Starting phenix.real_space_refine on Tue Sep 24 17:18:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/09_2024/7adb_11722.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/09_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_11722/09_2024/7adb_11722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/09_2024/7adb_11722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/09_2024/7adb_11722.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adb_11722/09_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): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 20.72, per 1000 atoms: 0.40 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: 9.85 Conformation dependent library (CDL) restraints added in 4.9 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: 13.98 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: 21.56 Time building geometry restraints manager: 11.68 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.390 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 105.650 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.160 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.570 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 264 poor density : 429 time to evaluate : 4.412 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: 0.5526 time to fit residues: 586.8148 Evaluate side-chains 360 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 283 time to evaluate : 4.417 ------------------------------------------------------------------------------- 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 : 11.281 142.880 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 fitting. rotamer outliers: 3 poor density : 320 time to evaluate : 4.468 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: 0.6862 (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: 0.5705 time to fit residues: 305.3401 Evaluate side-chains 259 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 4.530 ------------------------------------------------------------------------------- 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: 1.9990 chunk 178 optimal weight: 4.9990 chunk 477 optimal weight: 30.0000 chunk 390 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 574 optimal weight: 6.9990 chunk 621 optimal weight: 1.9990 chunk 512 optimal weight: 10.0000 chunk 570 optimal weight: 5.9990 chunk 196 optimal weight: 20.0000 chunk 461 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 295 HIS d 32 GLN ** 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** A 337 ASN U 160 HIS V 147 GLN ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 808 ASN Y 232 ASN ** Y1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 52220 Z= 0.174 Angle : 0.567 10.047 70811 Z= 0.287 Chirality : 0.041 0.171 8094 Planarity : 0.004 0.085 8994 Dihedral : 11.232 142.795 7837 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.36 % 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: -1.63 (0.10), residues: 6307 helix: 0.16 (0.11), residues: 2331 sheet: -1.20 (0.16), residues: 908 loop : -2.06 (0.10), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 334 HIS 0.008 0.001 HIS V 160 PHE 0.024 0.001 PHE A 24 TYR 0.023 0.001 TYR e 110 ARG 0.012 0.000 ARG e 109 *********************** 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 298 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 295 time to evaluate : 4.481 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: 0.0869 (ptt) cc_final: 0.0546 (ptt) REVERT: a 327 MET cc_start: 0.9403 (pmm) cc_final: 0.9189 (pmm) REVERT: b 186 MET cc_start: 0.7320 (pmm) cc_final: 0.7019 (pmm) REVERT: b 380 MET cc_start: 0.9235 (ptm) cc_final: 0.8998 (ptp) REVERT: b 396 MET cc_start: 0.9272 (mmm) cc_final: 0.8932 (mmm) REVERT: c 21 MET cc_start: 0.6036 (ptp) cc_final: 0.5352 (ptp) REVERT: c 186 MET cc_start: 0.7682 (ptm) cc_final: 0.7319 (ppp) REVERT: c 245 MET cc_start: 0.7931 (tpt) cc_final: 0.7661 (tpt) REVERT: c 410 ASP cc_start: 0.9438 (m-30) cc_final: 0.8943 (p0) REVERT: d 374 GLN cc_start: 0.9696 (tp-100) cc_final: 0.9456 (tp-100) REVERT: d 396 