 chunk 256 optimal weight: 9.9990 chunk 496 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 369 optimal weight: 2.9990 chunk 574 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 135 ASN ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 361 ASN a 90 ASN ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 361 ASN b 41 GLN b 90 ASN b 135 ASN b 172 GLN b 361 ASN c 41 GLN c 90 ASN c 172 GLN c 361 ASN d 90 ASN d 135 ASN d 172 GLN d 361 ASN e 90 ASN e 172 GLN A 14 ASN A 157 ASN A 172 ASN A 282 GLN A 324 ASN A 330 GLN ** U 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 147 GLN V 239 GLN V 276 HIS V 283 GLN ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 60 ASN X 343 HIS ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 580 GLN X 618 GLN X 628 HIS X 808 ASN X 932 GLN X 952 GLN X1009 ASN X1010 GLN X1013 GLN X1017 GLN X1070 HIS X1116 HIS X1268 GLN X1312 ASN Y 80 HIS Y 196 GLN Y 266 ASN Y 277 ASN Y 320 ASN Y 341 ASN Y 365 GLN Y 545 HIS Y 702 GLN Y 865 HIS Y1084 GLN Y1295 ASN ** Y1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 52532 Z= 0.296 Angle : 0.683 25.289 71294 Z= 0.345 Chirality : 0.048 2.020 8160 Planarity : 0.004 0.057 9006 Dihedral : 13.159 177.769 8027 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.11 % Allowed : 6.33 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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: -1.80 (0.10), residues: 6306 helix: -0.15 (0.10), residues: 2451 sheet: -1.42 (0.16), residues: 860 loop : -2.02 (0.11), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 334 HIS 0.011 0.002 HIS e 388 PHE 0.019 0.002 PHE f 62 TYR 0.018 0.002 TYR b 72 ARG 0.014 0.001 ARG V 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 275 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 186 MET cc_start: 0.8819 (ptt) cc_final: 0.8607 (ptt) REVERT: f 327 MET cc_start: 0.9071 (ptm) cc_final: 0.8796 (ptm) REVERT: b 1 MET cc_start: 0.4764 (ptt) cc_final: 0.4266 (ptt) REVERT: c 219 MET cc_start: 0.8035 (mmp) cc_final: 0.7749 (mmm) REVERT: d 21 MET cc_start: 0.8528 (mpp) cc_final: 0.7520 (ptp) REVERT: e 327 MET cc_start: 0.9094 (mpp) cc_final: 0.8779 (mpp) REVERT: A 339 MET cc_start: 0.8676 (mmt) cc_final: 0.8010 (pmm) REVERT: A 389 MET cc_start: 0.8093 (tpt) cc_final: 0.7613 (tpt) REVERT: W 19 LEU cc_start: 0.9361 (tt) cc_final: 0.9037 (tp) REVERT: W 48 VAL cc_start: 0.9163 (t) cc_final: 0.8847 (t) REVERT: W 52 ARG cc_start: 0.9415 (ttp-170) cc_final: 0.9140 (ptm160) REVERT: X 107 ARG cc_start: 0.6856 (mmt180) cc_final: 0.6284 (tpp-160) REVERT: X 1230 MET cc_start: 0.7042 (tmm) cc_final: 0.6666 (tmm) REVERT: Y 237 MET cc_start: 0.7877 (tmm) cc_final: 0.7641 (tmm) REVERT: Y 1040 MET cc_start: 0.6642 (mpp) cc_final: 0.5604 (mpp) REVERT: Y 1145 PHE cc_start: 0.8002 (m-80) cc_final: 0.7727 (m-80) REVERT: Y 1183 SER cc_start: 0.8819 (m) cc_final: 0.8574 (p) REVERT: Y 1189 MET cc_start: 0.8264 (tmm) cc_final: 0.7997 (tpp) outliers start: 6 outliers final: 0 residues processed: 281 average time/residue: 0.5728 time to fit residues: 261.7509 Evaluate side-chains 239 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 319 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 478 optimal weight: 8.9990 chunk 391 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 575 optimal weight: 0.9990 chunk 622 