Starting phenix.real_space_refine on Tue Nov 19 09:51:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/11_2024/7adb_11722.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/11_2024/7adb_11722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/11_2024/7adb_11722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/11_2024/7adb_11722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/11_2024/7adb_11722.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/11_2024/7adb_11722.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 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 84 5.49 5 Mg 6 5.21 5 S 223 5.16 5 Be 5 3.05 5 C 31897 2.51 5 N 9072 2.21 5 O 10026 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 173 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 51330 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: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2510 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain: "V" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1828 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} 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': 1, 'PTRANS': 55, '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: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 497 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "L" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 682 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "R" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 364 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 1, 'rna3p': 15} Chain breaks: 1 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: 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: "d" 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: "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: "f" 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: "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} Chain: "f" 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 39513 SG CYS Y 70 94.114 111.046 92.022 1.00164.10 S ATOM 39527 SG CYS Y 72 93.362 107.519 92.259 1.00173.13 S ATOM 39635 SG CYS Y 85 90.800 109.992 92.691 1.00119.58 S ATOM 39659 SG CYS Y 88 93.949 110.750 95.561 1.00146.28 S ATOM 45347 SG CYS Y 814 105.619 176.997 88.573 1.00 80.35 S ATOM 45912 SG CYS Y 888 108.351 173.231 89.446 1.00 84.15 S ATOM 45963 SG CYS Y 895 104.963 173.401 87.191 1.00 81.30 S ATOM 45984 SG CYS Y 898 108.341 175.591 86.670 1.00 64.63 S Restraints were copied for chains: b, c, d, e, f Time building chain proxies: 26.00, per 1000 atoms: 0.51 Number of scatterers: 51330 At special positions: 0 Unit cell: (197.16, 217, 163.68, 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 84 15.00 Mg 6 11.99 F 15 9.00 O 10026 8.00 N 9072 7.00 C 31897 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.96 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Y1502 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 85 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 88 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 72 " pdb="ZN ZN Y1502 " - pdb=" SG CYS Y 70 " 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 : 12 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11748 Finding SS restraints... Secondary structure from input PDB file: 239 helices and 76 sheets defined 42.1% alpha, 15.1% beta 29 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 18.28 Creating SS restraints... Processing helix chain 'a' and resid 3 through 8 Processing helix chain 'a' and resid 10 through 21 Processing helix chain 'a' and resid 25 through 29 removed outlier: 4.021A pdb=" N ARG a 28 " --> pdb=" O ASN a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 45 Processing helix chain 'a' and resid 82 through 90 removed outlier: 4.281A pdb=" N ILE a 86 " --> pdb=" O SER a 82 " (cutoff:3.500A) Processing helix chain 'a' and resid 123 through 128 Processing helix chain 'a' and resid 155 through 166 removed outlier: 3.882A pdb=" N ALA a 159 " --> pdb=" O GLU a 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 199 Processing helix chain 'a' and resid 212 through 221 removed outlier: 3.596A pdb=" N ARG a 221 " --> pdb=" O THR a 217 " (cutoff:3.500A) Processing helix chain 'a' and resid 235 through 256 Processing helix chain 'a' and resid 266 through 278 removed outlier: 3.915A pdb=" N LEU a 270 " --> pdb=" O SER a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 285 through 289 removed outlier: 3.879A pdb=" N VAL a 289 " --> pdb=" O THR a 286 " (cutoff:3.500A) 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 326 through 337 removed outlier: 4.032A pdb=" N GLY a 337 " --> pdb=" O GLU a 333 " (cutoff:3.500A) Processing helix chain 'a' and resid 367 through 372 removed outlier: 3.529A pdb=" N LEU a 370 " --> pdb=" O LYS a 367 " (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 Processing helix chain 'b' and resid 3 through 8 Processing helix chain 'b' and resid 10 through 21 Processing helix chain 'b' and resid 25 through 29 removed outlier: 4.020A pdb=" N ARG b 28 " --> pdb=" O ASN b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 45 Processing helix chain 'b' and resid 82 through 90 removed outlier: 4.281A pdb=" N ILE b 86 " --> pdb=" O SER b 82 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 128 Processing helix chain 'b' and resid 155 through 166 removed outlier: 3.883A pdb=" N ALA b 159 " --> pdb=" O GLU b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 184 through 199 Processing helix chain 'b' and resid 212 through 221 removed outlier: 3.597A pdb=" N ARG b 221 " --> pdb=" O THR b 217 " (cutoff:3.500A) Processing helix chain 'b' and resid 235 through 256 Processing helix chain 'b' and resid 266 through 278 removed outlier: 3.914A pdb=" N LEU b 270 " --> pdb=" O SER b 266 " (cutoff:3.500A) Processing helix chain 'b' and resid 285 through 289 removed outlier: 3.879A pdb=" N VAL b 289 " --> pdb=" O THR b 286 " (cutoff:3.500A) 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 326 through 337 removed outlier: 4.032A pdb=" N GLY b 337 " --> pdb=" O GLU b 333 " (cutoff:3.500A) Processing helix chain 'b' and resid 367 through 372 removed outlier: 3.529A pdb=" N LEU b 370 " --> pdb=" O LYS b 367 " (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 Processing helix chain 'c' and resid 3 through 8 Processing helix chain 'c' and resid 10 through 21 Processing helix chain 'c' and resid 25 through 29 removed outlier: 4.021A pdb=" N ARG c 28 " --> pdb=" O ASN c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 45 Processing helix chain 'c' and resid 82 through 90 removed outlier: 4.281A pdb=" N ILE c 86 " --> pdb=" O SER c 82 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 128 Processing helix chain 'c' and resid 155 through 166 removed outlier: 3.882A pdb=" N ALA c 159 " --> pdb=" O GLU c 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 184 through 199 Processing helix chain 'c' and resid 212 through 221 removed outlier: 3.596A pdb=" N ARG c 221 " --> pdb=" O THR c 217 " (cutoff:3.500A) Processing helix chain 'c' and resid 235 through 256 Processing helix chain 'c' and resid 266 through 278 removed outlier: 3.914A pdb=" N LEU c 270 " --> pdb=" O SER c 266 " (cutoff:3.500A) Processing helix chain 'c' and resid 285 through 289 removed outlier: 3.879A pdb=" N VAL c 289 " --> pdb=" O THR c 286 " (cutoff:3.500A) 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 326 through 337 removed outlier: 4.032A pdb=" N GLY c 337 " --> pdb=" O GLU c 333 " (cutoff:3.500A) Processing helix chain 'c' and resid 367 through 372 removed outlier: 3.530A pdb=" N LEU c 370 " --> pdb=" O LYS c 367 " (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 Processing helix chain 'd' and resid 3 through 8 Processing helix chain 'd' and resid 10 through 21 Processing helix chain 'd' and resid 25 through 29 removed outlier: 4.020A pdb=" N ARG d 28 " --> pdb=" O ASN d 25 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 45 Processing helix chain 'd' and resid 82 through 90 removed outlier: 4.281A pdb=" N ILE d 86 " --> pdb=" O SER d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 128 Processing helix chain 'd' and resid 155 through 166 removed outlier: 3.882A pdb=" N ALA d 159 " --> pdb=" O GLU d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 199 Processing helix chain 'd' and resid 212 through 221 removed outlier: 3.597A pdb=" N ARG d 221 " --> pdb=" O THR d 217 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 256 Processing helix chain 'd' and resid 266 through 278 removed outlier: 3.914A pdb=" N LEU d 270 " --> pdb=" O SER d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 285 through 289 removed outlier: 3.880A pdb=" N VAL d 289 " --> pdb=" O THR d 286 " (cutoff:3.500A) 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 326 through 337 removed outlier: 4.033A pdb=" N GLY d 337 " --> pdb=" O GLU d 333 " (cutoff:3.500A) Processing helix chain 'd' and resid 367 through 372 removed outlier: 3.529A pdb=" N LEU d 370 " --> pdb=" O LYS d 367 " (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 Processing helix chain 'e' and resid 3 through 8 Processing helix chain 'e' and resid 10 through 21 Processing helix chain 'e' and resid 25 through 29 removed outlier: 4.020A pdb=" N ARG e 28 " --> pdb=" O ASN e 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 45 Processing helix chain 'e' and resid 82 through 90 removed outlier: 4.280A pdb=" N ILE e 86 " --> pdb=" O SER e 82 " (cutoff:3.500A) Processing helix chain 'e' and resid 123 through 128 Processing helix chain 'e' and resid 155 through 166 removed outlier: 3.883A pdb=" N ALA e 159 " --> pdb=" O GLU e 155 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 199 Processing helix chain 'e' and resid 212 through 221 removed outlier: 3.597A pdb=" N ARG e 221 " --> pdb=" O THR e 217 " (cutoff:3.500A) Processing helix chain 'e' and resid 235 through 256 Processing helix chain 'e' and resid 266 through 278 removed outlier: 3.914A pdb=" N LEU e 270 " --> pdb=" O SER e 266 " (cutoff:3.500A) Processing helix chain 'e' and resid 285 through 289 removed outlier: 3.880A pdb=" N VAL e 289 " --> pdb=" O THR e 286 " (cutoff:3.500A) 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 