MET cc_start: 0.9640 (mmp) cc_final: 0.9423 (mmm) REVERT: e 241 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8865 (tm-30) REVERT: e 380 MET cc_start: 0.9608 (mtp) cc_final: 0.9149 (tpp) REVERT: e 415 MET cc_start: 0.7567 (ptt) cc_final: 0.6457 (ptt) REVERT: f 147 MET cc_start: 0.6243 (mpp) cc_final: 0.5701 (mpp) REVERT: f 295 HIS cc_start: 0.9333 (m90) cc_final: 0.9028 (m-70) REVERT: f 396 MET cc_start: 0.7809 (mtp) cc_final: 0.7591 (mmp) REVERT: f 405 MET cc_start: 0.7286 (pmm) cc_final: 0.6829 (pmm) REVERT: f 415 MET cc_start: 0.8361 (ptt) cc_final: 0.7891 (ptt) REVERT: X 1243 MET cc_start: 0.7326 (ttm) cc_final: 0.6696 (ttt) REVERT: X 1304 MET cc_start: 0.7698 (mmp) cc_final: 0.7405 (mmm) REVERT: Y 1040 MET cc_start: 0.4324 (mpp) cc_final: 0.3517 (mpp) outliers start: 3 outliers final: 1 residues processed: 298 average time/residue: 0.5478 time to fit residues: 273.5673 Evaluate side-chains 249 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 4.414 ------------------------------------------------------------------------------- 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: 20.0000 chunk 298 optimal weight: 6.9990 chunk 63 optimal weight: 20.0000 chunk 274 optimal weight: 7.9990 chunk 386 optimal weight: 30.0000 chunk 577 optimal weight: 20.0000 chunk 610 optimal weight: 8.9990 chunk 301 optimal weight: 4.9990 chunk 546 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 90 ASN ** a 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 ASN b 344 HIS ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 42 HIS c 140 HIS ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 388 HIS ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 344 HIS ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 344 HIS f 140 HIS f 189 GLN ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 160 HIS ** V 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 41 GLN ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 799 ASN ** X 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1209 GLN X1220 GLN Y 277 ASN ** Y 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 651 HIS Y 817 HIS ** Y1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1197 ASN Y1218 HIS Y1259 GLN ** Y1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 52220 Z= 0.395 Angle : 0.804 11.892 70811 Z= 0.408 Chirality : 0.045 0.239 8094 Planarity : 0.006 0.165 8994 Dihedral : 11.627 145.131 7837 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.66 % 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: -1.63 (0.10), residues: 6307 helix: -0.04 (0.10), residues: 2361 sheet: -1.31 (0.17), residues: 871 loop : -1.85 (0.10), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Y1020 HIS 0.016 0.002 HIS Y 364 PHE 0.026 0.003 PHE X 972 TYR 0.050 0.003 TYR Y 999 ARG 0.043 0.001 ARG A 326 *********************** 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 269 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 265 time to evaluate : 4.500 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: a 1 MET cc_start: 0.8739 (tmm) cc_final: 0.8400 (tmm) REVERT: a 72 TYR cc_start: 0.8890 (m-80) cc_final: 0.8582 (m-10) REVERT: a 327 MET cc_start: 0.9376 (pmm) cc_final: 0.9100 (pmm) REVERT: a 380 MET cc_start: 0.9576 (mtm) cc_final: 0.9211 (ptp) REVERT: b 29 MET cc_start: 0.7809 (ptt) cc_final: 0.7458 (ptt) REVERT: b 396 MET cc_start: 0.9367 (mmm) cc_final: 0.8689 (mmm) REVERT: b 405 MET cc_start: 0.9537 (ptp) cc_final: 0.9233 (ptp) REVERT: c 186 MET cc_start: 0.8597 (ptm) cc_final: 0.7698 (ppp) REVERT: c 410 ASP cc_start: 0.9574 (m-30) cc_final: 0.9140 (p0) REVERT: c 415 MET cc_start: 0.8845 (ptt) cc_final: 0.8233 (ptt) REVERT: d 396 MET cc_start: 0.9693 (mmp) cc_final: 0.9347 (tpp) REVERT: e 374 GLN cc_start: 0.9825 (tp-100) cc_final: 0.9600 (tm-30) REVERT: e 380 MET cc_start: 0.9569 (mtp) cc_final: 0.9074 (tpp) REVERT: e 405 MET cc_start: 0.7628 (ptp) cc_final: 0.7300 (ptp) REVERT: e 415 MET cc_start: 0.7093 (ptt) cc_final: 0.6215 (ptt) REVERT: f 21 MET cc_start: 0.8258 (ptm) cc_final: 0.7590 (tmm) REVERT: f 147 MET cc_start: 