optimal weight: 5.9990 chunk 512 optimal weight: 6.9990 chunk 571 optimal weight: 30.0000 chunk 196 optimal weight: 7.9990 chunk 461 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 90 ASN ** f 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 140 HIS ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 344 HIS A 129 GLN U 132 HIS ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1326 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 52532 Z= 0.241 Angle : 0.618 25.811 71294 Z= 0.309 Chirality : 0.047 2.000 8160 Planarity : 0.004 0.084 9006 Dihedral : 13.145 179.627 8027 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.02 % Allowed : 4.55 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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: -1.39 (0.10), residues: 6306 helix: 0.19 (0.11), residues: 2462 sheet: -1.32 (0.16), residues: 850 loop : -1.74 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 334 HIS 0.009 0.001 HIS e 42 PHE 0.029 0.002 PHE A 24 TYR 0.034 0.002 TYR c 274 ARG 0.011 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 4.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 405 MET cc_start: 0.9043 (ptp) cc_final: 0.8824 (ppp) REVERT: f 415 MET cc_start: 0.8368 (ppp) cc_final: 0.8090 (ppp) REVERT: f 416 MET cc_start: 0.8363 (ptt) cc_final: 0.7795 (ptt) REVERT: a 29 MET cc_start: -0.0133 (ptt) cc_final: -0.0582 (ptt) REVERT: b 1 MET cc_start: 0.4196 (ptt) cc_final: 0.3855 (ptt) REVERT: b 21 MET cc_start: 0.5610 (ttp) cc_final: 0.4974 (tmm) REVERT: c 21 MET cc_start: 0.7501 (ttt) cc_final: 0.7110 (ttt) REVERT: c 219 MET cc_start: 0.8141 (mmp) cc_final: 0.7810 (mmm) REVERT: e 21 MET cc_start: 0.7990 (ptm) cc_final: 0.7766 (tmm) REVERT: e 416 MET cc_start: 0.7892 (ptt) cc_final: 0.7242 (ptt) REVERT: A 339 MET cc_start: 0.8574 (mmt) cc_final: 0.7855 (pmm) REVERT: A 389 MET cc_start: 0.8385 (tpt) cc_final: 0.8115 (tpt) REVERT: A 483 MET cc_start: 0.3746 (tmm) cc_final: 0.3240 (tpt) REVERT: W 52 ARG cc_start: 0.9370 (ttp-170) cc_final: 0.9143 (ptm160) REVERT: W 60 ASN cc_start: 0.9160 (m110) cc_final: 0.8910 (m-40) REVERT: X 107 ARG cc_start: 0.6076 (mmt180) cc_final: 0.5450 (tpp-160) REVERT: X 370 MET cc_start: 0.8987 (ptp) cc_final: 0.8688 (ptp) REVERT: X 1230 MET cc_start: 0.6596 (tmm) cc_final: 0.6351 (tmm) REVERT: Y 237 MET cc_start: 0.7931 (tmm) cc_final: 0.7354 (tmm) REVERT: Y 1145 PHE cc_start: 0.7931 (m-80) cc_final: 0.7714 (m-80) REVERT: Y 1183 SER cc_start: 0.8799 (m) cc_final: 0.8550 (p) REVERT: Y 1189 MET cc_start: 0.8328 (tmm) cc_final: 0.8047 (tpp) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.5662 time to fit residues: 252.6019 Evaluate side-chains 236 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 568 optimal weight: 6.9990 chunk 432 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 274 optimal weight: 10.0000 chunk 386 optimal weight: 9.9990 chunk 577 optimal weight: 8.9990 chunk 611 optimal weight: 0.2980 chunk 301 optimal weight: 8.9990 chunk 547 optimal weight: 10.0000 chunk 164 optimal weight: 20.