Starting phenix.real_space_refine on Fri Feb 23 09:16:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z84_14542/02_2024/7z84_14542_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z84_14542/02_2024/7z84_14542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z84_14542/02_2024/7z84_14542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z84_14542/02_2024/7z84_14542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z84_14542/02_2024/7z84_14542_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z84_14542/02_2024/7z84_14542_updated.pdb" } resolution = 2.87 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= 0.004 sd= 0.018 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 13 5.49 5 S 267 5.16 5 C 24594 2.51 5 N 6239 2.21 5 O 6626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 48": "OD1" <-> "OD2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E ASP 68": "OD1" <-> "OD2" Residue "E ASP 123": "OD1" <-> "OD2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E ASP 148": "OD1" <-> "OD2" Residue "G ASP 19": "OD1" <-> "OD2" Residue "G ASP 179": "OD1" <-> "OD2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G ASP 442": "OD1" <-> "OD2" Residue "G ASP 642": "OD1" <-> "OD2" Residue "G GLU 789": "OE1" <-> "OE2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 435": "OD1" <-> "OD2" Residue "C TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B ASP 94": "OD1" <-> "OD2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 129": "OD1" <-> "OD2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "I ASP 159": "OD1" <-> "OD2" Residue "I GLU 169": "OE1" <-> "OE2" Residue "I ASP 174": "OD1" <-> "OD2" Residue "H ASP 79": "OD1" <-> "OD2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 546": "OD1" <-> "OD2" Residue "M ASP 84": "OD1" <-> "OD2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 133": "OE1" <-> "OE2" Residue "N GLU 154": "OE1" <-> "OE2" Residue "N ASP 183": "OD1" <-> "OD2" Residue "N TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 55": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37772 Number of models: 1 Model: "" Number of chains: 23 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4738 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1656 Classifications: {'peptide': 208} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 193} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2544 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 307} Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 894 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 4629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4629 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} Chain breaks: 1 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3563 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 450} Chain breaks: 2 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 224 Unusual residues: {'3PE': 4, 'LFA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 122 Unusual residues: {'3PE': 2, 'LFA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 70.269 60.480 191.525 1.00 12.70 S ATOM 2741 SG CYS F 357 73.673 60.035 196.087 1.00 22.22 S ATOM 3062 SG CYS F 398 67.840 56.764 196.394 1.00 21.57 S ATOM 2697 SG CYS F 351 72.337 54.157 192.920 1.00 14.65 S ATOM 4054 SG CYS E 92 80.559 52.057 212.775 1.00 36.01 S ATOM 4088 SG CYS E 97 80.635 52.886 216.206 1.00 34.35 S ATOM 4366 SG CYS E 133 75.310 51.456 212.367 1.00 47.06 S ATOM 4392 SG CYS E 137 74.503 52.311 215.614 1.00 40.65 S ATOM 5476 SG CYS G 114 81.024 66.621 174.325 1.00 7.04 S ATOM 5416 SG CYS G 105 86.283 70.282 175.941 1.00 7.35 S ATOM 5436 SG CYS G 108 86.951 64.315 173.544 1.00 1.74 S ATOM 5830 SG CYS G 156 75.140 58.831 179.129 1.00 6.41 S ATOM 5811 SG CYS G 153 80.906 57.673 182.204 1.00 3.89 S ATOM 5859 SG CYS G 159 78.175 53.080 178.565 1.00 5.98 S ATOM 6203 SG CYS G 203 80.322 58.302 175.556 1.00 5.88 S ATOM 6428 SG CYS G 230 77.315 49.982 154.306 1.00 15.43 S ATOM 6713 SG CYS G 265 77.106 46.208 159.640 1.00 9.98 S ATOM 6476 SG CYS G 237 71.846 49.626 157.339 1.00 4.70 S ATOM 6452 SG CYS G 233 74.080 44.297 154.329 1.00 18.49 S ATOM 4877 SG CYS G 36 68.783 59.853 181.861 1.00 4.16 S ATOM 4953 SG CYS G 47 70.341 63.183 182.112 1.00 3.85 S ATOM 4979 SG CYS G 50 64.517 64.874 181.919 1.00 11.43 S ATOM 5128 SG CYS G 69 63.989 61.326 181.695 1.00 9.98 S ATOM 17321 SG CYS B 129 91.859 93.860 150.601 1.00 8.44 S ATOM 16818 SG CYS B 64 97.099 97.582 152.343 1.00 15.77 S ATOM 16812 SG CYS B 63 91.569 99.706 154.130 1.00 7.15 S ATOM 17538 SG CYS B 158 93.531 93.758 156.386 1.00 11.15 S ATOM 18869 SG CYS I 102 92.212 87.977 162.405 1.00 2.12 S ATOM 18844 SG CYS I 99 97.671 86.527 158.865 1.00 6.35 S ATOM 18887 SG CYS I 105 96.165 83.229 164.254 1.00 9.95 S ATOM 18602 SG CYS I 70 92.343 82.644 159.000 1.00 7.39 S ATOM 18916 SG CYS I 109 97.040 77.666 170.519 1.00 3.35 S ATOM 18579 SG CYS I 66 95.124 77.030 164.366 1.00 13.84 S ATOM 18539 SG CYS I 60 99.102 72.628 166.711 1.00 7.86 S ATOM 18557 SG CYS I 63 92.828 73.186 169.088 1.00 6.93 S Time building chain proxies: 18.77, per 1000 atoms: 0.50 Number of scatterers: 37772 At special positions: 0 Unit cell: (157.94, 215.18, 243.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 267 16.00 P 13 15.00 O 6626 8.00 N 6239 7.00 C 24594 6.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.10 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " Number of angles added : 93 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8682 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 24 sheets defined 54.4% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.85 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 100 through 107 removed outlier: 3.862A pdb=" N GLN F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 122 Processing helix chain 'F' and resid 137 through 152 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 311 through 317 removed outlier: 3.554A pdb=" N ALA F 317 " --> pdb=" O SER F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 391 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 removed outlier: 4.025A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.863A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.710A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.107A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 157 through 164 removed outlier: 4.216A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 97 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 122 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 