326 through 337 removed outlier: 4.032A pdb=" N GLY e 337 " --> pdb=" O GLU e 333 " (cutoff:3.500A) Processing helix chain 'e' and resid 367 through 372 removed outlier: 3.529A pdb=" N LEU e 370 " --> pdb=" O LYS e 367 " (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 Processing helix chain 'f' and resid 3 through 8 Processing helix chain 'f' and resid 10 through 21 Processing helix chain 'f' and resid 25 through 29 removed outlier: 4.020A pdb=" N ARG f 28 " --> pdb=" O ASN f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 45 Processing helix chain 'f' and resid 82 through 90 removed outlier: 4.281A pdb=" N ILE f 86 " --> pdb=" O SER f 82 " (cutoff:3.500A) Processing helix chain 'f' and resid 123 through 128 Processing helix chain 'f' and resid 155 through 166 removed outlier: 3.883A pdb=" N ALA f 159 " --> pdb=" O GLU f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 184 through 199 Processing helix chain 'f' and resid 212 through 221 removed outlier: 3.597A pdb=" N ARG f 221 " --> pdb=" O THR f 217 " (cutoff:3.500A) Processing helix chain 'f' and resid 235 through 256 Processing helix chain 'f' and resid 266 through 278 removed outlier: 3.915A pdb=" N LEU f 270 " --> pdb=" O SER f 266 " (cutoff:3.500A) Processing helix chain 'f' and resid 285 through 289 removed outlier: 3.879A pdb=" N VAL f 289 " --> pdb=" O THR f 286 " (cutoff:3.500A) 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 326 through 337 removed outlier: 4.032A pdb=" N GLY f 337 " --> pdb=" O GLU f 333 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 372 removed outlier: 3.530A pdb=" N LEU f 370 " --> pdb=" O LYS f 367 " (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 Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 19 through 39 removed outlier: 3.760A pdb=" N LYS A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.761A pdb=" N ASP A 84 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 133 Processing helix chain 'A' and resid 201 through 213 removed outlier: 4.266A pdb=" N LEU A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 206 " --> pdb=" O PRO A 202 " (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: 4.017A 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 332 removed outlier: 3.892A pdb=" N ALA A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 426 Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 441 through 452 removed outlier: 4.028A pdb=" N GLY A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.599A pdb=" N GLN A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 490 Processing helix chain 'U' and resid 34 through 50 removed outlier: 3.610A 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 212 through 233 removed outlier: 4.254A pdb=" N ASP U 233 " --> pdb=" O GLU U 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 256 through 260 removed outlier: 3.691A pdb=" N ASP U 259 " --> pdb=" O PRO U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 264 through 273 removed outlier: 3.680A pdb=" N GLU U 273 " --> pdb=" O CYS U 269 " (cutoff:3.500A) Processing helix chain 'U' and resid 277 through 282 removed outlier: 3.762A pdb=" N LEU U 281 " --> pdb=" O TYR U 277 " (cutoff:3.500A) Processing helix chain 'U' and resid 283 through 285 No H-bonds generated for 'chain 'U' and resid 283 through 285' Processing helix chain 'U' and resid 286 through 291 removed outlier: 4.130A pdb=" N LEU U 290 " --> pdb=" O GLU U 286 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS U 291 " --> pdb=" O VAL U 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 286 through 291' Processing helix chain 'U' and resid 297 through 309 removed outlier: 3.669A pdb=" N LEU U 307 " --> pdb=" O ILE U 303 " (cutoff:3.500A) Processing helix chain 'V' and resid 18 through 21 Processing helix chain 'V' and resid 34 through 49 removed outlier: 3.817A pdb=" N THR V 38 " --> pdb=" O GLY V 34 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER V 49 " --> pdb=" O ARG V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 87 removed outlier: 3.534A 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 163 Processing helix chain 'V' and resid 212 through 229 Processing helix chain 'W' and resid 6 through 13 removed outlier: 3.966A pdb=" N LYS W 12 " --> pdb=" O ASP W 8 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 32 Processing helix chain 'W' and resid 45 through 57 removed outlier: 3.506A pdb=" N ILE W 49 " --> pdb=" O LYS W 45 " (cutoff:3.500A) removed outlier: 3.673A 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 Processing helix chain 'X' and resid 28 through 39 removed outlier: 3.612A pdb=" N LEU X 32 " --> pdb=" O LEU X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 57 Processing helix chain 'X' and resid 81 through 89 Processing helix chain 'X' and resid 163 through 167 removed outlier: 3.505A pdb=" N SER X 166 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER X 167 " --> pdb=" O THR X 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 163 through 167' Processing helix chain 'X' and resid 205 through 212 removed outlier: 4.003A pdb=" N ILE X 209 " --> pdb=" O PRO X 205 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 224 Processing helix chain 'X' and resid 242 through 247 removed outlier: 3.681A pdb=" N LEU X 246 " --> pdb=" O PRO X 243 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG X 247 " --> pdb=" O GLU X 244 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 281 Processing helix chain 'X' and resid 288 through 295 removed outlier: 4.524A pdb=" N ILE X 292 " --> pdb=" O PRO X 288 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA X 293 " --> pdb=" O VAL X 289 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY X 294 " --> pdb=" O GLU X 290 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS X 295 " --> pdb=" O TYR X 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 288 through 295' Processing helix chain 'X' and resid 318 through 329 removed outlier: 3.844A pdb=" N GLY X 329 " --> pdb=" O LEU X 325 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 353 removed outlier: 3.584A 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 389 Processing helix chain 'X' and resid 398 through 409 Processing helix chain 'X' and resid 421 through 438 removed outlier: 4.064A pdb=" N ILE X 425 " --> pdb=" O SER X 421 " (cutoff:3.500A) Processing helix chain 'X' and resid 447 through 449 No H-bonds generated for 'chain 'X' and resid 447 through 449' Processing helix chain 'X' and resid 455 through 480 removed outlier: 3.552A pdb=" N MET X 459 " --> pdb=" O SER X 455 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG X 470 " --> pdb=" O VAL X 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 495 through 508 Processing helix chain 'X' and resid 519 through 528 Processing helix chain 'X' and resid 544 through 549 removed outlier: 3.659A pdb=" N ARG X 548 " --> pdb=" O GLY X 544 " (cutoff:3.500A) Processing helix chain 'X' and resid 551 through 555 Processing helix chain 'X' and resid 664 through 668 removed outlier: 3.568A pdb=" N LEU X 667 " --> pdb=" O GLY X 664 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE X 668 " --> pdb=" O ALA X 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 664 through 668' Processing helix chain 'X' and resid 670 through 674 Processing helix chain 'X' and resid 675 through 686 Processing helix chain 'X' and resid 704 through 712 removed outlier: 3.632A pdb=" N ALA X 709 " --> pdb=" O GLU X 705 " (cutoff:3.500A) removed outlier: 4.288A 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 896 through 906 Processing helix chain 'X' and resid 942 through 979 Processing helix chain 'X' and resid 982 through 990 Processing helix chain 'X' and resid 993 through 997 Processing helix chain 'X' and resid 1003 through 1038 removed outlier: 4.862A pdb=" N ASN X1009 " --> pdb=" O GLU X1005 " (cutoff:3.500A) Processing helix chain 'X' and resid 1099 through 1103 removed outlier: 3.564A pdb=" N GLY X1102 " --> pdb=" O ASN X1099 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL X1103 " --> pdb=" O PRO X1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 1099 through 1103' Processing helix chain 'X' and resid 1109 through 1134 removed outlier: 3.694A pdb=" N LEU X1113 " --> pdb=" O ILE X1109 " (cutoff:3.500A) Processing helix chain 'X' and resid 1137 through 1150 removed outlier: 3.859A pdb=" N LEU X1141 " --> pdb=" O GLU X1137 " (cutoff:3.500A) Processing helix chain 'X' and resid 1167 through 1177 removed outlier: 3.716A pdb=" N ARG X1171 " --> pdb=" O GLU X1167 " (cutoff:3.500A) Processing helix chain 'X' and resid 1192 through 1202 Processing helix chain 'X' and resid 1238 through 1243 removed outlier: 3.618A pdb=" N LYS X1242 " --> pdb=" O LEU X1238 " (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 1310 Processing helix chain 'X' and resid 1320 through 1332 removed outlier: 3.513A pdb=" N ASN X1324 " --> pdb=" O PRO X1320 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 33 Processing helix chain 'Y' and resid 96 through 101 removed outlier: 3.890A pdb=" N GLU Y 100 " --> pdb=" O LYS Y 96 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 117 Processing helix chain 'Y' and resid 123 through 128 Processing helix chain 'Y' and resid 131 through 140 removed outlier: 3.720A pdb=" N ILE Y 135 " --> pdb=" O PRO Y 131 " (cutoff:3.500A) Processing helix chain 'Y' and resid 161 through 168 Processing helix chain 'Y' and resid 181 through 191 Processing helix chain 'Y' and resid 194 through 208 Processing helix chain 'Y' and resid 211 through 230 Processing helix chain 'Y' and resid 233 through 236 Processing helix chain 'Y' and resid 246 through 250 Processing helix chain 'Y' and resid 263 through 285 removed outlier: 4.383A pdb=" N ASP Y 267 " --> pdb=" O SER Y 263 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU Y 268 " --> pdb=" O ASP Y 264 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP Y 284 " --> pdb=" O LYS Y 280 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU Y 285 " --> pdb=" O ARG Y 281 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 308 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 removed outlier: 3.503A