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 344 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** V 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 490 GLN ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 52532 Z= 0.219 Angle : 0.594 25.912 71294 Z= 0.297 Chirality : 0.046 1.996 8160 Planarity : 0.004 0.065 9006 Dihedral : 13.011 177.902 8027 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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: -1.15 (0.10), residues: 6306 helix: 0.37 (0.11), residues: 2459 sheet: -1.16 (0.17), residues: 849 loop : -1.60 (0.11), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 321 HIS 0.005 0.001 HIS Y 777 PHE 0.018 0.001 PHE X1265 TYR 0.020 0.001 TYR c 274 ARG 0.005 0.000 ARG W 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 405 MET cc_start: 0.9131 (ptp) cc_final: 0.8719 (ptp) REVERT: f 415 MET cc_start: 0.8364 (ppp) cc_final: 0.8147 (ppp) REVERT: f 416 MET cc_start: 0.8449 (ptt) cc_final: 0.7846 (ptt) REVERT: a 29 MET cc_start: -0.0215 (ptt) cc_final: -0.0490 (ptt) REVERT: a 327 MET cc_start: 0.8526 (ptm) cc_final: 0.8298 (ppp) REVERT: b 1 MET cc_start: 0.4448 (ptt) cc_final: 0.3959 (ptt) REVERT: b 21 MET cc_start: 0.5878 (ttp) cc_final: 0.5233 (tmm) REVERT: b 380 MET cc_start: 0.8745 (ptp) cc_final: 0.8513 (ptp) REVERT: c 219 MET cc_start: 0.8164 (mmp) cc_final: 0.7831 (mmm) REVERT: e 245 MET cc_start: 0.8884 (ppp) cc_final: 0.8674 (ppp) REVERT: e 416 MET cc_start: 0.8033 (ptt) cc_final: 0.7376 (ptt) REVERT: A 339 MET cc_start: 0.8606 (mmt) cc_final: 0.7895 (pmm) REVERT: A 389 MET cc_start: 0.8370 (tpt) cc_final: 0.7999 (mmt) REVERT: W 19 LEU cc_start: 0.9290 (tt) cc_final: 0.9038 (tp) REVERT: W 26 ARG cc_start: 0.9249 (tpt90) cc_final: 0.8903 (tpm170) REVERT: W 29 GLN cc_start: 0.9132 (mt0) cc_final: 0.8823 (mt0) REVERT: W 44 ASP cc_start: 0.8728 (t0) cc_final: 0.8426 (t70) REVERT: W 60 ASN cc_start: 0.9248 (m110) cc_final: 0.8931 (m-40) REVERT: X 370 MET cc_start: 0.9013 (ptp) cc_final: 0.8635 (ptp) REVERT: X 1085 MET cc_start: 0.8490 (mmm) cc_final: 0.8139 (mmm) REVERT: Y 932 MET cc_start: 0.6413 (mpp) cc_final: 0.5983 (mmp) REVERT: Y 1145 PHE cc_start: 0.7916 (m-80) cc_final: 0.7661 (m-80) REVERT: Y 1189 MET cc_start: 0.8317 (tmm) cc_final: 0.8071 (tpp) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.5466 time to fit residues: 236.2641 Evaluate side-chains 235 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 509 optimal weight: 20.0000 chunk 347 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 455 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 522 optimal weight: 30.0000 chunk 422 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 chunk 549 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN A 330 GLN ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 580 GLN ** X 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 739 GLN ** Y1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 52532 Z= 0.213 Angle : 0.590 25.997 71294 Z= 0.296 Chirality : 0.046 1.993 8160 Planarity : 0.004 0.049 9006 Dihedral : 12.751 178.112 8027 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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: -0.96 (0.10), residues: 6306 helix: 0.50 (0.11), residues: 2458 sheet: -1.14 (0.17), residues: 860 loop : -1.43 (0.11), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 381 HIS 0.005 0.001 HIS Y 364 PHE 0.013 0.001 PHE b 62 TYR 0.040 0.001 TYR X1231 ARG 0.008 0.000 ARG b 146 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 4.