removed outlier: 3.565A pdb=" N ILE G 202 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' Processing helix chain 'G' and resid 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 370 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 410 removed outlier: 4.422A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 559 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 603 No H-bonds generated for 'chain 'G' and resid 601 through 603' Processing helix chain 'G' and resid 615 through 617 No H-bonds generated for 'chain 'G' and resid 615 through 617' Processing helix chain 'G' and resid 650 through 663 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 690 removed outlier: 4.946A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 767 removed outlier: 3.525A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 767' Processing helix chain 'G' and resid 827 through 829 No H-bonds generated for 'chain 'G' and resid 827 through 829' Processing helix chain 'G' and resid 831 through 833 No H-bonds generated for 'chain 'G' and resid 831 through 833' Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 54 through 65 removed outlier: 5.088A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.540A pdb=" N TYR C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.609A pdb=" N MET C 285 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 376 through 397 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.040A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 564 through 575 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 104 through 116 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.847A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 4.730A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'H' and resid 6 through 43 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 4.588A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 136 removed outlier: 4.463A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.961A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 removed outlier: 3.673A pdb=" N GLN H 183 " --> pdb=" O ILE H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 302 Processing helix chain 'H' and resid 305 through 323 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 119 removed outlier: 3.641A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.575A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.761A pdb=" N SER L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 209 Proline residue: L 205 - end of helix removed outlier: 3.510A pdb=" N ALA L 209 " --> pdb=" O PRO L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 238 through 244 removed outlier: 4.883A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 254 Processing helix chain 'L' and resid 258 through 268 removed outlier: 4.172A pdb=" N GLY L 262 " --> pdb=" O VAL L 259 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA L 267 " --> pdb=" O TYR L 264 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG L 268 " --> pdb=" O LEU L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 300 removed outlier: 4.214A pdb=" N VAL L 300 " --> pdb=" O PHE L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 368 through 371 No H-bonds generated for 'chain 'L' and resid 368 through 371' Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 511 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 548 removed outlier: 6.164A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 562 removed outlier: 5.102A pdb=" N ARG L 562 " --> pdb=" O TRP L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.838A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER L 586 " --> pdb=" O GLY L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 612 Processing helix chain 'M' and resid 2 through 21 Proline residue: M 10 - end of helix removed outlier: 3.850A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 50 Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 156 removed outlier: 4.700A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 199 Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 219 through 234 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.720A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 Processing helix chain 'M' and resid 452 through 454 No H-bonds generated for 'chain 'M' and resid 452 through 454' Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 501 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 58 removed outlier: 4.507A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.191A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 120 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.472A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 3.835A pdb=" N ASP N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 288 removed outlier: 3.727A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 316 removed outlier: 3.999A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 347 Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 431 Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 25 through 45 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 112 removed outlier: 5.062A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 158 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.667A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 247 through 250 Processing sheet with id= C, first strand: chain 'F' and resid 251 through 253 Processing sheet with id= D, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= E, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.709A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= H, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.490A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= J, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.512A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.341A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= M, first strand: chain 'G' and resid 901 through 903 removed outlier: 7.723A pdb=" N TYR G 841 " --> pdb=" O PRO G 887 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.147A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.429A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 215 through 219 removed outlier: 3.552A pdb=" N VAL C 234 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 531 through 539 removed outlier: 3.630A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 20 through 25 removed outlier: 3.699A pdb=" N LYS B 21 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 7 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.530A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= U, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.999A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= W, first strand: chain 'L' and resid 60 through 66 removed outlier: 6.819A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.840A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1861 hydrogen bonds defined for protein. 