pdb=" N ALA Y 397 " --> pdb=" O THR Y 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 405 through 416 removed outlier: 4.171A pdb=" N TRP Y 409 " --> pdb=" O GLU Y 405 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP Y 410 " --> pdb=" O ALA Y 406 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE Y 411 " --> pdb=" O VAL Y 407 " (cutoff:3.500A) 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 450 through 458 removed outlier: 3.686A pdb=" N CYS Y 454 " --> pdb=" O HIS Y 450 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA Y 455 " --> pdb=" O PRO Y 451 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA Y 456 " --> pdb=" O LEU Y 452 " (cutoff:3.500A) Processing helix chain 'Y' and resid 473 through 484 Processing helix chain 'Y' and resid 503 through 515 Processing helix chain 'Y' and resid 529 through 539 Processing helix chain 'Y' and resid 573 through 580 Processing helix chain 'Y' and resid 597 through 613 Processing helix chain 'Y' and resid 614 through 634 removed outlier: 3.618A pdb=" N VAL Y 618 " --> pdb=" O LEU Y 614 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE Y 619 " --> pdb=" O LYS Y 615 " (cutoff:3.500A) Processing helix chain 'Y' and resid 640 through 644 removed outlier: 3.589A pdb=" N MET Y 644 " --> pdb=" O ILE Y 641 " (cutoff:3.500A) Processing helix chain 'Y' and resid 649 through 670 Processing helix chain 'Y' and resid 674 through 702 removed outlier: 3.957A pdb=" N ASP Y 684 " --> pdb=" O ASN Y 680 " (cutoff:3.500A) Processing helix chain 'Y' and resid 722 through 728 removed outlier: 3.746A 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: 4.007A pdb=" N LYS Y 781 " --> pdb=" O HIS Y 777 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY Y 782 " --> pdb=" O GLY Y 778 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR Y 786 " --> pdb=" O GLY Y 782 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA Y 787 " --> pdb=" O LEU Y 783 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA Y 791 " --> pdb=" O ALA Y 787 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN Y 792 " --> pdb=" O LEU Y 788 " (cutoff:3.500A) Processing helix chain 'Y' and resid 834 through 840 removed outlier: 3.893A pdb=" N ARG Y 838 " --> pdb=" O PRO Y 834 " (cutoff:3.500A) Processing helix chain 'Y' and resid 865 through 876 Processing helix chain 'Y' and resid 895 through 899 removed outlier: 3.658A pdb=" N TYR Y 899 " --> pdb=" O ALA Y 896 " (cutoff:3.500A) Processing helix chain 'Y' and resid 914 through 925 removed outlier: 3.862A 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 1137 through 1147 removed outlier: 3.716A pdb=" N VAL Y1141 " --> pdb=" O GLY Y1137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1216 through 1225 removed outlier: 3.792A pdb=" N ILE Y1220 " --> pdb=" O ALA Y1216 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG Y1222 " --> pdb=" O HIS Y1218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1225 through 1245 removed outlier: 3.718A pdb=" N VAL Y1229 " --> pdb=" O GLY Y1225 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN Y1244 " --> pdb=" O VAL Y1240 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1249 through 1261 removed outlier: 4.464A pdb=" N ILE Y1253 " --> pdb=" O ASN Y1249 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1282 through 1295 removed outlier: 3.954A pdb=" N ASN Y1295 " --> pdb=" O GLU Y1291 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1308 through 1315 removed outlier: 3.668A pdb=" N SER Y1313 " --> pdb=" O ILE Y1309 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU Y1314 " --> pdb=" O THR Y1310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1319 through 1325 removed outlier: 3.670A pdb=" N PHE Y1325 " --> pdb=" O SER Y1321 " (cutoff:3.500A) Processing helix chain 'Y' and resid 1327 through 1339 Processing helix chain 'Y' and resid 1347 through 1354 Processing helix chain 'Y' and resid 1361 through 1373 removed outlier: 3.942A pdb=" N TYR Y1365 " --> pdb=" O THR Y1361 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 49 through 57 removed outlier: 7.723A pdb=" N TYR a 80 " --> pdb=" O LEU a 113 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS a 115 " --> pdb=" O TYR a 80 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU a 114 " --> pdb=" O ARG a 102 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ARG a 102 " --> pdb=" O LEU a 114 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL a 116 " --> pdb=" O LYS a 100 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS a 100 " --> pdb=" O VAL a 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AA3, first strand: chain 'a' and resid 144 through 145 removed outlier: 4.260A pdb=" N ILE a 168 " --> pdb=" O LEU a 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 226 through 230 removed outlier: 7.191A pdb=" N LEU a 204 " --> pdb=" O GLU a 226 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N VAL a 228 " --> pdb=" O LEU a 204 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL a 206 " --> pdb=" O VAL a 228 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N SER a 230 " --> pdb=" O VAL a 206 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU a 208 " --> pdb=" O SER a 230 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL a 203 " --> pdb=" O ASP a 259 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL a 260 " --> pdb=" O THR a 314 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE a 316 " --> pdb=" O VAL a 260 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE a 262 " --> pdb=" O ILE a 316 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N THR a 318 " --> pdb=" O ILE a 262 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU a 264 " --> pdb=" O THR a 318 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N LEU a 320 " --> pdb=" O LEU a 264 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY a 174 " --> pdb=" O ALA a 317 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ALA a 319 " --> pdb=" O GLY a 174 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE a 176 " --> pdb=" O ALA a 319 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG a 173 " --> pdb=" O MET a 341 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU a 343 " --> pdb=" O ARG a 173 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU a 175 " --> pdb=" O LEU a 343 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU a 342 " --> pdb=" O GLY a 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 49 through 57 removed outlier: 7.723A pdb=" N TYR b 80 " --> pdb=" O LEU b 113 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS b 115 " --> pdb=" O TYR b 80 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU b 114 " --> pdb=" O ARG b 102 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ARG b 102 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL b 116 " --> pdb=" O LYS b 100 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS b 100 " --> pdb=" O VAL b 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'b' and resid 144 through 145 removed outlier: 4.260A pdb=" N ILE b 168 " --> pdb=" O LEU b 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 226 through 230 removed outlier: 7.191A pdb=" N LEU b 204 " --> pdb=" O GLU b 226 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL b 228 " --> pdb=" O LEU b 204 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL b 206 " --> pdb=" O VAL b 228 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N SER b 230 " --> pdb=" O VAL b 206 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU b 208 " --> pdb=" O SER b 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL b 203 " --> pdb=" O ASP b 259 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL b 260 " --> pdb=" O THR b 314 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE b 316 " --> pdb=" O VAL b 260 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE b 262 " --> pdb=" O ILE b 316 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR b 318 " --> pdb=" O ILE b 262 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU b 264 " --> pdb=" O THR b 318 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N LEU b 320 " --> pdb=" O LEU b 264 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY b 174 " --> pdb=" O ALA b 317 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ALA b 319 " --> pdb=" O GLY b 174 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE b 176 " --> pdb=" O ALA b 319 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG b 173 " --> pdb=" O MET b 341 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU b 343 " --> pdb=" O ARG b 173 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU b 175 " --> pdb=" O LEU b 343 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU b 342 " --> pdb=" O GLY b 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'c' and resid 49 through 57 removed outlier: 7.723A pdb=" N TYR c 80 " --> pdb=" O LEU c 113 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N LYS c 115 " --> pdb=" O TYR c 80 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU c 114 " --> pdb=" O ARG c 102 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ARG c 102 " --> pdb=" O LEU c 114 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL c 116 " --> pdb=" O LYS c 100 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS c 100 " --> pdb=" O VAL c 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 138 through 139 Processing sheet with id=AB2, first strand: chain 'c' and resid 144 through 145 removed outlier: 4.260A pdb=" N ILE c 168 " --> pdb=" O LEU c 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 226 through 230 removed outlier: 7.191A pdb=" N LEU c 204 " --> pdb=" O GLU c 226 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL c 228 " --> pdb=" O LEU c 204 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL c 206 " --> pdb=" O VAL c 228 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N SER c 230 " --> pdb=" O VAL c 206 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU c 208 " --> pdb=" O SER c 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL c 203 " --> pdb=" O ASP c 259 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL c 260 " --> pdb=" O THR c 314 