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 396 MET cc_start: 0.9195 (tmm) cc_final: 0.8809 (ppp) REVERT: f 416 MET cc_start: 0.8409 (ptt) cc_final: 0.7910 (ptt) REVERT: a 21 MET cc_start: 0.8309 (mpp) cc_final: 0.8027 (mpp) REVERT: a 186 MET cc_start: 0.7996 (ptp) cc_final: 0.7751 (ptp) REVERT: a 327 MET cc_start: 0.8678 (ptm) cc_final: 0.8286 (ppp) REVERT: b 1 MET cc_start: 0.5208 (ptt) cc_final: 0.4733 (ptt) REVERT: b 21 MET cc_start: 0.5873 (ttp) cc_final: 0.5181 (tmm) REVERT: b 147 MET cc_start: 0.6667 (tpt) cc_final: 0.6410 (tpp) REVERT: c 219 MET cc_start: 0.8152 (mmp) cc_final: 0.7834 (mmm) REVERT: e 416 MET cc_start: 0.7963 (ptt) cc_final: 0.7716 (ptt) REVERT: A 339 MET cc_start: 0.8556 (mmt) cc_final: 0.8148 (pmm) REVERT: A 389 MET cc_start: 0.8412 (tpt) cc_final: 0.8076 (mmt) REVERT: W 26 ARG cc_start: 0.9492 (tpt90) cc_final: 0.9237 (tpp-160) REVERT: W 29 GLN cc_start: 0.9168 (mt0) cc_final: 0.8966 (mp10) REVERT: W 44 ASP cc_start: 0.8810 (t0) cc_final: 0.8495 (t70) REVERT: W 60 ASN cc_start: 0.9290 (m110) cc_final: 0.8952 (m-40) REVERT: Y 102 MET cc_start: 0.7680 (mmp) cc_final: 0.7237 (ttt) REVERT: Y 932 MET cc_start: 0.6571 (mpp) cc_final: 0.5962 (mmp) REVERT: Y 1189 MET cc_start: 0.8319 (tmm) cc_final: 0.8089 (tpp) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.5558 time to fit residues: 235.2992 Evaluate side-chains 232 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 4.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 205 optimal weight: 20.0000 chunk 551 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 359 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 612 optimal weight: 7.9990 chunk 508 optimal weight: 4.9990 chunk 283 optimal weight: 40.0000 chunk 50 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 41 GLN ** e 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 52532 Z= 0.201 Angle : 0.582 26.065 71294 Z= 0.292 Chirality : 0.046 1.989 8160 Planarity : 0.004 0.055 9006 Dihedral : 12.604 178.439 8027 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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: -0.79 (0.11), residues: 6306 helix: 0.60 (0.11), residues: 2463 sheet: -0.94 (0.17), residues: 828 loop : -1.34 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 381 HIS 0.004 0.001 HIS Y 777 PHE 0.023 0.001 PHE A 102 TYR 0.020 0.001 TYR c 110 ARG 0.009 0.000 ARG Y1206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 396 MET cc_start: 0.9216 (tmm) cc_final: 0.8823 (ppp) REVERT: f 416 MET cc_start: 0.8453 (ptt) cc_final: 0.8024 (ptt) REVERT: a 327 MET cc_start: 0.8733 (ptm) cc_final: 0.8359 (ppp) REVERT: a 396 MET cc_start: 0.8369 (mmm) cc_final: 0.8128 (mmm) REVERT: b 1 MET cc_start: 0.4915 (ptt) cc_final: 0.4541 (ptt) REVERT: b 21 MET cc_start: 0.6286 (ttp) cc_final: 0.5384 (tmm) REVERT: c 219 MET cc_start: 0.8150 (mmp) cc_final: 0.7811 (mmm) REVERT: e 416 MET cc_start: 0.8251 (ptt) cc_final: 0.7914 (ptt) REVERT: A 204 MET cc_start: 0.6474 (tpt) cc_final: 0.6136 (tpt) REVERT: A 339 MET cc_start: 0.8604 (mmt) cc_final: 0.8099 (pmm) REVERT: A 389 MET cc_start: 0.8483 (tpt) cc_final: 0.8107 (mmt) REVERT: W 44 ASP cc_start: 0.8981 (t0) cc_final: 0.8727 (t70) REVERT: W 60 ASN cc_start: 0.9310 (m110) cc_final: 0.8982 (m-40) REVERT: X 1230 MET cc_start: 0.7177 (tmm) cc_final: 0.6858 (tmm) REVERT: Y 102 MET cc_start: 0.7611 (mmp) cc_final: 0.7221 (ttt) REVERT: Y 237 MET cc_start: 0.8209 (tmm) cc_final: 0.7537 (tmm) REVERT: Y 932 MET cc_start: 0.6981 (mpp) cc_final: 0.6401 (mmp) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.5419 time to fit residues: 227.2340 Evaluate side-chains 231 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 4.