5331 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.73 Time building geometry restraints manager: 16.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 16045 1.42 - 1.64: 22166 1.64 - 1.86: 409 1.86 - 2.08: 0 2.08 - 2.31: 92 Bond restraints: 38712 Sorted by residual: bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.67e+00 bond pdb=" O13 3PE J 202 " pdb=" P 3PE J 202 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.65e+00 bond pdb=" O13 3PE L 803 " pdb=" P 3PE L 803 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.60e+00 bond pdb=" O13 3PE J 201 " pdb=" P 3PE J 201 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.53e+00 bond pdb=" O13 3PE H 401 " pdb=" P 3PE H 401 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.46e+00 ... (remaining 38707 not shown) Histogram of bond angle deviations from ideal: 69.39 - 82.74: 88 82.74 - 96.09: 1 96.09 - 109.44: 3671 109.44 - 122.79: 45789 122.79 - 136.14: 2937 Bond angle restraints: 52486 Sorted by residual: angle pdb=" C TYR C 268 " pdb=" N ILE C 269 " pdb=" CA ILE C 269 " ideal model delta sigma weight residual 120.24 124.68 -4.44 6.30e-01 2.52e+00 4.97e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.03 12.78 2.21e+00 2.05e-01 3.34e+01 angle pdb=" CB MET M 136 " pdb=" CG MET M 136 " pdb=" SD MET M 136 " ideal model delta sigma weight residual 112.70 129.67 -16.97 3.00e+00 1.11e-01 3.20e+01 angle pdb=" CB LYS L 515 " pdb=" CG LYS L 515 " pdb=" CD LYS L 515 " ideal model delta sigma weight residual 111.30 124.17 -12.87 2.30e+00 1.89e-01 3.13e+01 angle pdb=" CB MET N 255 " pdb=" CG MET N 255 " pdb=" SD MET N 255 " ideal model delta sigma weight residual 112.70 129.36 -16.66 3.00e+00 1.11e-01 3.08e+01 ... (remaining 52481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.21: 21999 34.21 - 68.41: 816 68.41 - 102.62: 56 102.62 - 136.82: 5 136.82 - 171.03: 1 Dihedral angle restraints: 22877 sinusoidal: 9304 harmonic: 13573 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 135.31 44.69 0 5.00e+00 4.00e-02 7.99e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.05 34.95 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 86.56 171.03 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 22874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.237: 5813 4.237 - 8.473: 0 8.473 - 12.710: 0 12.710 - 16.947: 0 16.947 - 21.183: 28 Chirality restraints: 5841 Sorted by residual: chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.63 -21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.18 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5838 not shown) Planarity restraints: 6553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C VAL N 63 " 0.073 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.028 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 200 " 0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO C 201 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 93 " 0.021 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP J 93 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP J 93 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP J 93 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 93 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 93 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 93 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 93 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 93 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP J 93 " 0.001 2.00e-02 2.50e+03 ... (remaining 6550 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 5004 2.76 - 3.29: 36145 3.29 - 3.83: 69392 3.83 - 4.36: 83538 4.36 - 4.90: 141039 Nonbonded interactions: 335118 Sorted by model distance: nonbonded pdb=" OH TYR L 318 " pdb=" O GLY L 418 " model vdw 2.221 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.242 2.440 nonbonded pdb=" OH TYR G 255 " pdb=" O GLY G 776 " model vdw 2.244 2.440 nonbonded pdb=" O TRP G 668 " pdb=" OG1 THR G 669 " model vdw 2.248 2.440 nonbonded pdb=" OE2 GLU N 324 " pdb=" OH TYR N 397 " model vdw 2.256 2.440 ... (remaining 335113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 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: 0.040 Extract box with map and model: 3.820 Check model and map are aligned: 0.510 Set scattering table: 0.340 Process input model: 101.850 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.130 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:15.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 38712 Z= 0.286 Angle : 0.765 16.974 52486 Z= 0.388 Chirality : 1.464 21.183 5841 Planarity : 0.006 0.104 6553 Dihedral : 16.759 171.031 14195 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.02 % Favored : 97.96 % Rotamer: Outliers : 1.65 % Allowed : 20.05 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.07 % 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: -0.27 (0.11), residues: 4711 helix: 0.35 (0.09), residues: 2673 sheet: -0.40 (0.27), residues: 323 loop : -0.80 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP J 93 HIS 0.007 0.001 HIS C 518 PHE 0.042 0.002 PHE L 341 TYR 0.032 0.002 TYR M 435 ARG 0.022 0.001 ARG L 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 489 time to evaluate : 4.277 Fit side-chains REVERT: F 80 GLU cc_start: 0.7466 (mp0) cc_final: 0.7064 (pm20) REVERT: F 126 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8036 (p90) REVERT: G 62 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7034 (tpt170) REVERT: L 198 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7958 (mtt180) REVERT: L 258 MET cc_start: 0.8059 (mmm) cc_final: 0.6660 (tmm) REVERT: M 441 HIS cc_start: 0.8170 (m170) cc_final: 0.7792 (m170) REVERT: N 106 TYR cc_start: 0.8626 (m-80) cc_final: 0.8265 (m-80) REVERT: N 135 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8691 (tt) REVERT: N 388 MET cc_start: 0.7978 (mtm) cc_final: 0.7638 (mtp) outliers start: 64 outliers final: 41 residues processed: 547 average time/residue: 1.4518 time to fit residues: 967.9721 Evaluate side-chains 492 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 449 time to evaluate : 4.