0.6955 (mpp) cc_final: 0.6364 (mpp) REVERT: f 245 MET cc_start: 0.5288 (ttt) cc_final: 0.4656 (tpt) REVERT: f 396 MET cc_start: 0.7966 (mtp) cc_final: 0.7744 (mmp) REVERT: f 405 MET cc_start: 0.8054 (pmm) cc_final: 0.7806 (pmm) REVERT: f 415 MET cc_start: 0.8398 (ptt) cc_final: 0.7994 (ptt) REVERT: A 305 MET cc_start: -0.4836 (ptt) cc_final: -0.5351 (ptt) REVERT: X 1304 MET cc_start: 0.7825 (mmp) cc_final: 0.7343 (tpt) REVERT: X 1315 MET cc_start: 0.7528 (mpp) cc_final: 0.7155 (mpp) outliers start: 4 outliers final: 1 residues processed: 269 average time/residue: 0.5163 time to fit residues: 238.6932 Evaluate side-chains 229 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 4.412 ------------------------------------------------------------------------------- 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: 9.9990 chunk 346 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 454 optimal weight: 4.9990 chunk 252 optimal weight: 20.0000 chunk 521 optimal weight: 8.9990 chunk 422 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 311 optimal weight: 0.0020 chunk 548 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 overall best weight: 5.7996 ------------------------------------------------------------------------------- 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 ** 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 140 HIS e 126 ASN ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 HIS ** 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 613 ASN X 688 GLN ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1236 ASN ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1049 GLN Y1197 ASN Y1295 ASN ** Y1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 52220 Z= 0.265 Angle : 0.637 9.414 70811 Z= 0.327 Chirality : 0.042 0.217 8094 Planarity : 0.005 0.127 8994 Dihedral : 11.597 148.958 7837 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -1.39 (0.10), residues: 6307 helix: 0.17 (0.11), residues: 2401 sheet: -1.37 (0.17), residues: 879 loop : -1.67 (0.11), residues: 3027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 62 HIS 0.006 0.001 HIS Y 364 PHE 0.015 0.002 PHE X 35 TYR 0.029 0.002 TYR a 274 ARG 0.015 0.001 ARG c 160 *********************** 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 265 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 4.455 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: a 1 MET cc_start: 0.8757 (tmm) cc_final: 0.8365 (tmm) REVERT: a 29 MET cc_start: 0.1710 (ptt) cc_final: 0.1241 (ptt) REVERT: a 72 TYR cc_start: 0.8815 (m-80) cc_final: 0.8473 (m-10) REVERT: a 380 MET cc_start: 0.9586 (mtm) cc_final: 0.9328 (ptp) REVERT: b 29 MET cc_start: 0.7833 (ptt) cc_final: 0.7470 (ptt) REVERT: b 405 MET cc_start: 0.9513 (ptp) cc_final: 0.9219 (ptp) REVERT: c 21 MET cc_start: 0.5444 (ptt) cc_final: 0.3419 (ptt) REVERT: c 186 MET cc_start: 0.8473 (ptm) cc_final: 0.7599 (ppp) REVERT: c 245 MET cc_start: 0.8293 (tpt) cc_final: 0.7932 (tpt) REVERT: c 264 LEU cc_start: 0.8975 (tt) cc_final: 0.8439 (mp) REVERT: c 410 ASP cc_start: 0.9579 (m-30) cc_final: 0.9119 (p0) REVERT: c 415 MET cc_start: 0.8832 (ptt) cc_final: 0.8026 (ptt) REVERT: e 21 MET cc_start: 0.7103 (ptm) cc_final: 0.6851 (ptm) REVERT: e 374 GLN cc_start: 0.9825 (tp-100) cc_final: 0.9604 (tm-30) REVERT: e 405 MET cc_start: 0.7839 (ptp) cc_final: 0.7586 (ptp) REVERT: e 415 MET cc_start: 0.7240 (ptt) cc_final: 0.6267 (ptt) REVERT: f 21 MET cc_start: 0.8354 (ptm) cc_final: 0.6998 (ppp) REVERT: f 147 MET cc_start: 0.6933 (mpp) cc_final: 0.6396 (mpp) REVERT: f 245 MET cc_start: 0.5484 (ttt) cc_final: 0.4895 (tpt) REVERT: f 396 MET cc_start: 0.7957 (mtp) cc_final: 0.7755 (mmp) REVERT: f 415 MET cc_start: 0.8289 (ptt) cc_final: 0.8064 (ptt) REVERT: A 305 MET cc_start: -0.5108 (ptt) cc_final: -0.5329 (ptt) REVERT: W 18 ASP cc_start: 0.8004 (p0) cc_final: 0.7791 (p0) REVERT: X 681 MET cc_start: 0.7795 (ptp) cc_final: 0.7294 (ptp) REVERT: X 1243 MET cc_start: 0.7525 (ttm) cc_final: 0.5952 (ttt) REVERT: X 1304 MET cc_start: 0.7836 (mmp) cc_final: 0.7551 (mmm) REVERT: Y 180 MET cc_start: 