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 590 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 348 optimal weight: 7.9990 chunk 447 optimal weight: 10.0000 chunk 346 optimal weight: 20.0000 chunk 515 optimal weight: 50.0000 chunk 341 optimal weight: 2.9990 chunk 610 optimal weight: 8.9990 chunk 381 optimal weight: 0.7980 chunk 371 optimal weight: 2.9990 chunk 281 optimal weight: 50.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 85 GLN ** f 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 HIS ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 618 GLN ** X 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 52532 Z= 0.220 Angle : 0.604 26.056 71294 Z= 0.303 Chirality : 0.047 1.985 8160 Planarity : 0.004 0.081 9006 Dihedral : 12.583 178.547 8027 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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: -0.76 (0.10), residues: 6306 helix: 0.61 (0.11), residues: 2465 sheet: -0.93 (0.17), residues: 847 loop : -1.30 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 334 HIS 0.009 0.001 HIS X 150 PHE 0.019 0.001 PHE A 102 TYR 0.033 0.001 TYR X1231 ARG 0.010 0.000 ARG Y 883 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 4.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 186 MET cc_start: 0.8507 (ptt) cc_final: 0.8291 (ppp) REVERT: f 341 MET cc_start: 0.7865 (tpp) cc_final: 0.7574 (mmm) REVERT: f 396 MET cc_start: 0.9246 (tmm) cc_final: 0.8944 (ppp) REVERT: f 416 MET cc_start: 0.8522 (ptt) cc_final: 0.8226 (ptt) REVERT: a 396 MET cc_start: 0.8269 (mmm) cc_final: 0.8015 (mmm) REVERT: b 1 MET cc_start: 0.4772 (ptt) cc_final: 0.4452 (ptt) REVERT: b 21 MET cc_start: 0.6306 (ttp) cc_final: 0.5402 (tmm) REVERT: b 147 MET cc_start: 0.6583 (tpt) cc_final: 0.6225 (tpp) REVERT: c 219 MET cc_start: 0.8203 (mmp) cc_final: 0.7866 (mmm) REVERT: d 219 MET cc_start: 0.8305 (mmp) cc_final: 0.8094 (mmm) REVERT: d 396 MET cc_start: 0.7862 (tpp) cc_final: 0.7630 (tpp) REVERT: e 396 MET cc_start: 0.9190 (mpp) cc_final: 0.8931 (mpp) REVERT: e 416 MET cc_start: 0.8356 (ptt) cc_final: 0.7729 (ptt) REVERT: A 204 MET cc_start: 0.6645 (tpt) cc_final: 0.6302 (tpt) REVERT: A 339 MET cc_start: 0.8271 (mmt) cc_final: 0.7807 (pmm) REVERT: A 389 MET cc_start: 0.8478 (tpt) cc_final: 0.8205 (tpt) REVERT: W 44 ASP cc_start: 0.9052 (t0) cc_final: 0.8836 (t70) REVERT: W 64 LEU cc_start: 0.9487 (pp) cc_final: 0.9069 (pp) REVERT: Y 102 MET cc_start: 0.7545 (mmp) cc_final: 0.7211 (ttt) REVERT: Y 237 MET cc_start: 0.8196 (tmm) cc_final: 0.7536 (tmm) REVERT: Y 932 MET cc_start: 0.7047 (mpp) cc_final: 0.6532 (mmp) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.5571 time to fit residues: 233.0865 Evaluate side-chains 229 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 377 optimal weight: 20.0000 chunk 243 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 chunk 119 optimal weight: 0.0770 chunk 118 optimal weight: 9.9990 chunk 387 optimal weight: 8.9990 chunk 415 optimal weight: 8.9990 chunk 301 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 479 optimal weight: 3.