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 470 SER Chi-restraints excluded: chain G residue 791 SER Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 861 SER Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain H residue 73 TRP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 497 SER Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 608 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 455 GLN Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 396 optimal weight: 9.9990 chunk 356 optimal weight: 20.0000 chunk 197 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 240 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 368 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 274 optimal weight: 6.9990 chunk 426 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 386 GLN ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 HIS G 765 GLN G 768 ASN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS B 116 GLN H 45 ASN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 163 ASN ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.254 38712 Z= 0.818 Angle : 2.188 51.141 52486 Z= 1.434 Chirality : 0.447 6.581 5841 Planarity : 0.006 0.072 6553 Dihedral : 9.999 175.722 5824 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.83 % Rotamer: Outliers : 4.01 % Allowed : 17.34 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.34 (0.12), residues: 4711 helix: 0.88 (0.10), residues: 2677 sheet: -0.08 (0.27), residues: 309 loop : -0.63 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 93 HIS 0.010 0.001 HIS G 178 PHE 0.030 0.002 PHE L 341 TYR 0.023 0.002 TYR L 428 ARG 0.008 0.001 ARG I 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 441 time to evaluate : 3.804 Fit side-chains revert: symmetry clash REVERT: F 80 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7146 (pm20) REVERT: F 95 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8712 (tp30) REVERT: F 307 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8405 (mt) REVERT: G 209 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8102 (m) REVERT: C 190 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7976 (tp40) REVERT: C 219 ASN cc_start: 0.6675 (t0) cc_final: 0.6125 (t0) REVERT: C 378 ARG cc_start: 0.8428 (ttp-170) cc_final: 0.8166 (ttp-110) REVERT: I 83 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8636 (mmtt) REVERT: I 126 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.9000 (mttp) REVERT: I 167 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: L 35 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8445 (t) REVERT: L 353 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6721 (mp) REVERT: L 578 PHE cc_start: 0.7673 (t80) cc_final: 0.7340 (t80) REVERT: M 291 MET cc_start: 0.9029 (mtp) cc_final: 0.8796 (mtp) REVERT: M 384 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8763 (tt) REVERT: N 388 MET cc_start: 0.8183 (mtm) cc_final: 0.7817 (mtp) REVERT: N 482 MET cc_start: 0.8335 (tpp) cc_final: 0.8103 (mmm) REVERT: J 55 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8738 (mm-30) outliers start: 156 outliers final: 69 residues processed: 538 average time/residue: 1.4880 time to fit residues: 975.9367 Evaluate side-chains 509 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 428 time to evaluate : 4.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 313 SER Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 73 TRP Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 258 ASP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 59 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 237 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 355 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 427 optimal weight: 8.9990 chunk 461 optimal weight: 9.9990 chunk 380 optimal weight: 10.0000 chunk 424 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 343 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 GLN G 299 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.244 38712 Z= 0.774 Angle : 2.174 50.753 52486 Z= 1.428 Chirality : 0.445 6.552 5841 Planarity : 0.005 0.069 6553 Dihedral : 9.723 175.580 5793 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.92 % Rotamer: Outliers : 4.27 % Allowed : 17.32 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.62 (0.12), residues: 4711 helix: 1.15 (0.10), residues: 2662 sheet: -0.03 (0.27), residues: 318 loop : -0.56 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 93 HIS 0.010 0.001 HIS G 178 PHE 0.029 0.002 PHE L 341 TYR 0.022 0.002 TYR N 424 ARG 0.007 0.001 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 443 time to evaluate : 4.649 Fit side-chains REVERT: F 22 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8647 (mm-40) REVERT: F 80 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: F 307 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8461 (mt) REVERT: G 98 MET cc_start: 0.9044 (mmp) cc_final: 0.8692 (mmp) REVERT: G 209 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8113 (m) REVERT: G 490 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8548 (tp40) REVERT: G 541 MET cc_start: 0.9039 (mmt) cc_final: 0.8618 (mmt) REVERT: G 834 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: C 112 MET cc_start: 0.9025 (ttm) cc_final: 0.8819 (ttm) REVERT: C 219 ASN cc_start: 0.6594 (t0) cc_final: 0.6104 (t0) REVERT: C 378 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.8165 (ttp-110) REVERT: B 23 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: I 126 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9025 (mttp) REVERT: H 322 TRP cc_start: 0.7902 (t-100) cc_final: 0.7015 (t60) REVERT: L 139 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8229 (ttp) REVERT: L 353 ILE cc_start: 0.7105 (OUTLIER) cc_final: 0.6706 (mp) REVERT: L 360 GLN cc_start: 0.6071 (OUTLIER) cc_final: 0.5659 (mt0) REVERT: L 427 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8306 (mt) REVERT: L 578 PHE cc_start: 0.7698 (t80) cc_final: 0.7353 (t80) REVERT: M 291 MET cc_start: 0.9026 (mtp) cc_final: 0.8783 (mtp) REVERT: M 384 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8785 (tt) REVERT: M 447 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7418 (mtpt) REVERT: N 388 MET cc_start: 0.8238 (mtm) cc_final: 0.7858 (mtp) REVERT: K 26 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7942 (mtm110) REVERT: J 72 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8370 (mpt) outliers start: 166 outliers final: 76 residues processed: 553 average time/residue: 1.4723 time to fit residues: 990.0552 Evaluate side-chains 