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE c 316 " --> pdb=" O VAL c 260 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE c 262 " --> pdb=" O ILE c 316 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N THR c 318 " --> pdb=" O ILE c 262 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU c 264 " --> pdb=" O THR c 318 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N LEU c 320 " --> pdb=" O LEU c 264 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY c 174 " --> pdb=" O ALA c 317 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA c 319 " --> pdb=" O GLY c 174 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE c 176 " --> pdb=" O ALA c 319 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG c 173 " --> pdb=" O MET c 341 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU c 343 " --> pdb=" O ARG c 173 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU c 175 " --> pdb=" O LEU c 343 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU c 342 " --> pdb=" O GLY c 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'd' and resid 49 through 57 removed outlier: 7.722A pdb=" N TYR d 80 " --> pdb=" O LEU d 113 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS d 115 " --> pdb=" O TYR d 80 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU d 114 " --> pdb=" O ARG d 102 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ARG d 102 " --> pdb=" O LEU d 114 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL d 116 " --> pdb=" O LYS d 100 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS d 100 " --> pdb=" O VAL d 116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 138 through 139 Processing sheet with id=AB6, first strand: chain 'd' and resid 144 through 145 removed outlier: 4.260A pdb=" N ILE d 168 " --> pdb=" O LEU d 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 226 through 230 removed outlier: 7.190A pdb=" N LEU d 204 " --> pdb=" O GLU d 226 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL d 228 " --> pdb=" O LEU d 204 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL d 206 " --> pdb=" O VAL d 228 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N SER d 230 " --> pdb=" O VAL d 206 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU d 208 " --> pdb=" O SER d 230 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL d 203 " --> pdb=" O ASP d 259 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL d 260 " --> pdb=" O THR d 314 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE d 316 " --> pdb=" O VAL d 260 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE d 262 " --> pdb=" O ILE d 316 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N THR d 318 " --> pdb=" O ILE d 262 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU d 264 " --> pdb=" O THR d 318 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N LEU d 320 " --> pdb=" O LEU d 264 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY d 174 " --> pdb=" O ALA d 317 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA d 319 " --> pdb=" O GLY d 174 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE d 176 " --> pdb=" O ALA d 319 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG d 173 " --> pdb=" O MET d 341 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU d 343 " --> pdb=" O ARG d 173 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU d 175 " --> pdb=" O LEU d 343 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU d 342 " --> pdb=" O GLY d 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'e' and resid 49 through 57 removed outlier: 7.723A pdb=" N TYR e 80 " --> pdb=" O LEU e 113 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N LYS e 115 " --> pdb=" O TYR e 80 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU e 114 " --> pdb=" O ARG e 102 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ARG e 102 " --> pdb=" O LEU e 114 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL e 116 " --> pdb=" O LYS e 100 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS e 100 " --> pdb=" O VAL e 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'e' and resid 138 through 139 Processing sheet with id=AC1, first strand: chain 'e' and resid 144 through 145 removed outlier: 4.260A pdb=" N ILE e 168 " --> pdb=" O LEU e 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 226 through 230 removed outlier: 7.191A pdb=" N LEU e 204 " --> pdb=" O GLU e 226 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL e 228 " --> pdb=" O LEU e 204 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL e 206 " --> pdb=" O VAL e 228 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N SER e 230 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU e 208 " --> pdb=" O SER e 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL e 203 " --> pdb=" O ASP e 259 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL e 260 " --> pdb=" O THR e 314 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE e 316 " --> pdb=" O VAL e 260 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE e 262 " --> pdb=" O ILE e 316 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR e 318 " --> pdb=" O ILE e 262 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU e 264 " --> pdb=" O THR e 318 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N LEU e 320 " --> pdb=" O LEU e 264 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY e 174 " --> pdb=" O ALA e 317 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA e 319 " --> pdb=" O GLY e 174 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE e 176 " --> pdb=" O ALA e 319 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG e 173 " --> pdb=" O MET e 341 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU e 343 " --> pdb=" O ARG e 173 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU e 175 " --> pdb=" O LEU e 343 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU e 342 " --> pdb=" O GLY e 364 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'f' and resid 49 through 57 removed outlier: 7.723A pdb=" N TYR f 80 " --> pdb=" O LEU f 113 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N LYS f 115 " --> pdb=" O TYR f 80 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU f 114 " --> pdb=" O ARG f 102 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ARG f 102 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL f 116 " --> pdb=" O LYS f 100 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LYS f 100 " --> pdb=" O VAL f 116 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'f' and resid 138 through 139 Processing sheet with id=AC5, first strand: chain 'f' and resid 144 through 145 removed outlier: 4.260A pdb=" N ILE f 168 " --> pdb=" O LEU f 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 226 through 230 removed outlier: 7.191A pdb=" N LEU f 204 " --> pdb=" O GLU f 226 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL f 228 " --> pdb=" O LEU f 204 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL f 206 " --> pdb=" O VAL f 228 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N SER f 230 " --> pdb=" O VAL f 206 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU f 208 " --> pdb=" O SER f 230 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL f 203 " --> pdb=" O ASP f 259 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL f 260 " --> pdb=" O THR f 314 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE f 316 " --> pdb=" O VAL f 260 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE f 262 " --> pdb=" O ILE f 316 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR f 318 " --> pdb=" O ILE f 262 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU f 264 " --> pdb=" O THR f 318 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N LEU f 320 " --> pdb=" O LEU f 264 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY f 174 " --> pdb=" O ALA f 317 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ALA f 319 " --> pdb=" O GLY f 174 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE f 176 " --> pdb=" O ALA f 319 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG f 173 " --> pdb=" O MET f 341 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N LEU f 343 " --> pdb=" O ARG f 173 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU f 175 " --> pdb=" O LEU f 343 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU f 342 " --> pdb=" O GLY f 364 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 138 through 145 removed outlier: 6.767A pdb=" N SER A 151 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL A 145 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASN A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 195 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 163 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 221 through 229 removed outlier: 4.526A pdb=" N ILE A 223 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS A 239 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA A 234 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL A 274 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE A 236 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 293 through 299 removed outlier: 4.167A pdb=" N SER A 295 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 12 through 13 removed outlier: 5.466A pdb=" N LYS U 25 " --> pdb=" O MET U 205 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N MET U 205 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N THR U 27 " --> pdb=" O ILE U 203 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE U 203 " --> pdb=" O THR U 27 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU U 29 " --> pdb=" O LEU U 201 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU U 201 " --> pdb=" O GLU U 29 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'U' and resid 52 through 53 removed outlier: 3.608A pdb=" N GLY U 53 " --> pdb=" O GLY U 149 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'U' and resid 115 through 116 removed outlier: 4.595A pdb=" N THR U 101 " --> pdb=" O THR U 116 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU U 58 " --> pdb=" O LYS U 145 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN U 147 " --> pdb=" O VAL U 56 