0.7251 (tpp) cc_final: 0.6920 (tpp) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.5071 time to fit residues: 231.6593 Evaluate side-chains 235 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 4.404 ------------------------------------------------------------------------------- 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: 20.0000 chunk 550 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 150 optimal weight: 0.0970 chunk 611 optimal weight: 0.9990 chunk 507 optimal weight: 5.9990 chunk 283 optimal weight: 40.0000 chunk 50 optimal weight: 10.0000 chunk 202 optimal weight: 4.9990 chunk 321 optimal weight: 30.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- 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 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 90 ASN ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 GLN ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 23 HIS ** 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 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 450 HIS Y1197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 52220 Z= 0.228 Angle : 0.615 10.234 70811 Z= 0.312 Chirality : 0.042 0.223 8094 Planarity : 0.005 0.134 8994 Dihedral : 11.532 147.671 7837 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.02 % Allowed : 1.80 % Favored : 98.18 % 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: -1.21 (0.10), residues: 6307 helix: 0.32 (0.11), residues: 2416 sheet: -1.41 (0.17), residues: 817 loop : -1.52 (0.11), residues: 3074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 62 HIS 0.005 0.001 HIS Y 469 PHE 0.019 0.001 PHE A 24 TYR 0.020 0.002 TYR Y 999 ARG 0.018 0.001 ARG c 212 *********************** 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 267 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 266 time to evaluate : 4.445 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: 0.8777 (tmm) cc_final: 0.8312 (tmm) REVERT: a 29 MET cc_start: 0.1727 (ptt) cc_final: 0.1309 (ptt) REVERT: a 72 TYR cc_start: 0.8810 (m-80) cc_final: 0.8529 (m-10) REVERT: a 380 MET cc_start: 0.9613 (mtm) cc_final: 0.9239 (ptp) REVERT: b 186 MET cc_start: 0.8035 (pmm) cc_final: 0.7699 (pmm) REVERT: b 396 MET cc_start: 0.9334 (mmm) cc_final: 0.8605 (mmm) REVERT: b 405 MET cc_start: 0.9486 (ptp) cc_final: 0.9183 (ptp) REVERT: c 21 MET cc_start: 0.5291 (ptt) cc_final: 0.3119 (ptt) REVERT: c 186 MET cc_start: 0.8485 (ptm) cc_final: 0.7679 (ppp) REVERT: c 245 MET cc_start: 0.8299 (tpt) cc_final: 0.7940 (tpt) REVERT: c 264 LEU cc_start: 0.8991 (tt) cc_final: 0.8506 (mp) REVERT: c 380 MET cc_start: 0.9489 (tpt) cc_final: 0.9281 (tpp) REVERT: c 410 ASP cc_start: 0.9516 (m-30) cc_final: 0.9038 (p0) REVERT: c 415 MET cc_start: 0.8804 (ptt) cc_final: 0.7961 (ptt) REVERT: d 21 MET cc_start: 0.6450 (ptm) cc_final: 0.4543 (ppp) REVERT: d 245 MET cc_start: 0.8247 (mmt) cc_final: 0.7454 (mmm) REVERT: e 21 MET cc_start: 0.7377 (ptm) cc_final: 0.7175 (ptm) REVERT: e 374 GLN cc_start: 0.9835 (tp-100) cc_final: 0.9609 (tm-30) REVERT: e 380 MET cc_start: 0.9261 (mmm) cc_final: 0.8986 (tpt) REVERT: e 405 MET cc_start: 0.7904 (ptp) cc_final: 0.7648 (ptp) REVERT: e 415 MET cc_start: 0.7335 (ptt) cc_final: 0.6281 (ptt) REVERT: f 21 MET cc_start: 0.8419 (ptm) cc_final: 0.7119 (ppp) REVERT: f 147 MET cc_start: 0.6884 (mpp) cc_final: 0.6387 (mpp) REVERT: f 245 MET cc_start: 0.5770 (ttt) cc_final: 0.5297 (tpt) REVERT: f 292 ASN cc_start: 0.8560 (t0) cc_final: 0.7590 (p0) REVERT: f 415 MET cc_start: 0.8339 (ptt) cc_final: 0.8084 (ptt) REVERT: A 305 MET cc_start: -0.4709 (ptt) cc_final: -0.5015 (ptt) REVERT: W 18 ASP cc_start: 0.7954 (p0) cc_final: 0.7738 (p0) REVERT: X 1243 MET cc_start: 0.7314 (ttm) cc_final: 0.6151 (ttt) REVERT: X 1304 MET cc_start: 0.7870 (mmp) cc_final: 0.7584 (mmm) REVERT: Y 180 MET cc_start: 0.7445 (tpp) cc_final: 0.6971 (tpp) REVERT: Y 1040 MET cc_start: 0.5682 (mpp) cc_final: 0.5457 (mpp) outliers start: 1 outliers final: 0 residues processed: 267 average time/residue: 0.4961 time to fit residues: 228.3000 Evaluate side-chains 236 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 4.402 ------------------------------------------------------------------------------- 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: 10.0000 chunk 68 optimal weight: 9.9990 chunk 348 optimal weight: 8.9990 chunk 446 optimal weight: 0.9980 chunk 345 optimal weight: 10.0000 chunk 514 optimal weight: 3.9990 chunk 341 optimal weight: 9.9990 chunk 609 optimal weight: 0.9990 chunk 381 optimal weight: 9.9990 chunk 371 optimal weight: 9.9990 chunk 281 optimal weight: 50.