528 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 437 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 664 ARG Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 139 MET Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 258 ASP Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 217 LYS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 422 optimal weight: 8.9990 chunk 321 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 204 optimal weight: 20.0000 chunk 287 optimal weight: 9.9990 chunk 429 optimal weight: 5.9990 chunk 454 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 chunk 406 optimal weight: 0.5980 chunk 122 optimal weight: 0.3980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN F 400 HIS ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38712 Z= 0.729 Angle : 2.158 50.783 52486 Z= 1.422 Chirality : 0.440 6.431 5841 Planarity : 0.004 0.071 6553 Dihedral : 9.288 174.553 5785 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.29 % Allowed : 18.76 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.94 (0.12), residues: 4711 helix: 1.44 (0.10), residues: 2669 sheet: -0.02 (0.28), residues: 307 loop : -0.48 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 93 HIS 0.007 0.001 HIS G 178 PHE 0.028 0.001 PHE L 341 TYR 0.024 0.001 TYR N 424 ARG 0.007 0.000 ARG L 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 454 time to evaluate : 4.231 Fit side-chains REVERT: F 80 GLU cc_start: 0.7498 (mp0) cc_final: 0.7113 (pm20) REVERT: F 373 ARG cc_start: 0.8388 (mpp80) cc_final: 0.7897 (mtm-85) REVERT: G 209 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8106 (m) REVERT: G 541 MET cc_start: 0.9038 (mmt) cc_final: 0.8644 (mmt) REVERT: C 378 ARG cc_start: 0.8385 (ttp-170) cc_final: 0.8120 (ttp-110) REVERT: B 23 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6985 (mt-10) REVERT: B 170 MET cc_start: 0.8918 (mtp) cc_final: 0.8592 (mtm) REVERT: I 126 LYS cc_start: 0.9309 (OUTLIER) cc_final: 0.8995 (mttp) REVERT: H 322 TRP cc_start: 0.8005 (t-100) cc_final: 0.7028 (t60) REVERT: L 35 VAL cc_start: 0.8656 (m) cc_final: 0.8416 (t) REVERT: L 40 LEU cc_start: 0.8883 (mp) cc_final: 0.8579 (mt) REVERT: L 353 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6569 (mp) REVERT: L 360 GLN cc_start: 0.6001 (OUTLIER) cc_final: 0.5593 (mt0) REVERT: M 291 MET cc_start: 0.8988 (mtp) cc_final: 0.8775 (mtp) REVERT: M 384 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8742 (tt) REVERT: M 447 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7371 (mtpt) REVERT: N 379 MET cc_start: 0.9141 (mmt) cc_final: 0.8631 (mmt) REVERT: N 388 MET cc_start: 0.8149 (mtm) cc_final: 0.7841 (mtp) REVERT: K 26 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7892 (mtm110) REVERT: J 55 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8671 (mm-30) REVERT: J 72 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8482 (mpt) outliers start: 128 outliers final: 64 residues processed: 537 average time/residue: 1.5343 time to fit residues: 998.6820 Evaluate side-chains 507 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 433 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain E residue 47 ARG Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain L residue 581 LYS Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 447 LYS Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 217 LYS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 55 GLU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 378 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 387 optimal weight: 20.0000 chunk 314 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 407 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN B 76 HIS ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN ** M 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN N 404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.245 38712 Z= 0.902 Angle : 2.209 50.833 52486 Z= 1.441 Chirality : 0.449 6.673 5841 Planarity : 0.006 0.065 6553 Dihedral : 10.078 175.658 5776 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.70 % Favored : 97.26 % Rotamer: Outliers : 4.55 % Allowed : 17.86 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.53 (0.12), residues: 4711 helix: 1.07 (0.10), residues: 2658 sheet: -0.16 (0.27), residues: 306 loop : -0.57 (0.14), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 143 HIS 0.010 0.002 HIS G 178 PHE 0.028 0.003 PHE L 341 TYR 0.026 0.003 TYR H 156 ARG 0.011 0.001 ARG I 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 429 time to evaluate : 4.316 Fit side-chains REVERT: F 80 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: F 302 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8640 (tp30) REVERT: F 307 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8480 (mt) REVERT: G 490 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8546 (tp40) REVERT: G 834 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: C 219 ASN cc_start: 0.6631 (t0) cc_final: 0.6093 (t0) REVERT: C 378 ARG cc_start: 0.8573 (ttp-170) cc_final: 0.8197 (ttp-110) REVERT: B 23 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: B 41 LYS cc_start: 0.9102 (mttp) cc_final: 0.8396 (tmtt) REVERT: I 126 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9065 (mttp) REVERT: H 286 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.6870 (tmt90) REVERT: H 322 TRP cc_start: 0.7957 (t-100) cc_final: 0.7010 (t60) REVERT: L 258 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7303 (tmm) REVERT: L 360 GLN cc_start: 0.6082 (OUTLIER) cc_final: 0.5674 (mt0) REVERT: L 427 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8259 (mt) REVERT: L 578 PHE cc_start: 0.7792 (t80) cc_final: 0.7437 (t80) REVERT: M 384 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8798 (tt) REVERT: M 442 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7290 (mtp180) REVERT: N 12 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8557 (mt) REVERT: K 4 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8795 (tt) REVERT: K 26 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7925 (mtm110) REVERT: J 69 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8234 (t80) REVERT: J 72 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8346 (mpt) outliers start: 177 outliers final: 83 residues processed: 552 average time/residue: 1.5016 time to fit residues: 1007.3923 Evaluate side-chains 522 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 421 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 247 GLU Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 832 VAL Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 360 GLN Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain M residue 258 ASP Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 442 ARG Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 26 ARG Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 152 optimal weight: 6.9990 chunk 409 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 454 optimal weight: 6.9990 chunk 377 optimal weight: 4.9990 chunk 210 optimal weight: 0.5980 chunk 37 optimal weight: 0.0770 chunk 150 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 overall best weight: 2.