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N VAL U 56 " --> pdb=" O GLN U 147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 90 through 92 Processing sheet with id=AD5, first strand: chain 'U' and resid 108 through 111 removed outlier: 6.332A pdb=" N GLY U 108 " --> pdb=" O HIS U 132 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS U 132 " --> pdb=" O GLY U 108 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL U 110 " --> pdb=" O ILE U 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 16 through 17 removed outlier: 6.374A pdb=" N ASP V 199 " --> pdb=" O PRO V 30 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 55 through 61 removed outlier: 5.812A pdb=" N VAL V 56 " --> pdb=" O GLN V 147 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLN V 147 " --> pdb=" O VAL V 56 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 90 through 92 Processing sheet with id=AD9, first strand: chain 'V' and resid 104 through 105 removed outlier: 3.838A pdb=" N LYS V 104 " --> pdb=" O ILE V 140 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE V 140 " --> pdb=" O LYS V 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'V' and resid 109 through 111 Processing sheet with id=AE2, first strand: chain 'V' and resid 152 through 153 removed outlier: 3.940A pdb=" N ALA V 175 " --> pdb=" O VAL V 153 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X' and resid 59 through 60 removed outlier: 3.574A pdb=" N ILE X 59 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS X 99 " --> pdb=" O VAL X 71 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR X 73 " --> pdb=" O ARG X 97 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ARG X 97 " --> pdb=" O TYR X 73 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU X 75 " --> pdb=" O PRO X 95 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ALA X 94 " --> pdb=" O GLU X 126 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU X 126 " --> pdb=" O ALA X 94 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU X 96 " --> pdb=" O MET X 124 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE X 104 " --> pdb=" O ASP X 116 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASP X 116 " --> pdb=" O ILE X 104 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 136 through 137 removed outlier: 3.560A pdb=" N GLN X 513 " --> pdb=" O VAL X 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 451 through 454 removed outlier: 6.592A pdb=" N SER X 147 " --> pdb=" O SER X 531 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER X 574 " --> pdb=" O CYS X 559 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 154 through 160 removed outlier: 5.995A pdb=" N TYR X 172 " --> pdb=" O PHE X 188 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE X 188 " --> pdb=" O TYR X 172 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 228 through 231 Processing sheet with id=AE8, first strand: chain 'X' and resid 239 through 240 removed outlier: 3.789A pdb=" N MET X 239 " --> pdb=" O ILE X 285 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 255 through 257 removed outlier: 6.354A pdb=" N ALA X 257 " --> pdb=" O VAL X 261 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL X 261 " --> pdb=" O ALA X 257 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 296 through 297 removed outlier: 4.482A pdb=" N MET X 315 " --> pdb=" O VAL X 297 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 301 through 302 removed outlier: 7.537A pdb=" N TYR X 301 " --> pdb=" O ILE X 310 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE X 310 " --> pdb=" O TYR X 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'X' and resid 580 through 581 removed outlier: 5.498A pdb=" N GLU X 602 " --> pdb=" O LYS X 593 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'X' and resid 580 through 581 Processing sheet with id=AF5, first strand: chain 'X' and resid 616 through 617 removed outlier: 3.832A pdb=" N ILE X 616 " --> pdb=" O ARG X 637 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG X 637 " --> pdb=" O ILE X 616 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'X' and resid 623 through 624 removed outlier: 3.695A pdb=" N HIS X 628 " --> pdb=" O ASP X 624 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 700 through 701 Processing sheet with id=AF8, first strand: chain 'X' and resid 716 through 717 removed outlier: 6.654A pdb=" N ALA X 716 " --> pdb=" O LEU X 783 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'X' and resid 722 through 727 removed outlier: 6.644A pdb=" N VAL X 733 " --> pdb=" O GLN X 725 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL X 727 " --> pdb=" O ARG X 731 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG X 731 " --> pdb=" O VAL X 727 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 757 through 758 removed outlier: 3.746A pdb=" N THR X 757 " --> pdb=" O ILE X 765 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE X 765 " --> pdb=" O THR X 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'X' and resid 798 through 804 removed outlier: 9.057A pdb=" N ILE X1096 " --> pdb=" O ASN X 799 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG X 801 " --> pdb=" O ILE X1096 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU X1098 " --> pdb=" O ARG X 801 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA X 803 " --> pdb=" O LEU X1098 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU X 817 " --> pdb=" O VAL X1097 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE X 816 " --> pdb=" O LYS X1078 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN X1080 " --> pdb=" O ILE X 816 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL X 818 " --> pdb=" O ASN X1080 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 830 through 841 removed outlier: 3.605A pdb=" N SER X 840 " --> pdb=" O LYS X1048 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS X1048 " --> pdb=" O SER X 840 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU X1047 " --> pdb=" O THR X 935 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR X 935 " --> pdb=" O LEU X1047 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE X1049 " --> pdb=" O VAL X 933 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL X 933 " --> pdb=" O ILE X1049 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS X1051 " --> pdb=" O VAL X 931 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL X 931 " --> pdb=" O LYS X1051 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR X1053 " --> pdb=" O ILE X 929 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 1087 through 1088 Processing sheet with id=AG5, first strand: chain 'X' and resid 1244 through 1246 removed outlier: 3.643A pdb=" N HIS X1244 " --> pdb=" O ARG Y 352 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG X1246 " --> pdb=" O SER Y 350 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER Y 350 " --> pdb=" O ARG X1246 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N CYS Y 366 " --> pdb=" O VAL Y 440 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE Y 442 " --> pdb=" O CYS Y 366 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU Y 368 " --> pdb=" O ILE Y 442 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 1244 through 1246 removed outlier: 3.643A pdb=" N HIS X1244 " --> pdb=" O ARG Y 352 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG X1246 " --> pdb=" O SER Y 350 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER Y 350 " --> pdb=" O ARG X1246 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE Y 447 " --> pdb=" O ARG Y 352 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL Y 354 " --> pdb=" O ILE Y 447 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU Y 449 " --> pdb=" O VAL Y 354 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N THR Y 356 " --> pdb=" O LEU Y 449 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 1335 through 1339 removed outlier: 3.552A pdb=" N ILE Y 20 " --> pdb=" O ASP Y1342 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 34 through 37 removed outlier: 7.384A pdb=" N HIS Y 104 " --> pdb=" O PHE Y 35 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU Y 37 " --> pdb=" O HIS Y 104 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLU Y 106 " --> pdb=" O GLU Y 37 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU Y 107 " --> pdb=" O THR Y 240 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR Y 240 " --> pdb=" O LEU Y 107 " (cutoff:3.500A) removed outlier: 10.657A pdb=" N SER Y 109 " --> pdb=" O ILE Y 238 " (cutoff:3.500A) removed outlier: 10.294A pdb=" N ILE Y 238 " --> pdb=" O SER Y 109 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 144 through 145 Processing sheet with id=AH1, first strand: chain 'Y' and resid 317 through 319 removed outlier: 6.582A pdb=" N ARG Y 322 " --> pdb=" O GLY Y 318 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 548 through 557 Processing sheet with id=AH3, first strand: chain 'Y' and resid 707 through 708 Processing sheet with id=AH4, first strand: chain 'Y' and resid 820 through 822 removed outlier: 3.631A pdb=" N VAL Y 880 " --> pdb=" O MET Y 822 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 848 through 849 removed outlier: 3.638A pdb=" N VAL Y 858 " --> pdb=" O VAL Y 848 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 991 through 996 removed outlier: 4.037A pdb=" N GLU Y 993 " --> pdb=" O LEU Y 984 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU Y 981 " --> pdb=" O SER Y 961 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 965 through 967 Processing sheet with id=AH8, first strand: chain 'Y' and resid 1002 through 1003 removed outlier: 3.656A pdb=" N VAL Y1002 " --> pdb=" O ASN Y1019 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Y' and resid 1033 through 1035 removed outlier: 3.702A pdb=" N GLY Y1033 " --> pdb=" O ILE Y1115 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL Y1035 " --> pdb=" O VAL Y1113 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL Y1113 " --> pdb=" O VAL Y1035 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Y' and resid 1046 through 1047 removed outlier: 3.543A pdb=" N THR Y1047 " --> pdb=" O VAL Y1060 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL Y1060 " --> pdb=" O THR Y1047 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 1077 through 1079 Processing sheet with id=AI3, first strand: chain 'Y' and resid 1162 through 1164 Processing sheet with id=AI4, first strand: chain 'Y' and resid 1279 through 1281 2032 hydrogen bonds defined for protein. 