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 135 ASN ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 52532 Z= 0.193 Angle : 0.588 26.061 71294 Z= 0.294 Chirality : 0.047 1.977 8160 Planarity : 0.004 0.100 9006 Dihedral : 12.533 178.931 8027 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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: -0.65 (0.11), residues: 6306 helix: 0.69 (0.11), residues: 2462 sheet: -0.92 (0.17), residues: 861 loop : -1.21 (0.11), residues: 2983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 33 HIS 0.006 0.001 HIS Y 777 PHE 0.012 0.001 PHE b 62 TYR 0.013 0.001 TYR e 72 ARG 0.018 0.000 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 4.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 341 MET cc_start: 0.7915 (tpp) cc_final: 0.7351 (mmm) REVERT: f 396 MET cc_start: 0.9232 (tmm) cc_final: 0.8902 (ppp) REVERT: f 416 MET cc_start: 0.8445 (ptt) cc_final: 0.8169 (ptt) REVERT: a 21 MET cc_start: 0.8611 (mpp) cc_final: 0.8411 (mpp) REVERT: a 327 MET cc_start: 0.8621 (ptm) cc_final: 0.8191 (ppp) REVERT: b 1 MET cc_start: 0.4626 (ptt) cc_final: 0.4391 (ptt) REVERT: b 21 MET cc_start: 0.6390 (ttp) cc_final: 0.5284 (tmm) REVERT: b 147 MET cc_start: 0.6642 (tpt) cc_final: 0.6311 (tpp) REVERT: c 219 MET cc_start: 0.8073 (mmp) cc_final: 0.7744 (mmm) REVERT: d 396 MET cc_start: 0.7853 (tpp) cc_final: 0.7598 (tpp) REVERT: e 245 MET cc_start: 0.9039 (ppp) cc_final: 0.8623 (ppp) REVERT: e 416 MET cc_start: 0.8258 (ptt) cc_final: 0.7647 (ptt) REVERT: A 204 MET cc_start: 0.6860 (tpt) cc_final: 0.6546 (tpt) REVERT: A 339 MET cc_start: 0.8340 (mmt) cc_final: 0.7969 (pmm) REVERT: A 389 MET cc_start: 0.8490 (tpt) cc_final: 0.8218 (tpt) REVERT: W 60 ASN cc_start: 0.9358 (m110) cc_final: 0.9095 (m-40) REVERT: X 370 MET cc_start: 0.8562 (ptp) cc_final: 0.8352 (ptp) REVERT: X 1085 MET cc_start: 0.8604 (mpp) cc_final: 0.8321 (mtm) REVERT: X 1304 MET cc_start: 0.7710 (tpt) cc_final: 0.7434 (tpt) REVERT: Y 102 MET cc_start: 0.7434 (mmp) cc_final: 0.7197 (ttt) REVERT: Y 130 MET cc_start: 0.5364 (ptm) cc_final: 0.4680 (tmm) REVERT: Y 237 MET cc_start: 0.8164 (tmm) cc_final: 0.7512 (tmm) REVERT: Y 932 MET cc_start: 0.6949 (mpp) cc_final: 0.6452 (mmp) REVERT: Y 1040 MET cc_start: 0.7478 (mpp) cc_final: 0.6662 (mpp) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.5288 time to fit residues: 220.9698 Evaluate side-chains 227 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 4.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 554 optimal weight: 0.0870 chunk 584 optimal weight: 30.0000 chunk 533 optimal weight: 10.0000 chunk 568 optimal weight: 10.0000 chunk 342 optimal weight: 9.9990 chunk 247 optimal weight: 0.0020 chunk 446 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 chunk 513 optimal weight: 6.9990 chunk 537 optimal weight: 4.9990 chunk 566 optimal weight: 2.9990 overall best weight: 1.