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 238 ASN G 839 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN H 152 GLN H 312 ASN ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38712 Z= 0.741 Angle : 2.166 50.794 52486 Z= 1.425 Chirality : 0.441 6.482 5841 Planarity : 0.004 0.067 6553 Dihedral : 9.600 175.310 5776 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.12 % Favored : 97.86 % Rotamer: Outliers : 3.55 % Allowed : 19.30 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.12), residues: 4711 helix: 1.39 (0.10), residues: 2658 sheet: -0.08 (0.28), residues: 298 loop : -0.48 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 93 HIS 0.009 0.001 HIS G 178 PHE 0.028 0.001 PHE L 341 TYR 0.024 0.002 TYR N 424 ARG 0.011 0.000 ARG L 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 441 time to evaluate : 3.891 Fit side-chains REVERT: F 80 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7206 (pm20) REVERT: F 373 ARG cc_start: 0.8476 (mpp80) cc_final: 0.7943 (mtm-85) REVERT: G 541 MET cc_start: 0.9031 (mmt) cc_final: 0.8626 (mmt) REVERT: G 834 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: C 110 ASP cc_start: 0.8775 (p0) cc_final: 0.8546 (p0) REVERT: C 190 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7939 (tp40) REVERT: C 240 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: C 378 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.8180 (ttp-110) REVERT: B 41 LYS cc_start: 0.9108 (mttp) cc_final: 0.8400 (tmtt) REVERT: B 84 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8305 (pp20) REVERT: B 170 MET cc_start: 0.9015 (mtp) cc_final: 0.8704 (mtm) REVERT: I 83 LYS cc_start: 0.8719 (mppt) cc_final: 0.8513 (mmtt) REVERT: I 126 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9040 (mttp) REVERT: H 322 TRP cc_start: 0.7983 (t-100) cc_final: 0.7027 (t60) REVERT: A 81 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8321 (mt-10) REVERT: L 40 LEU cc_start: 0.8914 (mp) cc_final: 0.8571 (mt) REVERT: L 578 PHE cc_start: 0.7722 (t80) cc_final: 0.7380 (t80) REVERT: M 291 MET cc_start: 0.9074 (mtp) cc_final: 0.8709 (mtm) REVERT: M 384 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8771 (tt) REVERT: N 64 THR cc_start: 0.8002 (m) cc_final: 0.7722 (m) REVERT: N 379 MET cc_start: 0.9107 (mmt) cc_final: 0.8528 (mmt) REVERT: N 388 MET cc_start: 0.8189 (mtm) cc_final: 0.7876 (mtp) REVERT: J 72 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8455 (mpt) outliers start: 138 outliers final: 75 residues processed: 535 average time/residue: 1.4810 time to fit residues: 964.7469 Evaluate side-chains 514 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 430 time to evaluate : 4.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 532 THR Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain L residue 575 LEU Chi-restraints excluded: chain M residue 258 ASP Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 281 ASN Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 135 ILE Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 438 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 332 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 382 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 453 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 276 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.242 38712 Z= 0.874 Angle : 2.201 50.795 52486 Z= 1.438 Chirality : 0.448 6.662 5841 Planarity : 0.006 0.067 6553 Dihedral : 9.996 175.925 5776 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 3.65 % Allowed : 19.20 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.12), residues: 4711 helix: 1.14 (0.10), residues: 2655 sheet: -0.19 (0.27), residues: 306 loop : -0.56 (0.15), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 143 HIS 0.011 0.002 HIS G 178 PHE 0.029 0.002 PHE L 341 TYR 0.024 0.003 TYR H 156 ARG 0.013 0.001 ARG L 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 418 time to evaluate : 4.227 Fit side-chains REVERT: F 80 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: F 307 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8472 (mt) REVERT: G 114 CYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8063 (t) REVERT: G 490 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8545 (tp40) REVERT: G 834 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: C 240 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8388 (mt-10) REVERT: C 378 ARG cc_start: 0.8572 (ttp-170) cc_final: 0.8247 (ttp-110) REVERT: B 41 LYS cc_start: 0.9113 (mttp) cc_final: 0.8413 (tmtt) REVERT: I 126 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9066 (mttp) REVERT: I 167 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8284 (mt-10) REVERT: H 8 LEU cc_start: 0.9174 (tm) cc_final: 0.8804 (tm) REVERT: H 12 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8883 (mm) REVERT: H 322 TRP cc_start: 0.7934 (t-100) cc_final: 0.7016 (t60) REVERT: L 258 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7173 (tmm) REVERT: L 578 PHE cc_start: 0.7797 (t80) cc_final: 0.7445 (t80) REVERT: M 384 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8798 (tt) REVERT: M 442 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.7254 (mtp180) REVERT: N 379 MET cc_start: 0.9152 (mmt) cc_final: 0.8573 (mmt) REVERT: J 72 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8378 (mpt) outliers start: 142 outliers final: 90 residues processed: 520 average time/residue: 1.5188 time to fit residues: 972.5257 Evaluate side-chains 519 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 416 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 532 THR Chi-restraints excluded: chain G residue 586 LEU Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 773 GLU Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 142 SER Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 453 HIS Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 