5718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 29 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 28.70 Time building geometry restraints manager: 14.96 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: 16684 1.34 - 1.46: 6599 1.46 - 1.57: 28368 1.57 - 1.69: 161 1.69 - 1.81: 408 Bond restraints: 52220 Sorted by residual: bond pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " 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 f1002 " pdb="BE BEF f1002 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.87e+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 1.84e+01 bond pdb=" F2 BEF d1002 " pdb="BE BEF d1002 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" F2 BEF b 501 " pdb="BE BEF b 501 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 52215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 70029 2.53 - 5.06: 665 5.06 - 7.59: 98 7.59 - 10.13: 11 10.13 - 12.66: 8 Bond angle restraints: 70811 Sorted by residual: angle pdb=" N ILE Y 500 " pdb=" CA ILE Y 500 " pdb=" C ILE Y 500 " ideal model delta sigma weight residual 111.91 108.02 3.89 8.90e-01 1.26e+00 1.91e+01 angle pdb=" F2 BEF f1002 " pdb="BE BEF f1002 " pdb=" F3 BEF f1002 " ideal model delta sigma weight residual 119.96 107.30 12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" C LEU A 183 " pdb=" N TYR A 184 " pdb=" CA TYR A 184 " ideal model delta sigma weight residual 122.58 113.86 8.72 2.07e+00 2.33e-01 1.78e+01 angle pdb=" F2 BEF b 501 " pdb="BE BEF b 501 " pdb=" F3 BEF b 501 " ideal model delta sigma weight residual 119.96 107.33 12.63 3.00e+00 1.11e-01 1.77e+01 angle pdb=" F2 BEF c1002 " pdb="BE BEF c1002 " pdb=" F3 BEF c1002 " ideal model delta sigma weight residual 119.96 107.37 12.59 3.00e+00 1.11e-01 1.76e+01 ... (remaining 70806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.10: 30322 28.10 - 56.19: 1570 56.19 - 84.29: 175 84.29 - 112.38: 26 112.38 - 140.48: 5 Dihedral angle restraints: 32098 sinusoidal: 13897 harmonic: 18201 Sorted by residual: dihedral pdb=" C5' ADP e1000 " pdb=" O5' ADP e1000 " pdb=" PA ADP e1000 " pdb=" O2A ADP e1000 " ideal model delta sinusoidal sigma weight residual 300.00 164.30 135.70 1 2.00e+01 2.50e-03 4.12e+01 dihedral pdb=" O1B ADP c1000 " pdb=" O3A ADP c1000 " pdb=" PB ADP c1000 " pdb=" PA ADP c1000 " ideal model delta sinusoidal sigma weight residual 300.00 170.81 129.18 1 2.00e+01 2.50e-03 3.92e+01 dihedral pdb=" C5' ADP d1000 " pdb=" O5' ADP d1000 " pdb=" PA ADP d1000 " pdb=" O2A ADP d1000 " ideal model delta sinusoidal sigma weight residual 300.00 172.21 127.80 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 32095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5846 0.039 - 0.078: 1555 0.078 - 0.117: 593 0.117 - 0.156: 90 0.156 - 0.195: 10 Chirality restraints: 8094 Sorted by residual: chirality pdb=" CB ILE e 382 " pdb=" CA ILE e 382 " pdb=" CG1 ILE e 382 " pdb=" CG2 ILE e 382 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CB ILE a 382 " pdb=" CA ILE a 382 " pdb=" CG1 ILE a 382 " pdb=" CG2 ILE a 382 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CB ILE c 382 " pdb=" CA ILE c 382 " pdb=" CG1 ILE c 382 " pdb=" CG2 ILE c 382 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.43e-01 ... (remaining 8091 not shown) Planarity restraints: 8994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS a 388 " 0.049 5.00e-02 4.00e+02 7.43e-02 8.84e+00 pdb=" N PRO a 389 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO a 389 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO a 389 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS f 388 " 0.049 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO f 389 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO f 389 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO f 389 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS e 388 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.82e+00 pdb=" N PRO e 389 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO e 389 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO e 389 " -0.041 5.00e-02 4.00e+02 ... (remaining 8991 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 756 2.60 - 3.18: 44628 3.18 - 3.75: 82851 3.75 - 4.33: 109708 4.33 - 4.90: 175639 Nonbonded interactions: 413582 Sorted by model distance: nonbonded pdb=" O2B ADP c1000 " pdb="MG MG c1001 " model vdw 2.026 2.170 nonbonded pdb=" O3' C R 99 " pdb="MG MG Y1501 " model vdw 2.056 2.170 nonbonded pdb="MG MG c1001 " pdb=" O HOH c1102 " model vdw 2.066 2.170 nonbonded pdb=" O2B ADP d1000 " pdb="MG MG d1001 " model vdw 2.074 2.170 nonbonded pdb=" O2B ADP e1000 " pdb="MG MG e1001 " model vdw 2.078 2.170 ... (remaining 413577 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' 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' and resid 1 through 417) } 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.190 Check model and map are aligned: 0.350 Set scattering table: 0.490 Process input model: 133.990 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 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 52220 Z= 0.203 Angle : 0.650 12.656 70811 Z= 0.355 Chirality : 0.042 0.195 8094 Planarity : 0.004 0.074 8994 Dihedral : 15.815 140.477 20350 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.90 % Allowed : 6.71 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.09), residues: 6307 helix: -1.70 (0.09), residues: 2376 sheet: -1.78 (0.15), residues: 912 loop : -2.90 (0.09), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 997 HIS 0.003 0.001 HIS d 295 PHE 0.030 0.001 PHE A 24 TYR 0.012 0.001 TYR Y 679 ARG 0.014 0.000 ARG X 10 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 264 poor density : 429 time to evaluate : 5.949 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: 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 54 VAL cc_start: 0.9158 (OUTLIER) cc_final: 0.8569 (p) REVERT: a 245 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7467 (mmt) REVERT: a 281 SER cc_start: 0.4187 (OUTLIER) cc_final: 0.1925 (p) REVERT: a 338 THR cc_start: 0.6324 (OUTLIER) cc_final: 0.6012 (t) REVERT: b 4 THR cc_start: 0.9068 (OUTLIER) cc_final: 0.8707 (m) REVERT: b 29 MET cc_start: 0.9129 (ptp) cc_final: 0.8897 (ptp) REVERT: b 54 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8130 (p) REVERT: b 403 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9201 (tt) REVERT: b 411 ASP cc_start: 0.9184 (OUTLIER) cc_final: 0.8834 (t0) REVERT: b 415 MET cc_start: 0.8462 (ptm) cc_final: 0.7973 (ptt) REVERT: c 54 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8432 (p) REVERT: c 166 SER cc_start: 0.8547 (OUTLIER) cc_final: 0.8163 (m) REVERT: c 186 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7411 (pmm) REVERT: c 194 SER cc_start: 0.7680 (OUTLIER) cc_final: 0.6818 (p) REVERT: c 309 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7346 (pm20) REVERT: c 390 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8079 (mmm) REVERT: c 410 ASP cc_start: 0.9452 (m-30) cc_final: 0.8936 (p0) REVERT: c 411 ASP cc_start: 0.9390 (OUTLIER) cc_final: 0.8907 (t0) REVERT: c 415 MET cc_start: 0.8877 (ptm) cc_final: 0.8563 (ptt) REVERT: d 166 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8221 (m) REVERT: d 233 ASP cc_start: 0.8945 (m-30) cc_final: 0.8617 (p0) REVERT: d 300 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6762 (t80) REVERT: d 309 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7442 (pm20) REVERT: d 380 MET cc_start: 0.9706 (mtp) cc_final: 0.9482 (mtt) REVERT: e 233 ASP cc_start: 0.9311 (m-30) cc_final: 0.8573 (p0) REVERT: e 241 GLN cc_start: 0.9510 (tm-30) cc_final: 0.9275 (tm-30) REVERT: e 380 MET cc_start: 0.9609 (mtp) cc_final: 0.9347 (tpt) REVERT: f 54 VAL cc_start: 0.7906 (OUTLIER) cc_final: 0.7092 (p) REVERT: f 114 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8069 (mp) REVERT: f 166 SER cc_start: 0.7725 (OUTLIER) cc_final: 0.7507 (m) REVERT: f 309 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: f 403 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7851 (tp) REVERT: A 305 MET cc_start: -0.2145 (mtt) cc_final: -0.2694 (ptp) REVERT: W 49 ILE cc_start: 0.8953 (pt) cc_final: 0.8247 (pt) REVERT: Y 1040 MET cc_start: 0.4290 (mpp) cc_final: 0.3850 (mtm) outliers start: 264 outliers final: 54 residues processed: 649 average time/residue: 0.6908 time to fit residues: 738.2866 Evaluate side-chains 360 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 533 optimal weight: 6.9990 chunk 479 optimal weight: 7.9990 chunk 265 optimal weight: 30.0000 chunk 163 optimal weight: 0.0870 chunk 323 optimal weight: 0.0870 chunk 255 optimal weight: 7.9990 chunk 495 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 301 optimal weight: 20.0000 chunk 368 optimal weight: 3.9990 chunk 573 optimal weight: 3.9990 overall best weight: 2.