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- 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 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 344 HIS ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 388 HIS e 126 ASN ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 42 HIS f 344 HIS ** V 23 HIS ** 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 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 52220 Z= 0.249 Angle : 0.635 10.242 70811 Z= 0.324 Chirality : 0.042 0.179 8094 Planarity : 0.005 0.093 8994 Dihedral : 11.530 147.038 7837 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: -1.05 (0.10), residues: 6307 helix: 0.37 (0.11), residues: 2410 sheet: -1.26 (0.17), residues: 878 loop : -1.36 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 62 HIS 0.008 0.001 HIS X 273 PHE 0.023 0.002 PHE A 24 TYR 0.019 0.002 TYR Y 999 ARG 0.013 0.001 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 256 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 4.490 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: a 29 MET cc_start: 0.1962 (ptt) cc_final: 0.1525 (ptt) REVERT: a 380 MET cc_start: 0.9596 (mtm) cc_final: 0.9218 (ptp) REVERT: b 396 MET cc_start: 0.9322 (mmm) cc_final: 0.8566 (mmm) REVERT: c 21 MET cc_start: 0.5334 (ptt) cc_final: 0.3431 (ptt) REVERT: c 186 MET cc_start: 0.8484 (ptm) cc_final: 0.7691 (ppp) REVERT: c 245 MET cc_start: 0.8372 (tpt) cc_final: 0.8064 (tpt) REVERT: c 264 LEU cc_start: 0.8936 (tt) cc_final: 0.8482 (mp) REVERT: c 380 MET cc_start: 0.9495 (tpt) cc_final: 0.9169 (tpp) REVERT: c 390 MET cc_start: 0.8800 (mmm) cc_final: 0.8595 (mmm) REVERT: c 410 ASP cc_start: 0.9384 (m-30) cc_final: 0.8881 (p0) REVERT: c 415 MET cc_start: 0.8894 (ptt) cc_final: 0.8177 (ptt) REVERT: d 21 MET cc_start: 0.6676 (ptm) cc_final: 0.4787 (ppp) REVERT: d 245 MET cc_start: 0.7901 (mmm) cc_final: 0.7637 (mmm) REVERT: e 205 MET cc_start: 0.9234 (mmp) cc_final: 0.8350 (mmm) REVERT: e 380 MET cc_start: 0.9297 (mmm) cc_final: 0.9060 (tpt) REVERT: e 405 MET cc_start: 0.8009 (ptp) cc_final: 0.7786 (ptp) REVERT: e 415 MET cc_start: 0.7666 (ptt) cc_final: 0.6570 (ptt) REVERT: f 21 MET cc_start: 0.8626 (ptm) cc_final: 0.7357 (ppp) REVERT: f 147 MET cc_start: 0.7171 (mpp) cc_final: 0.6650 (mpp) REVERT: f 219 MET cc_start: 0.8602 (mmp) cc_final: 0.8118 (tpp) REVERT: f 245 MET cc_start: 0.6143 (ttt) cc_final: 0.5593 (ttm) REVERT: f 396 MET cc_start: 0.8269 (mtt) cc_final: 0.7584 (mmp) REVERT: f 415 MET cc_start: 0.8422 (ptt) cc_final: 0.8152 (ptt) REVERT: A 305 MET cc_start: -0.4619 (ptt) cc_final: -0.5000 (ptt) REVERT: A 321 ASN cc_start: 0.7684 (t0) cc_final: 0.7445 (t0) REVERT: W 18 ASP cc_start: 0.7990 (p0) cc_final: 0.7726 (p0) REVERT: X 681 MET cc_start: 0.7944 (ptp) cc_final: 0.7396 (ptm) REVERT: X 1243 MET cc_start: 0.7265 (ttm) cc_final: 0.6967 (tpp) REVERT: X 1304 MET cc_start: 0.7903 (mmp) cc_final: 0.7648 (mmm) REVERT: Y 180 MET cc_start: 0.7605 (tpp) cc_final: 0.7060 (tpp) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.5112 time to fit residues: 226.1167 Evaluate side-chains 225 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 4.