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN V 103 ASN V 268 ASN ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 448 GLN ** Y1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 52532 Z= 0.162 Angle : 0.584 26.035 71294 Z= 0.290 Chirality : 0.047 1.967 8160 Planarity : 0.004 0.073 9006 Dihedral : 12.439 178.934 8027 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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 (0.11), residues: 6306 helix: 0.73 (0.11), residues: 2483 sheet: -0.87 (0.17), residues: 814 loop : -1.12 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 33 HIS 0.005 0.001 HIS X1244 PHE 0.011 0.001 PHE c 62 TYR 0.013 0.001 TYR c 110 ARG 0.006 0.000 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 4.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 341 MET cc_start: 0.7951 (tpp) cc_final: 0.7239 (mmm) REVERT: f 396 MET cc_start: 0.9210 (tmm) cc_final: 0.8897 (ppp) REVERT: a 327 MET cc_start: 0.8585 (ptm) cc_final: 0.8118 (ppp) REVERT: a 396 MET cc_start: 0.8203 (mmm) cc_final: 0.7891 (mmm) REVERT: b 1 MET cc_start: 0.4630 (ptt) cc_final: 0.4397 (ptt) REVERT: b 21 MET cc_start: 0.6418 (ttp) cc_final: 0.5196 (tmm) REVERT: b 147 MET cc_start: 0.6597 (tpt) cc_final: 0.6350 (tpp) REVERT: c 219 MET cc_start: 0.7915 (mmp) cc_final: 0.7599 (mmm) REVERT: d 396 MET cc_start: 0.7808 (tpp) cc_final: 0.7578 (tpp) REVERT: e 245 MET cc_start: 0.8992 (ppp) cc_final: 0.8622 (ppp) REVERT: e 416 MET cc_start: 0.8148 (ptt) cc_final: 0.7925 (ptt) REVERT: A 204 MET cc_start: 0.6775 (tpt) cc_final: 0.6486 (tpt) REVERT: A 339 MET cc_start: 0.8478 (mmt) cc_final: 0.7975 (pmm) REVERT: A 389 MET cc_start: 0.8479 (tpt) cc_final: 0.8219 (tpt) REVERT: W 26 ARG cc_start: 0.9336 (tpp-160) cc_final: 0.9091 (tpp-160) REVERT: W 60 ASN cc_start: 0.9297 (m110) cc_final: 0.8733 (m-40) REVERT: X 370 MET cc_start: 0.8618 (ptp) cc_final: 0.8346 (ptp) REVERT: X 1085 MET cc_start: 0.8570 (mpp) cc_final: 0.8265 (mtm) REVERT: X 1119 MET cc_start: 0.7770 (tpp) cc_final: 0.7514 (tpp) REVERT: Y 130 MET cc_start: 0.5309 (ptm) cc_final: 0.4559 (tmm) REVERT: Y 237 MET cc_start: 0.8126 (tmm) cc_final: 0.7482 (tmm) REVERT: Y 932 MET cc_start: 0.6965 (mpp) cc_final: 0.6485 (mmp) REVERT: Y 1040 MET cc_start: 0.7474 (mpp) cc_final: 0.6627 (mpp) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.5425 time to fit residues: 224.3644 Evaluate side-chains 225 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 4.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 373 optimal weight: 20.0000 chunk 601 optimal weight: 0.0980 chunk 366 optimal weight: 9.9990 chunk 285 optimal weight: 0.4980 chunk 417 optimal weight: 10.0000 chunk 630 optimal weight: 10.0000 chunk 580 optimal weight: 0.8980 chunk 502 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 387 optimal weight: 7.9990 chunk 307 optimal weight: 8.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 190 ASN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 275 ASN ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 72 GLN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 52532 Z= 0.163 Angle : 0.586 25.975 71294 Z= 0.290 Chirality : 0.047 1.959 8160 Planarity : 0.004 0.068 9006 Dihedral : 12.387 178.464 8027 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % 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: -0.51 (0.11), residues: 6306 helix: 0.75 (0.11), residues: 2484 sheet: -0.73 (0.17), residues: 849 loop : -1.13 (0.11), residues: 2973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 334 HIS 0.006 0.001 HIS X 150 PHE 0.022 0.001 PHE f 412 TYR 0.012 0.001 TYR c 110 ARG 0.008 0.000 ARG W 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12612 Ramachandran restraints generated. 