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 32 GLN a 42 HIS ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 198 ASN a 295 HIS a 388 HIS b 32 GLN b 42 HIS b 140 HIS ** b 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 198 ASN b 295 HIS b 388 HIS c 32 GLN ** c 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 198 ASN c 295 HIS d 90 ASN d 198 ASN e 42 HIS ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 140 HIS e 198 ASN ** e 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 388 HIS f 198 ASN f 295 HIS A 96 GLN A 129 GLN A 157 ASN A 303 HIS A 324 ASN A 412 ASN U 103 ASN U 160 HIS U 227 GLN W 29 GLN X 139 ASN X 193 ASN ** X 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 684 ASN X 688 GLN ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 832 HIS X 932 GLN X1116 HIS ** X1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Y 365 GLN Y 477 GLN Y 739 GLN ** Y 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 52220 Z= 0.192 Angle : 0.598 9.529 70811 Z= 0.304 Chirality : 0.042 0.200 8094 Planarity : 0.005 0.094 8994 Dihedral : 11.281 142.879 7837 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -2.16 (0.10), residues: 6307 helix: -0.37 (0.10), residues: 2319 sheet: -1.40 (0.16), residues: 903 loop : -2.32 (0.10), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 115 HIS 0.010 0.001 HIS V 160 PHE 0.029 0.001 PHE d 300 TYR 0.015 0.001 TYR d 274 ARG 0.013 0.001 ARG Y1284 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 320 time to evaluate : 5.964 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: a 29 MET cc_start: 0.0830 (ptt) cc_final: 0.0511 (ptt) REVERT: a 380 MET cc_start: 0.9358 (mtm) cc_final: 0.9156 (ptp) REVERT: b 380 MET cc_start: 0.9174 (ptm) cc_final: 0.8931 (ptp) REVERT: b 411 ASP cc_start: 0.9222 (t70) cc_final: 0.8914 (t0) REVERT: c 21 MET cc_start: 0.6632 (ptp) cc_final: 0.5820 (ptp) REVERT: c 186 MET cc_start: 0.7807 (ptm) cc_final: 0.7397 (ppp) REVERT: c 245 MET cc_start: 0.7831 (tpt) cc_final: 0.7238 (tpt) REVERT: c 410 ASP cc_start: 0.9444 (m-30) cc_final: 0.8961 (p0) REVERT: c 415 MET cc_start: 0.9019 (ptm) cc_final: 0.8793 (ptt) REVERT: d 186 MET cc_start: 0.6517 (pmm) cc_final: 0.6255 (pmm) REVERT: d 233 ASP cc_start: 0.9053 (m-30) cc_final: 0.8732 (p0) REVERT: d 245 MET cc_start: 0.7762 (mmt) cc_final: 0.7183 (mmm) REVERT: d 374 GLN cc_start: 0.9684 (tp-100) cc_final: 0.9459 (tp-100) REVERT: d 380 MET cc_start: 0.9736 (mtp) cc_final: 0.9533 (mtt) REVERT: d 396 MET cc_start: 0.9616 (mmp) cc_final: 0.9384 (mmm) REVERT: e 380 MET cc_start: 0.9627 (mtp) cc_final: 0.9348 (tpt) REVERT: e 405 MET cc_start: 0.6900 (ptp) cc_final: 0.6580 (ptp) REVERT: e 415 MET cc_start: 0.7599 (ptt) cc_final: 0.6492 (ptt) REVERT: f 147 MET cc_start: 0.6324 (mpp) cc_final: 0.5908 (mpp) REVERT: f 396 MET cc_start: 0.8050 (mtp) cc_final: 0.7751 (mmt) REVERT: f 405 MET cc_start: 0.7175 (pmm) cc_final: 0.6861 (pmm) REVERT: f 415 MET cc_start: 0.8321 (ptt) cc_final: 0.8098 (ptt) REVERT: V 103 ASN cc_start: 0.7268 (m-40) cc_final: 0.7038 (m-40) REVERT: X 1304 MET cc_start: 0.7774 (mmp) cc_final: 0.7475 (mmm) REVERT: Y 180 MET cc_start: 0.7266 (tpp) cc_final: 0.6963 (mmm) REVERT: Y 1040 MET cc_start: 0.3906 (mpp) cc_final: 0.3008 (mpp) outliers start: 3 outliers final: 0 residues processed: 323 average time/residue: 0.6841 time to fit residues: 368.9029 Evaluate side-chains 259 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 5.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 318 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 chunk 477 optimal weight: 30.0000 chunk 390 optimal weight: 0.8980 chunk 158 optimal weight: 0.0770 chunk 574 optimal weight: 9.9990 chunk 621 optimal weight: 0.9990 chunk 512 optimal weight: 1.9990 chunk 570 optimal weight: 8.9990 chunk 196 optimal weight: 20.0000 chunk 461 optimal weight: 0.0970 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 295 HIS ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 160 HIS V 147 GLN ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 232 ASN ** Y1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 52220 Z= 0.160 Angle : 0.568 10.279 70811 Z= 0.285 Chirality : 0.042 0.176 8094 Planarity : 0.004 0.084 8994 Dihedral : 11.208 142.541 7837 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.71 (0.10), residues: 6307 helix: 0.10 (0.11), residues: 2330 sheet: -1.25 (0.16), residues: 922 loop : -2.11 (0.10), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 334 HIS 0.008 0.001 HIS V 160 PHE 0.024 0.001 PHE A 24 TYR 0.015 0.001 TYR X 47 ARG 0.011 0.000 ARG V 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 298 time to evaluate : 5.957 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: a 29 MET cc_start: 0.0841 (ptt) cc_final: 0.0536 (ptt) REVERT: a 327 MET cc_start: 0.9394 (pmm) cc_final: 0.9193 (pmm) REVERT: b 29 MET cc_start: 0.7478 (ptt) cc_final: 0.7143 (ptt) REVERT: b 186 MET cc_start: 0.7127 (pmm) cc_final: 0.6799 (pmm) REVERT: b 380 MET cc_start: 0.9242 (ptm) cc_final: 0.8988 (ptp) REVERT: b 396 MET cc_start: 0.9275 (mmm) cc_final: 0.8922 (mmm) REVERT: c 21 MET cc_start: 0.6050 (ptp) cc_final: 0.5516 (ptp) REVERT: c 186 MET cc_start: 0.7595 (ptm) cc_final: 0.7379 (ppp) REVERT: c 245 MET cc_start: 0.7881 (tpt) cc_final: 0.7362 (tpt) REVERT: c 410 ASP cc_start: 0.9411 (m-30) cc_final: 0.8917 (p0) REVERT: d 374 GLN cc_start: 0.9687 (tp-100) cc_final: 0.9472 (tp-100) REVERT: d 396 MET cc_start: 0.9633 (mmp) cc_final: 0.9427 (mmm) REVERT: e 241 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8870 (tm-30) REVERT: e 380 MET cc_start: 0.9615 (mtp) cc_final: 0.9146 (tpp) REVERT: e 415 MET cc_start: 0.7593 (ptt) cc_final: 0.6618 (ptt) REVERT: f 21 MET cc_start: 0.8314 (mtm) cc_final: 0.8094 (ptm) REVERT: f 147 MET cc_start: 0.6161 (mpp) cc_final: 0.5660 (mpp) REVERT: f 295 HIS cc_start: 0.9339 (m90) cc_final: 0.9058 (m-70) REVERT: f 405 MET cc_start: 0.7230 (pmm) cc_final: 0.6796 (pmm) REVERT: f 415 MET cc_start: 0.8302 (ptt) cc_final: 0.7612 (ptt) REVERT: f 416 MET cc_start: 0.7581 (tmm) cc_final: 0.7329 (ppp) REVERT: V 103 ASN cc_start: 0.7178 (m-40) cc_final: 0.6929 (m-40) REVERT: X 1243 MET cc_start: 0.7296 (ttm) cc_final: 0.6681 (ttt) REVERT: X 1304 MET cc_start: 0.7716 (mmp) cc_final: 0.7441 (mmm) REVERT: Y 1040 MET cc_start: 0.3918 (mpp) cc_final: 0.3620 (mtm) outliers start: 3 outliers final: 0 residues processed: 301 average time/residue: 0.6734 time to fit residues: 339.6932 Evaluate side-chains 254 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 6.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 568 optimal weight: 20.0000 chunk 432 optimal weight: 0.3980 chunk 298 optimal weight: 4.9990 chunk 63 optimal weight: 30.0000 chunk 274 optimal weight: 8.9990 chunk 386 optimal weight: 20.0000 chunk 577 optimal weight: 0.0870 chunk 610 optimal weight: 0.9980 chunk 301 optimal weight: 20.0000 chunk 546 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 overall best weight: 3.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 90 ASN ** a 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 140 HIS c 388 HIS ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 HIS ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 160 HIS ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 688 GLN ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 808 ASN Y1259 GLN ** Y1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 52220 Z= 0.189 Angle : 0.568 9.081 70811 Z= 0.287 Chirality : 0.041 0.178 8094 Planarity : 0.004 0.068 8994 Dihedral : 11.221 143.603 7837 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.02 % Allowed : 3.04 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.37 (0.10), residues: 6307 helix: 0.31 (0.11), residues: 2385 sheet: -1.05 (0.16), residues: 908 loop : -1.88 (0.10), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 997 HIS 0.008 0.001 HIS X1070 PHE 0.026 0.001 PHE A 24 TYR 0.035 0.001 TYR Y 999 ARG 0.023 0.000 ARG a 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 5.974 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: a 1 MET cc_start: 0.8868 (tmm) cc_final: 0.8485 (tmm) REVERT: a 29 MET cc_start: 0.0955 (ptt) cc_final: 0.0686 (ptt) REVERT: a 327 MET cc_start: 0.9396 (pmm) cc_final: 0.9183 (pmm) REVERT: b 29 MET cc_start: 0.7719 (ptt) cc_final: 0.7379 (ptt) REVERT: b 186 MET cc_start: 0.7371 (pmm) cc_final: 0.7112 (pmm) REVERT: b 380 MET cc_start: 0.9257 (ptm) cc_final: 0.9030 (ptp) REVERT: c 186 MET cc_start: 0.7801 (ptm) cc_final: 0.7365 (ppp) REVERT: c 405 MET cc_start: 0.9076 (ptp) cc_final: 0.8835 (ptp) REVERT: c 410 ASP cc_start: 0.9474 (m-30) cc_final: 0.8966 (p0) REVERT: c 415 MET cc_start: 0.8474 (ptt) cc_final: 0.7532 (ptt) REVERT: d 245 MET cc_start: 0.7730 (mmt) cc_final: 0.7174 (mmm) REVERT: d 374 GLN cc_start: 0.9728 (tp-100) cc_final: 0.9500 (tp-100) REVERT: d 396 MET cc_start: 0.9647 (mmp) cc_final: 0.9346 (mmm) REVERT: e 380 MET cc_start: 0.9587 (mtp) cc_final: 0.9140 (tpp) REVERT: e 405 MET cc_start: 0.7354 (ptp) cc_final: 0.7119 (ptp) REVERT: e 415 MET cc_start: 0.7533 (ptt) cc_final: 0.6499 (ptt) REVERT: f 147 MET cc_start: 0.6378 (mpp) cc_final: 0.5866 (mpp) REVERT: f 245 MET cc_start: 0.4676 (ttt) cc_final: 0.3899 (tpt) REVERT: f 292 ASN cc_start: 0.8490 (t0) cc_final: 0.7523 (p0) REVERT: f 405 MET cc_start: 0.7109 (pmm) cc_final: 0.6760 (pmm) REVERT: f 415 MET cc_start: 0.8047 (ptt) cc_final: 0.7488 (ptt) REVERT: A 337 ASN cc_start: 0.9043 (m-40) cc_final: 0.8813 (p0) REVERT: X 1304 MET cc_start: 0.7693 (mmp) cc_final: 0.7437 (mmm) REVERT: Y 372 MET cc_start: 0.7062 (mmm) cc_final: 0.6761 (mmm) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.6420 time to fit residues: 309.5256 Evaluate side-chains 239 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 5.