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 376 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 363 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 387 optimal weight: 7.9990 chunk 415 optimal weight: 2.9990 chunk 301 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 478 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 90 ASN a 198 ASN ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 ASN ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 HIS ** 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 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1116 HIS ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 52220 Z= 0.191 Angle : 0.609 14.848 70811 Z= 0.307 Chirality : 0.042 0.306 8094 Planarity : 0.004 0.091 8994 Dihedral : 11.479 146.822 7837 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -0.87 (0.11), residues: 6307 helix: 0.52 (0.11), residues: 2406 sheet: -1.15 (0.17), residues: 872 loop : -1.27 (0.11), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 62 HIS 0.004 0.001 HIS f 42 PHE 0.025 0.001 PHE A 24 TYR 0.016 0.001 TYR Y 999 ARG 0.020 0.000 ARG b 28 *********************** REFINEMENT MACRO_CYCLE 8 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 253 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 4.418 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: a 1 MET cc_start: 0.9141 (tmm) cc_final: 0.8925 (tmm) REVERT: a 29 MET cc_start: 0.1872 (ptt) cc_final: 0.1468 (ptt) REVERT: a 72 TYR cc_start: 0.8745 (m-80) cc_final: 0.8374 (m-10) REVERT: a 380 MET cc_start: 0.9597 (mtm) cc_final: 0.9204 (ptp) REVERT: b 186 MET cc_start: 0.7840 (pmm) cc_final: 0.7335 (pmm) REVERT: b 380 MET cc_start: 0.9454 (pmm) cc_final: 0.9048 (pmm) REVERT: b 396 MET cc_start: 0.9304 (mmm) cc_final: 0.8620 (mmm) REVERT: b 405 MET cc_start: 0.9553 (ptp) cc_final: 0.9273 (ptp) REVERT: c 21 MET cc_start: 0.5231 (ptt) cc_final: 0.3426 (ptt) REVERT: c 186 MET cc_start: 0.8415 (ptm) cc_final: 0.7769 (ppp) REVERT: c 245 MET cc_start: 0.8363 (tpt) cc_final: 0.8055 (tpt) REVERT: c 264 LEU cc_start: 0.8905 (tt) cc_final: 0.8464 (mp) REVERT: c 380 MET cc_start: 0.9423 (tpt) cc_final: 0.9047 (tpp) REVERT: c 396 MET cc_start: 0.9224 (mmp) cc_final: 0.8996 (mmm) REVERT: c 410 ASP cc_start: 0.9463 (m-30) cc_final: 0.9099 (p0) REVERT: c 415 MET cc_start: 0.8943 (ptt) cc_final: 0.8200 (ptt) REVERT: d 21 MET cc_start: 0.6754 (ptm) cc_final: 0.5283 (ppp) REVERT: e 205 MET cc_start: 0.9209 (mmp) cc_final: 0.8317 (mmm) REVERT: e 380 MET cc_start: 0.9280 (mmm) cc_final: 0.9033 (tpt) REVERT: e 405 MET cc_start: 0.8228 (ptp) cc_final: 0.8019 (ptp) REVERT: e 415 MET cc_start: 0.7487 (ptt) cc_final: 0.6287 (ptt) REVERT: f 21 MET cc_start: 0.8794 (ptm) cc_final: 0.7599 (ppp) REVERT: f 147 MET cc_start: 0.7031 (mpp) cc_final: 0.6567 (mpp) REVERT: f 245 MET cc_start: 0.6113 (ttt) cc_final: 0.5583 (ttm) REVERT: f 396 MET cc_start: 0.8060 (mtt) cc_final: 0.7542 (mmp) REVERT: f 415 MET cc_start: 0.8139 (ptt) cc_final: 0.7724 (ptt) REVERT: A 305 MET cc_start: -0.4376 (ptt) cc_final: -0.4669 (ptt) REVERT: A 321 ASN cc_start: 0.7697 (t0) cc_final: 0.7445 (t0) REVERT: X 1304 MET cc_start: 0.7787 (mmp) cc_final: 0.7543 (mmm) REVERT: Y 180 MET cc_start: 0.7400 (tpp) cc_final: 0.6956 (tpp) REVERT: Y 400 MET cc_start: 0.7530 (tmm) cc_final: 0.7314 (tmm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.5253 time to fit residues: 231.5195 Evaluate side-chains 224 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 554 optimal weight: 0.9990 chunk 583 optimal weight: 50.0000 chunk 532 optimal weight: 8.9990 chunk 567 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 chunk 247 optimal weight: 30.0000 chunk 445 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 512 optimal weight: 7.9990 chunk 536 optimal weight: 0.8980 chunk 565 optimal weight: 8.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 239 HIS ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 90 ASN e 126 ASN ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 73 GLN ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y1350 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.169 52220 Z= 0.267 Angle : 0.644 11.128 70811 Z= 0.328 Chirality : 0.042 0.226 8094 Planarity : 0.005 0.082 8994 Dihedral : 11.526 146.536 7837 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.63 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.92 (0.11), residues: 6307 helix: 0.44 (0.11), residues: 2419 sheet: -1.17 (0.17), residues: 873 loop : -1.28 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 381 HIS 0.014 0.001 HIS Y 450 PHE 0.026 0.002 PHE A 24 TYR 0.017 0.002 TYR Y 999 ARG 0.013 0.001 ARG c 160 *********************** REFINEMENT MACRO_CYCLE 9 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 249 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 4.495 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: a 1 MET cc_start: 0.9249 (tmm) cc_final: 0.8992 (tmm) REVERT: a 29 MET cc_start: 0.1986 (ptt) cc_final: 0.1514 (ptt) REVERT: a 72 TYR cc_start: 0.8830 (m-80) cc_final: 0.8454 (m-10) REVERT: a 380 MET cc_start: 0.9623 (mtm) cc_final: 0.9188 (ptp) REVERT: b 380 MET cc_start: 0.9484 (pmm) cc_final: 0.9049 (pmm) REVERT: b 396 MET cc_start: 0.9317 (mmm) cc_final: 0.8659 (mmm) REVERT: c 21 MET cc_start: 0.5538 (ptt) cc_final: 0.3678 (ptt) REVERT: c 186 MET cc_start: 0.8589 (ptm) cc_final: 0.7799 (ppp) REVERT: c 245 MET cc_start: 0.8390 (tpt) cc_final: 0.8087 (tpt) REVERT: c 264 LEU cc_start: 0.8924 (tt) cc_final: 0.8498 (mp) REVERT: c 380 MET cc_start: 0.9450 (tpt) cc_final: 0.9080 (tpp) REVERT: c 396 MET cc_start: 0.9159 (mmp) cc_final: 0.8798 (mmm) REVERT: c 410 ASP cc_start: 0.9487 (m-30) cc_final: 0.9181 (p0) REVERT: c 415 MET cc_start: 0.8967 (ptt) cc_final: 0.8278 (ptt) REVERT: d 21 MET cc_start: 0.7310 (ptm) cc_final: 0.5901 (ppp) REVERT: e 21 MET cc_start: 0.6873 (ptm) cc_final: 0.6344 (ppp) REVERT: e 205 MET cc_start: 0.9269 (mmp) cc_final: 0.8361 (mmm) REVERT: e 380 MET cc_start: 0.9251 (mmm) cc_final: 0.9014 (tpt) REVERT: e 405 MET cc_start: 0.8321 (ptp) cc_final: 0.8121 (ptp) REVERT: e 415 MET cc_start: 0.7754 (ptt) cc_final: 0.6632 (ptt) REVERT: f 21 MET cc_start: 0.8812 (ptm) cc_final: 0.7693 (ppp) REVERT: f 219 MET cc_start: 0.8516 (mmp) cc_final: 0.8009 (tpp) REVERT: f 245 MET cc_start: 0.6598 (ttt) cc_final: 0.6171 (ttm) REVERT: f 396 MET cc_start: 0.8108 (mtt) cc_final: 0.7585 (mmp) REVERT: f 415 MET cc_start: 0.8283 (ptt) cc_final: 0.8064 (ptt) REVERT: A 1 MET cc_start: 0.8123 (tpt) cc_final: 0.7879 (tpt) REVERT: A 305 MET cc_start: -0.4291 (ptt) cc_final: -0.4653 (ptt) REVERT: A 321 ASN cc_start: 0.7821 (t0) cc_final: 0.7570 (t0) REVERT: W 18 ASP cc_start: 0.7906 (p0) cc_final: 0.7661 (p0) REVERT: X 681 MET cc_start: 0.8008 (ptp) cc_final: 0.7789 (ptm) REVERT: X 1304 MET cc_start: 0.7884 (mmp) cc_final: 0.7482 (tpt) REVERT: Y 180 MET cc_start: 0.7659 (tpp) cc_final: 0.7160 (tpp) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.5161 time to fit residues: 224.0600 Evaluate side-chains 222 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 372 optimal weight: 0.9990 chunk 600 optimal weight: 10.0000 chunk 366 optimal weight: 0.0270 chunk 284 optimal weight: 6.9990 chunk 417 optimal weight: 0.3980 chunk 629 optimal weight: 10.0000 chunk 579 optimal weight: 9.9990 chunk 501 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 387 optimal weight: 7.9990 chunk 307 optimal weight: 6.9990 overall best weight: 2.6844 ------------------------------------------------------------------------------- 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** ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 275 ASN e 126 ASN ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 194 GLN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 752 ASN ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 799 ASN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5580 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= 0.187 Angle : 0.604 11.062 70811 Z= 0.303 Chirality : 0.042 0.204 8094 Planarity : 0.004 0.071 8994 Dihedral : 11.452 146.346 7837 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.02 % Allowed : 0.35 % Favored : 99.63 % 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: -0.85 (0.11), residues: 6307 helix: 0.59 (0.11), residues: 2402 sheet: -1.33 (0.17), residues: 927 loop : -1.22 (0.11), residues: 2978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 62 HIS 0.009 0.001 HIS d 42 PHE 0.026 0.001 PHE A 24 TYR 0.024 0.001 TYR a 274 ARG 0.011 0.000 ARG c 160 ********************** REFINEMENT MACRO_CYCLE 10 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 251 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 4.