6306 Oldfield, 0 Emsley, 6306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 4.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 341 MET cc_start: 0.8012 (tpp) cc_final: 0.7176 (mmm) REVERT: f 396 MET cc_start: 0.9212 (tmm) cc_final: 0.8907 (ppp) REVERT: a 327 MET cc_start: 0.8588 (ptm) cc_final: 0.8118 (ppp) REVERT: a 396 MET cc_start: 0.8257 (mmm) cc_final: 0.8006 (mmm) REVERT: b 1 MET cc_start: 0.5093 (ptt) cc_final: 0.4868 (ptt) REVERT: b 21 MET cc_start: 0.6261 (ttp) cc_final: 0.5127 (tmm) REVERT: b 147 MET cc_start: 0.6469 (tpt) cc_final: 0.6251 (tpp) REVERT: c 219 MET cc_start: 0.7930 (mmp) cc_final: 0.7637 (mmm) REVERT: d 396 MET cc_start: 0.7885 (tpp) cc_final: 0.7658 (tpp) REVERT: e 245 MET cc_start: 0.8969 (ppp) cc_final: 0.8572 (ppp) REVERT: e 416 MET cc_start: 0.8177 (ptt) cc_final: 0.7924 (ptt) REVERT: A 204 MET cc_start: 0.7180 (tpt) cc_final: 0.6973 (tpt) REVERT: A 339 MET cc_start: 0.8334 (mmt) cc_final: 0.7960 (pmm) REVERT: A 389 MET cc_start: 0.8424 (tpt) cc_final: 0.8125 (tpt) REVERT: W 60 ASN cc_start: 0.9121 (m110) cc_final: 0.8718 (m-40) REVERT: X 369 MET cc_start: 0.9267 (tmm) cc_final: 0.9054 (tmm) REVERT: X 370 MET cc_start: 0.8605 (ptp) cc_final: 0.8346 (ptp) REVERT: X 1085 MET cc_start: 0.8510 (mpp) cc_final: 0.8215 (mtm) REVERT: Y 130 MET cc_start: 0.5526 (ptm) cc_final: 0.4772 (tmm) REVERT: Y 237 MET cc_start: 0.8083 (tmm) cc_final: 0.7451 (tmm) REVERT: Y 932 MET cc_start: 0.7005 (mpp) cc_final: 0.6511 (mmp) REVERT: Y 1040 MET cc_start: 0.7542 (mpp) cc_final: 0.6673 (mpp) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.5382 time to fit residues: 224.5383 Evaluate side-chains 224 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 4.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 633 random chunks: chunk 398 optimal weight: 9.9990 chunk 534 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 463 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 502 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 516 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 126 ASN ** f 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 117 ASN ** d 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN V 23 HIS ** W 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.033263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.020790 restraints weight = 795478.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.021029 restraints weight = 588296.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.021365 restraints weight = 472370.770| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 52532 Z= 0.254 Angle : 0.643 25.929 71294 Z= 0.324 Chirality : 0.047 1.960 8160 Planarity : 0.004 0.085 9006 Dihedral : 12.511 179.402 8027 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.12 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.11), residues: 6306 helix: 0.66 (0.11), residues: 2484 sheet: -0.98 (0.17), residues: 817 loop : -1.07 (0.11), residues: 3005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 381 HIS 0.009 0.001 HIS Y 777 PHE 0.017 0.002 PHE b 62 TYR 0.021 0.002 TYR X1231 ARG 0.021 0.001 ARG f 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7325.82 seconds wall clock time: 132 minutes 9.23 seconds (7929.23 seconds total)