258 ASP Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 371 MET Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 442 ARG Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 462 LEU Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 280 optimal weight: 30.0000 chunk 180 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 308 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 356 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN H 152 GLN ** H 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38712 Z= 0.786 Angle : 2.182 50.774 52486 Z= 1.431 Chirality : 0.445 6.581 5841 Planarity : 0.005 0.069 6553 Dihedral : 9.846 176.026 5776 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.57 % Favored : 97.41 % Rotamer: Outliers : 3.73 % Allowed : 19.20 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.69 (0.12), residues: 4711 helix: 1.24 (0.10), residues: 2652 sheet: -0.23 (0.27), residues: 311 loop : -0.53 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP J 93 HIS 0.010 0.001 HIS G 178 PHE 0.028 0.002 PHE L 341 TYR 0.021 0.002 TYR L 428 ARG 0.013 0.001 ARG L 198 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 426 time to evaluate : 4.157 Fit side-chains REVERT: F 80 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7188 (pm20) REVERT: F 302 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8362 (tp30) REVERT: F 307 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8483 (mt) REVERT: G 114 CYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7990 (t) REVERT: G 490 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8540 (tp40) REVERT: G 834 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.7539 (mp10) REVERT: C 127 PHE cc_start: 0.9202 (OUTLIER) cc_final: 0.8798 (t80) REVERT: C 190 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8051 (tp40) REVERT: C 240 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8380 (mt-10) REVERT: C 378 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.8227 (ttp-110) REVERT: B 23 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6983 (mt-10) REVERT: B 41 LYS cc_start: 0.9106 (mttp) cc_final: 0.8413 (tmtt) REVERT: I 126 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9055 (mttp) REVERT: H 8 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8783 (tm) REVERT: H 12 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8897 (mm) REVERT: H 286 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.6869 (tmt90) REVERT: H 322 TRP cc_start: 0.7964 (t-100) cc_final: 0.6998 (t60) REVERT: L 258 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7113 (tmm) REVERT: L 578 PHE cc_start: 0.7778 (t80) cc_final: 0.7432 (t80) REVERT: M 384 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8791 (tt) REVERT: M 442 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.7235 (mtp180) REVERT: N 295 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8353 (mttt) REVERT: N 379 MET cc_start: 0.9108 (mmt) cc_final: 0.8571 (mmt) REVERT: N 388 MET cc_start: 0.8265 (mtm) cc_final: 0.7946 (mtp) REVERT: J 72 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8416 (mpt) outliers start: 145 outliers final: 91 residues processed: 531 average time/residue: 1.4963 time to fit residues: 963.1289 Evaluate side-chains 530 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 420 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 490 GLN Chi-restraints excluded: chain G residue 496 LYS Chi-restraints excluded: chain G residue 532 THR Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 884 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 8 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 258 MET Chi-restraints excluded: chain L residue 286 VAL Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 130 VAL Chi-restraints excluded: chain M residue 258 ASP Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 442 ARG Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 295 LYS Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 412 optimal weight: 7.9990 chunk 433 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 422 optimal weight: 3.9990 chunk 254 optimal weight: 0.6980 chunk 183 optimal weight: 0.0770 chunk 331 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 381 optimal weight: 6.9990 chunk 399 optimal weight: 0.9980 chunk 420 optimal weight: 6.9990 overall best weight: 2.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN H 152 GLN ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38712 Z= 0.737 Angle : 2.167 50.783 52486 Z= 1.426 Chirality : 0.441 6.463 5841 Planarity : 0.004 0.073 6553 Dihedral : 9.417 174.306 5775 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.96 % Allowed : 20.23 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.97 (0.12), residues: 4711 helix: 1.47 (0.10), residues: 2649 sheet: -0.16 (0.28), residues: 311 loop : -0.42 (0.15), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 PHE 0.027 0.001 PHE L 341 TYR 0.026 0.002 TYR M 435 ARG 0.015 0.000 ARG L 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 443 time to evaluate : 4.006 Fit side-chains REVERT: F 80 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: F 302 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8409 (tp30) REVERT: G 541 MET cc_start: 0.9037 (mmt) cc_final: 0.8594 (mmt) REVERT: G 834 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.7638 (mp10) REVERT: C 190 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7981 (tp40) REVERT: C 240 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8357 (mt-10) REVERT: C 378 ARG cc_start: 0.8419 (ttp-170) cc_final: 0.8142 (ttp-110) REVERT: B 23 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6969 (mt-10) REVERT: B 41 LYS cc_start: 0.9097 (mttp) cc_final: 0.8383 (tmtt) REVERT: B 170 MET cc_start: 0.8999 (mtp) cc_final: 0.8694 (mtm) REVERT: I 83 LYS cc_start: 0.8716 (mppt) cc_final: 0.8472 (mmpt) REVERT: I 126 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9042 (mttp) REVERT: H 322 TRP cc_start: 0.7985 (t-100) cc_final: 0.7018 (t60) REVERT: L 40 LEU cc_start: 0.8905 (mp) cc_final: 0.8573 (mt) REVERT: M 291 MET cc_start: 0.9074 (mtp) cc_final: 0.8747 (mtm) REVERT: M 384 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8767 (tt) REVERT: N 295 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8303 (mttt) REVERT: N 379 MET cc_start: 0.9044 (mmt) cc_final: 0.8494 (mmt) REVERT: N 388 MET cc_start: 0.8112 (mtm) cc_final: 0.7697 (mtt) REVERT: J 72 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8467 (mpt) outliers start: 115 outliers final: 80 residues