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.1834 (ptt) cc_final: 0.1403 (ptt) REVERT: a 72 TYR cc_start: 0.8767 (m-80) cc_final: 0.8416 (m-10) REVERT: a 147 MET cc_start: 0.6832 (mmm) cc_final: 0.6197 (mmm) REVERT: a 380 MET cc_start: 0.9613 (mtm) cc_final: 0.9190 (ptp) REVERT: b 21 MET cc_start: 0.3299 (ptm) cc_final: 0.2511 (ppp) REVERT: b 380 MET cc_start: 0.9491 (pmm) cc_final: 0.9031 (pmm) REVERT: b 396 MET cc_start: 0.9276 (mmm) cc_final: 0.8615 (mmm) REVERT: c 21 MET cc_start: 0.5242 (ptt) cc_final: 0.3192 (ptt) REVERT: c 186 MET cc_start: 0.8433 (ptm) cc_final: 0.7806 (ppp) REVERT: c 245 MET cc_start: 0.8357 (tpt) cc_final: 0.8051 (tpt) REVERT: c 264 LEU cc_start: 0.8899 (tt) cc_final: 0.8512 (mp) REVERT: c 380 MET cc_start: 0.9430 (tpt) cc_final: 0.9033 (tpp) REVERT: c 396 MET cc_start: 0.9119 (mmp) cc_final: 0.8746 (mmm) REVERT: c 410 ASP cc_start: 0.9516 (m-30) cc_final: 0.9164 (p0) REVERT: c 415 MET cc_start: 0.9006 (ptt) cc_final: 0.8320 (ptt) REVERT: d 21 MET cc_start: 0.7216 (ptm) cc_final: 0.5465 (ppp) REVERT: d 186 MET cc_start: 0.7437 (pmm) cc_final: 0.7208 (pmm) REVERT: e 21 MET cc_start: 0.6924 (ptm) cc_final: 0.6349 (ppp) REVERT: e 205 MET cc_start: 0.9276 (mmp) cc_final: 0.8348 (mmm) REVERT: e 380 MET cc_start: 0.9245 (mmm) cc_final: 0.8999 (tpt) REVERT: e 415 MET cc_start: 0.7742 (ptt) cc_final: 0.6639 (ptt) REVERT: f 21 MET cc_start: 0.8924 (ptm) cc_final: 0.7838 (ppp) REVERT: f 219 MET cc_start: 0.8610 (mmp) cc_final: 0.8201 (tpp) REVERT: f 245 MET cc_start: 0.6545 (ttt) cc_final: 0.6138 (ttm) REVERT: f 396 MET cc_start: 0.8062 (mtt) cc_final: 0.7536 (mmp) REVERT: A 1 MET cc_start: 0.8008 (tpt) cc_final: 0.7769 (tpt) REVERT: A 305 MET cc_start: -0.4253 (ptt) cc_final: -0.4628 (ptt) REVERT: A 321 ASN cc_start: 0.7833 (t0) cc_final: 0.7577 (t0) REVERT: X 1304 MET cc_start: 0.7815 (mmp) cc_final: 0.7585 (mmm) REVERT: Y 180 MET cc_start: 0.7528 (tpp) cc_final: 0.7049 (tpp) REVERT: Y 400 MET cc_start: 0.7432 (tmm) cc_final: 0.7185 (tmm) REVERT: Y 1040 MET cc_start: 0.5808 (mpp) cc_final: 0.5515 (mpp) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.5215 time to fit residues: 227.0648 Evaluate side-chains 226 residues out of total 5391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 4.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 632 random chunks: chunk 398 optimal weight: 4.9990 chunk 534 optimal weight: 7.9990 chunk 153 optimal weight: 9.9990 chunk 462 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 502 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 515 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** c 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 90 ASN e 126 ASN ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 194 GLN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 554 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 277 ASN ** Y 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.036431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.021273 restraints weight = 791883.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.021623 restraints weight = 523980.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.021913 restraints weight = 384984.262| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 52220 Z= 0.185 Angle : 0.601 14.069 70811 Z= 0.303 Chirality : 0.042 0.241 8094 Planarity : 0.004 0.102 8994 Dihedral : 11.388 144.746 7837 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.02 % Allowed : 0.15 % Favored : 99.83 % 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: -0.76 (0.11), residues: 6307 helix: 0.68 (0.11), residues: 2396 sheet: -1.31 (0.17), residues: 913 loop : -1.18 (0.11), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 62 HIS 0.008 0.001 HIS d 42 PHE 0.016 0.001 PHE A 24 TYR 0.018 0.001 TYR a 274 ARG 0.010 0.000 ARG c 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7480.60 seconds wall clock time: 134 minutes 57.48 seconds (8097.48 seconds total)