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 508 optimal weight: 6.9990 chunk 346 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 454 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 521 optimal weight: 50.0000 chunk 422 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 311 optimal weight: 1.9990 chunk 548 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 ASN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 388 HIS ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 HIS ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 23 HIS X 41 GLN ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 766 ASN ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 651 HIS Y 817 HIS Y1049 GLN Y1218 HIS ** Y1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 52220 Z= 0.260 Angle : 0.623 9.522 70811 Z= 0.317 Chirality : 0.041 0.185 8094 Planarity : 0.004 0.068 8994 Dihedral : 11.328 143.953 7837 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.17 (0.10), residues: 6307 helix: 0.44 (0.11), residues: 2375 sheet: -1.16 (0.16), residues: 968 loop : -1.65 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 62 HIS 0.012 0.002 HIS Y 651 PHE 0.023 0.002 PHE X1025 TYR 0.033 0.002 TYR Y 144 ARG 0.016 0.001 ARG X1211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 6.029 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: a 1 MET cc_start: 0.8796 (tmm) cc_final: 0.8405 (tmm) REVERT: a 72 TYR cc_start: 0.8941 (m-10) cc_final: 0.8393 (m-80) REVERT: a 245 MET cc_start: 0.7429 (mmt) cc_final: 0.6387 (mtp) REVERT: a 327 MET cc_start: 0.9397 (pmm) cc_final: 0.9107 (pmm) REVERT: b 396 MET cc_start: 0.9349 (mmm) cc_final: 0.8617 (mmm) REVERT: c 21 MET cc_start: 0.6276 (ptm) cc_final: 0.5723 (ptm) REVERT: c 186 MET cc_start: 0.8110 (ptm) cc_final: 0.7744 (ptp) REVERT: c 245 MET cc_start: 0.7879 (tpt) cc_final: 0.7598 (tpt) REVERT: c 410 ASP cc_start: 0.9508 (m-30) cc_final: 0.9014 (p0) REVERT: c 415 MET cc_start: 0.8655 (ptt) cc_final: 0.7906 (ptt) REVERT: d 396 MET cc_start: 0.9681 (mmp) cc_final: 0.9274 (mmm) REVERT: e 205 MET cc_start: 0.9306 (mmm) cc_final: 0.8615 (mmm) REVERT: e 380 MET cc_start: 0.9574 (mtp) cc_final: 0.9094 (tpp) REVERT: e 415 MET cc_start: 0.7335 (ptt) cc_final: 0.6276 (ptt) REVERT: f 147 MET cc_start: 0.6795 (mpp) cc_final: 0.6270 (mpp) REVERT: f 245 MET cc_start: 0.5304 (ttt) cc_final: 0.4478 (tpt) REVERT: f 292 ASN cc_start: 0.8501 (t0) cc_final: 0.7515 (p0) REVERT: f 405 MET cc_start: 0.7757 (pmm) cc_final: 0.7198 (pmm) REVERT: f 415 MET cc_start: 0.8264 (ptt) cc_final: 0.7675 (ptt) REVERT: A 305 MET cc_start: -0.5372 (ptt) cc_final: -0.6454 (ptt) REVERT: A 337 ASN cc_start: 0.9022 (m-40) cc_final: 0.8792 (p0) REVERT: V 103 ASN cc_start: 0.7481 (m-40) cc_final: 0.7198 (p0) REVERT: W 18 ASP cc_start: 0.8031 (p0) cc_final: 0.7807 (p0) REVERT: X 681 MET cc_start: 0.7993 (ptp) cc_final: 0.7697 (ptm) REVERT: X 1304 MET cc_start: 0.7864 (mmp) cc_final: 0.7605 (mmm) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.6349 time to fit residues: 293.1543 Evaluate side-chains 234 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 5.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 205 optimal weight: 10.0000 chunk 550 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 358 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 611 optimal weight: 3.9990 chunk 507 optimal weight: 10.0000 chunk 283 optimal weight: 50.0000 chunk 50 optimal weight: 30.0000 chunk 202 optimal weight: 0.7980 chunk 321 optimal weight: 30.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 32 GLN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 90 ASN ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 344 HIS ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1209 GLN X1236 ASN X1268 GLN ** Y1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 52220 Z= 0.214 Angle : 0.592 9.227 70811 Z= 0.300 Chirality : 0.041 0.174 8094 Planarity : 0.004 0.069 8994 Dihedral : 11.360 144.076 7837 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -1.04 (0.11), residues: 6307 helix: 0.49 (0.11), residues: 2397 sheet: -1.14 (0.16), residues: 955 loop : -1.51 (0.11), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 62 HIS 0.005 0.001 HIS b 344 PHE 0.020 0.001 PHE A 24 TYR 0.039 0.002 TYR a 274 ARG 0.014 0.001 ARG c 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 5.989 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: a 1 MET cc_start: 0.8826 (tmm) cc_final: 0.8380 (tmm) REVERT: a 29 MET cc_start: 0.1592 (ptt) cc_final: 0.1159 (ptt) REVERT: a 72 TYR cc_start: 0.8828 (m-10) cc_final: 0.8546 (m-10) REVERT: b 186 MET cc_start: 0.7641 (pmm) cc_final: 0.7257 (pmm) REVERT: c 245 MET cc_start: 0.8021 (tpt) cc_final: 0.7760 (tpt) REVERT: c 264 LEU cc_start: 0.8933 (tt) cc_final: 0.8399 (mp) REVERT: c 410 ASP cc_start: 0.9534 (m-30) cc_final: 0.9034 (p0) REVERT: c 415 MET cc_start: 0.8670 (ptt) cc_final: 0.7846 (ptt) REVERT: e 205 MET cc_start: 0.9267 (mmm) cc_final: 0.8577 (mmm) REVERT: e 405 MET cc_start: 0.7624 (ptp) cc_final: 0.7420 (ptp) REVERT: e 415 MET cc_start: 0.7302 (ptt) cc_final: 0.6376 (ptt) REVERT: f 21 MET cc_start: 0.8280 (ppp) cc_final: 0.7755 (ppp) REVERT: f 147 MET cc_start: 0.6804 (mpp) cc_final: 0.6305 (mpp) REVERT: f 245 MET cc_start: 0.5201 (ttt) cc_final: 0.4805 (tpt) REVERT: f 292 ASN cc_start: 0.8542 (t0) cc_final: 0.7591 (p0) REVERT: f 415 MET cc_start: 0.8206 (ptt) cc_final: 0.7737 (ptt) REVERT: A 204 MET cc_start: 0.6330 (ttt) cc_final: 0.6063 (tpt) REVERT: A 305 MET cc_start: -0.5318 (ptt) cc_final: -0.6389 (ptt) REVERT: A 337 ASN cc_start: 0.9027 (m-40) cc_final: 0.8796 (p0) REVERT: W 18 ASP cc_start: 0.7759 (p0) cc_final: 0.7503 (p0) REVERT: X 681 MET cc_start: 0.7947 (ptp) cc_final: 0.7552 (ptp) REVERT: X 1304 MET cc_start: 0.7817 (mmp) cc_final: 0.7591 (mmm) REVERT: Y 1040 MET cc_start: 0.5675 (mpp) cc_final: 0.5456 (mtt) outliers start: 1 outliers final: 0 residues processed: 266 average time/residue: 0.6333 time to fit residues: 288.0365 Evaluate side-chains 234 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 589 optimal weight: 20.0000 chunk 68 optimal weight: 2.9990 chunk 348 optimal weight: 9.9990 chunk 446 optimal weight: 7.9990 chunk 345 optimal weight: 9.9990 chunk 514 optimal weight: 0.7980 chunk 341 optimal weight: 8.9990 chunk 609 optimal weight: 20.0000 chunk 381 optimal weight: 10.0000 chunk 371 optimal weight: 4.9990 chunk 281 optimal weight: 0.4980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 32 GLN ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 295 HIS ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 344 HIS ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 140 HIS ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 450 HIS Y1295 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 52220 Z= 0.196 Angle : 0.583 10.189 70811 Z= 0.294 Chirality : 0.042 0.234 8094 Planarity : 0.004 0.079 8994 Dihedral : 11.336 145.236 7837 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.33 % Cis-general : 0.10 % 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: -0.89 (0.11), residues: 6307 helix: 0.60 (0.11), residues: 2403 sheet: -1.09 (0.16), residues: 947 loop : -1.39 (0.11), residues: 2957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 62 HIS 0.006 0.001 HIS d 344 PHE 0.021 0.001 PHE A 24 TYR 0.016 0.001 TYR Y 999 ARG 0.013 0.000 ARG c 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12614 Ramachandran restraints generated. 6307 Oldfield, 0 Emsley, 6307 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 5.761 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: a 1 MET cc_start: 0.8814 (tmm) cc_final: 0.8348 (tmm) REVERT: a 29 MET cc_start: 0.1241 (ptt) cc_final: 0.0841 (ptt) REVERT: a 245 MET cc_start: 0.7670 (tpt) cc_final: 0.7229 (tpt) REVERT: b 396 MET cc_start: 0.9299 (mmm) cc_final: 0.8636 (mmm) REVERT: c 21 MET cc_start: 0.4950 (ptt) cc_final: 0.3116 (ptt) REVERT: c 245 MET cc_start: 0.8102 (tpt) cc_final: 0.7862 (tpt) REVERT: c 264 LEU cc_start: 0.8918 (tt) cc_final: 0.8414 (mp) REVERT: c 410 ASP cc_start: 0.9543 (m-30) cc_final: 0.9035 (p0) REVERT: c 415 MET cc_start: 0.8673 (ptt) cc_final: 0.7899 (ptt) REVERT: d 21 MET cc_start: 0.6425 (ptm) cc_final: 0.4356 (ppp) REVERT: d 245 MET cc_start: 0.8122 (mmt) cc_final: 0.7857 (mmt) REVERT: e 205 MET cc_start: 0.9251 (mmm) cc_final: 0.8599 (mmm) REVERT: e 380 MET cc_start: 0.9277 (mmm) cc_final: 0.8984 (tpt) REVERT: e 415 MET cc_start: 0.7421 (ptt) cc_final: 0.6386 (ptt) REVERT: f 21 MET cc_start: 0.8251 (ppp) cc_final: 0.7968 (ppp) REVERT: f 147 MET cc_start: 0.6824 (mpp) cc_final: 0.6330 (mpp) REVERT: f 245 MET cc_start: 0.5567 (ttt) cc_final: 0.4993 (tpt) REVERT: f 292 ASN cc_start: 0.8525 (t0) cc_final: 0.7531 (p0) REVERT: A 204 MET cc_start: 0.6227 (ttt) cc_final: 0.5985 (tpt) REVERT: A 305 MET cc_start: -0.5609 (ptt) cc_final: -0.6485 (ptt) REVERT: A 337 ASN cc_start: 0.8974 (m-40) cc_final: 0.8757 (p0) REVERT: W 18 ASP cc_start: 0.7953 (p0) cc_final: 0.7735 (p0) REVERT: X 681 MET cc_start: 0.8019 (ptp) cc_final: 0.7518 (ptp) REVERT: X 1243 MET cc_start: 0.7181 (ttm) cc_final: 0.6129 (ttm) REVERT: X 1304 MET cc_start: 0.7816 (mmp) cc_final: 0.7599 (mmm) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.6629 time to fit residues: 297.5779 Evaluate side-chains 234 residues out of total 5391 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 5.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/programs/real_space_refine.py", line 213, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6284 > 50: distance: 81 - 149: 29.214 distance: 83 - 87: 33.983 distance: 84 - 146: 34.395 distance: 87 - 88: 57.489 distance: 88 - 89: 68.356 distance: 88 - 91: 39.477 distance: 89 - 90: 41.147 distance: 89 - 94: 5.571 distance: 94 - 95: 6.297 distance: 95 - 96: 41.203 distance: 96 - 97: 40.086 distance: 96 - 102: 40.284 distance: 98 - 99: 68.669 distance: 102 - 103: 41.193 distance: 103 - 104: 56.809 distance: 103 - 106: 34.523 distance: 104 - 105: 38.923 distance: 104 - 111: 56.640 distance: 106 - 107: 4.126 distance: 107 - 108: 20.713 distance: 108 - 109: 33.211 distance: 108 - 110: 44.855 distance: 111 - 112: 29.020 distance: 112 - 113: 10.871 distance: 112 - 115: 28.584 distance: 113 - 114: 31.118 distance: 113 - 123: 31.548 distance: 116 - 117: 39.828 distance: 117 - 119: 33.015 distance: 118 - 120: 40.263 distance: 119 - 121: 28.842 distance: 120 - 121: 51.629 distance: 121 - 122: 14.359 distance: 123 - 124: 56.767 distance: 124 - 125: 49.584 distance: 125 - 126: 41.819 distance: 125 - 127: 32.231 distance: 127 - 128: 34.605 distance: 128 - 129: 54.631 distance: 128 - 131: 23.843 distance: 129 - 138: 47.400 distance: 131 - 132: 16.943 distance: 132 - 133: 19.028 distance: 132 - 134: 37.791 distance: 133 - 135: 16.716 distance: 134 - 136: 17.031 distance: 136 - 137: 28.404 distance: 138 - 139: 17.716 distance: 139 - 140: 43.607 distance: 139 - 142: 35.010 distance: 140 - 141: 34.841 distance: 140 - 146: 36.898 distance: 142 - 143: 29.119 distance: 143 - 144: 19.929 distance: 143 - 145: 22.053 distance: 147 - 148: 57.075 distance: 147 - 150: 39.205 distance: 148 - 149: 11.290 distance: 148 - 155: 30.720 distance: 152 - 153: 39.276 distance: 152 - 154: 15.292 distance: 155 - 156: 3.377 distance: 155 - 200: 31.786 distance: 156 - 157: 5.967 distance: 156 - 159: 21.511 distance: 157 - 158: 40.209 distance: 157 - 162: 14.624 distance: 158 - 197: 31.598 distance: 159 - 160: 5.477 distance: 159 - 161: 39.782 distance: 162 - 163: 49.975 distance: 162 - 168: 33.220 distance: 163 - 164: 49.437 distance: 163 - 166: 42.490 distance: 164 - 165: 47.139 distance: 164 - 169: 35.294 distance: 166 - 167: 48.241 distance: 167 - 168: 24.577