processed: 527 average time/residue: 1.5091 time to fit residues: 967.8631 Evaluate side-chains 522 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 432 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 532 THR Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 808 GLN Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain L residue 8 ILE Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 379 PHE Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 258 ASP Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 281 ASN Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 295 LYS Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 277 optimal weight: 10.0000 chunk 446 optimal weight: 0.9990 chunk 272 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 468 optimal weight: 3.9990 chunk 430 optimal weight: 6.9990 chunk 372 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN H 152 GLN ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.243 38712 Z= 0.744 Angle : 2.171 50.739 52486 Z= 1.427 Chirality : 0.442 6.495 5841 Planarity : 0.005 0.080 6553 Dihedral : 9.310 174.235 5773 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.62 % Allowed : 20.56 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.99 (0.12), residues: 4711 helix: 1.46 (0.10), residues: 2667 sheet: -0.13 (0.28), residues: 304 loop : -0.37 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 PHE 0.027 0.002 PHE L 341 TYR 0.023 0.002 TYR N 424 ARG 0.016 0.000 ARG L 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 431 time to evaluate : 3.988 Fit side-chains REVERT: F 80 GLU cc_start: 0.7565 (mp0) cc_final: 0.7122 (pm20) REVERT: F 302 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8415 (tp30) REVERT: G 541 MET cc_start: 0.9039 (mmt) cc_final: 0.8646 (mmt) REVERT: G 834 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: C 190 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7961 (tp40) REVERT: C 240 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: C 378 ARG cc_start: 0.8424 (ttp-170) cc_final: 0.8163 (ttp-110) REVERT: B 23 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: B 41 LYS cc_start: 0.9095 (mttp) cc_final: 0.8387 (tmtt) REVERT: B 170 MET cc_start: 0.9000 (mtp) cc_final: 0.8696 (mtm) REVERT: I 83 LYS cc_start: 0.8704 (mppt) cc_final: 0.8469 (mmpt) REVERT: I 126 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9039 (mttp) REVERT: H 286 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.6928 (tmt90) REVERT: H 322 TRP cc_start: 0.7966 (t-100) cc_final: 0.6979 (t60) REVERT: L 40 LEU cc_start: 0.8906 (mp) cc_final: 0.8575 (mt) REVERT: L 578 PHE cc_start: 0.7715 (t80) cc_final: 0.7377 (t80) REVERT: M 90 MET cc_start: 0.8651 (mmt) cc_final: 0.8438 (mmt) REVERT: M 291 MET cc_start: 0.9075 (mtp) cc_final: 0.8773 (mtm) REVERT: M 384 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8763 (tt) REVERT: M 442 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7147 (mtp180) REVERT: N 295 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8324 (mttt) REVERT: N 379 MET cc_start: 0.9114 (mmt) cc_final: 0.8432 (mmt) REVERT: N 388 MET cc_start: 0.8098 (mtm) cc_final: 0.7745 (mtp) REVERT: K 86 ARG cc_start: 0.8632 (ptp-110) cc_final: 0.8420 (ptp-110) REVERT: J 72 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8416 (mpt) outliers start: 102 outliers final: 76 residues processed: 505 average time/residue: 1.5420 time to fit residues: 942.3575 Evaluate side-chains 517 residues out of total 3887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 430 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 48 ASP Chi-restraints excluded: chain F residue 79 ASP Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 388 CYS Chi-restraints excluded: chain F residue 413 LYS Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 669 THR Chi-restraints excluded: chain G residue 834 GLN Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 482 GLU Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 537 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain I residue 4 LYS Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 126 LYS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 286 ARG Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 90 SER Chi-restraints excluded: chain L residue 200 MET Chi-restraints excluded: chain L residue 216 MET Chi-restraints excluded: chain L residue 241 ASP Chi-restraints excluded: chain L residue 398 SER Chi-restraints excluded: chain L residue 455 LEU Chi-restraints excluded: chain L residue 472 VAL Chi-restraints excluded: chain L residue 482 THR Chi-restraints excluded: chain L residue 490 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 258 ASP Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 281 ASN Chi-restraints excluded: chain M residue 384 LEU Chi-restraints excluded: chain M residue 426 THR Chi-restraints excluded: chain M residue 442 ARG Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 227 THR Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 295 LYS Chi-restraints excluded: chain K residue 27 ASN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 59 TYR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 72 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 296 optimal weight: 5.9990 chunk 397 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 343 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 373 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 383 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 839 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 400 GLN H 312 ASN ** M 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 ASN J 24 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.070850 restraints weight = 50481.585| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.22 r_work: 0.2850 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.243 38712 Z= 0.748 Angle : 2.173 50.730 52486 Z= 1.427 Chirality : 0.442 6.503 5841 Planarity : 0.004 0.074 6553 Dihedral : 9.241 174.524 5769 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.70 % Allowed : 20.51 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.98 (0.12), residues: 4711 helix: 1.45 (0.10), residues: 2668 sheet: -0.14 (0.28), residues: 300 loop : -0.36 (0.15), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP J 93 HIS 0.008 0.001 HIS G 178 PHE 0.026 0.002 PHE L 341 TYR 0.023 0.002 TYR N 424 ARG 0.016 0.000 ARG L 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14792.99 seconds wall clock time: 263 minutes 24.18 seconds (15804.18 seconds total)