Starting phenix.real_space_refine on Fri Feb 23 07:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/02_2024/7p7m_13240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/02_2024/7p7m_13240.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/02_2024/7p7m_13240_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/02_2024/7p7m_13240_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/02_2024/7p7m_13240_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/02_2024/7p7m_13240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/02_2024/7p7m_13240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/02_2024/7p7m_13240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/02_2024/7p7m_13240_updated.pdb" } resolution = 3.2 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= 0.015 sd= 0.054 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 12 5.49 5 S 267 5.16 5 C 24335 2.51 5 N 6171 2.21 5 O 6572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 60": "OD1" <-> "OD2" Residue "E TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G GLU 792": "OE1" <-> "OE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "H TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 359": "OE1" <-> "OE2" Residue "L PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 484": "OE1" <-> "OE2" Residue "M ASP 487": "OD1" <-> "OD2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N GLU 133": "OE1" <-> "OE2" Residue "N GLU 154": "OE1" <-> "OE2" Residue "N GLU 267": "OE1" <-> "OE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K ASP 93": "OD1" <-> "OD2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J ASP 116": "OD1" <-> "OD2" Residue "J GLU 161": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37390 Number of models: 1 Model: "" Number of chains: 25 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: 4728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4728 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 551} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} 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: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2444 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 4549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4549 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 577} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3638 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 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: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1218 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 5, 'TRANS': 154} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'HQH': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "L" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 236 Unusual residues: {'3PE': 5, 'LFA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "M" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 68.304 59.413 189.201 1.00 29.41 S ATOM 2741 SG CYS F 357 72.018 58.525 193.406 1.00 66.62 S ATOM 3062 SG CYS F 398 65.858 55.799 194.107 1.00 84.13 S ATOM 2697 SG CYS F 351 69.711 52.852 190.349 1.00 62.48 S ATOM 4054 SG CYS E 92 79.392 48.996 209.249 1.00 90.80 S ATOM 4088 SG CYS E 97 79.863 49.754 212.667 1.00 81.17 S ATOM 4366 SG CYS E 133 74.149 48.842 209.239 1.00110.33 S ATOM 4392 SG CYS E 137 73.610 49.597 212.541 1.00117.34 S ATOM 5476 SG CYS G 114 78.366 64.998 171.392 1.00 22.23 S ATOM 5416 SG CYS G 105 84.028 67.967 172.844 1.00 38.50 S ATOM 5436 SG CYS G 108 83.943 62.063 170.096 1.00 26.07 S ATOM 5830 SG CYS G 156 71.881 57.611 176.372 1.00 25.53 S ATOM 5811 SG CYS G 153 77.742 55.933 179.006 1.00 38.78 S ATOM 5859 SG CYS G 159 74.316 51.637 175.561 1.00 26.36 S ATOM 6203 SG CYS G 203 76.772 56.692 172.459 1.00 33.79 S ATOM 6428 SG CYS G 230 71.426 49.270 151.292 1.00 48.42 S ATOM 6713 SG CYS G 265 71.310 45.359 156.522 1.00 32.16 S ATOM 6476 SG CYS G 237 66.267 49.363 154.746 1.00 29.99 S ATOM 6452 SG CYS G 233 67.695 43.931 151.365 1.00 60.94 S ATOM 4877 SG CYS G 36 65.724 59.106 179.248 1.00 32.61 S ATOM 4953 SG CYS G 47 67.751 62.179 179.699 1.00 41.12 S ATOM 4979 SG CYS G 50 62.122 64.480 180.096 1.00 40.68 S ATOM 5128 SG CYS G 69 61.334 60.863 179.628 1.00 35.12 S ATOM 17223 SG CYS B 129 90.398 91.720 147.173 1.00 35.97 S ATOM 16720 SG CYS B 64 96.078 94.754 148.831 1.00 50.87 S ATOM 16714 SG CYS B 63 90.921 97.242 151.186 1.00 54.56 S ATOM 17440 SG CYS B 158 92.401 91.175 153.006 1.00 43.38 S ATOM 18818 SG CYS I 109 95.242 74.535 166.721 1.00 39.57 S ATOM 18481 SG CYS I 66 92.882 74.217 160.709 1.00 49.62 S ATOM 18441 SG CYS I 60 96.471 69.340 162.803 1.00 35.38 S ATOM 18459 SG CYS I 63 90.468 70.563 165.525 1.00 31.58 S ATOM 18771 SG CYS I 102 90.750 85.322 159.269 1.00 45.45 S ATOM 18746 SG CYS I 99 95.778 83.637 155.153 1.00 56.07 S ATOM 18789 SG CYS I 105 94.528 80.312 160.571 1.00 56.71 S ATOM 18504 SG CYS I 70 90.254 80.165 155.590 1.00 32.30 S Time building chain proxies: 19.72, per 1000 atoms: 0.53 Number of scatterers: 37390 At special positions: 0 Unit cell: (156.09, 220.22, 242, 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 12 15.00 O 6572 8.00 N 6171 7.00 C 24335 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: 14.77 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " 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 36 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 47 " 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="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " 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="FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 105 " 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="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 66 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 109 " pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 102 " Number of angles added : 93 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 26 sheets defined 54.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.29 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 75 Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 109 through 121 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 234 through 237 No H-bonds generated for 'chain 'F' and resid 234 through 237' Processing helix chain 'F' and resid 270 through 275 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 315 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: 3.628A pdb=" N ALA F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.956A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.516A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.145A 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 158 through 164 removed outlier: 3.562A pdb=" N GLU E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 4.152A 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 123 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 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 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: 4.273A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.771A 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 440 through 443 removed outlier: 4.417A pdb=" N ASP G 443 " --> pdb=" O ARG G 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 440 through 443' Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 494 Processing helix chain 'G' and resid 504 through 506 No H-bonds generated for 'chain 'G' and resid 504 through 506' 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 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 604 removed outlier: 3.842A pdb=" N GLU G 604 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 604' Processing helix chain 'G' and resid 638 through 641 No H-bonds generated for 'chain 'G' and resid 638 through 641' Processing helix chain 'G' and resid 650 through 662 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 686 through 688 No H-bonds generated for 'chain 'G' and resid 686 through 688' Processing helix chain 'G' and resid 764 through 770 removed outlier: 3.586A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 832 through 836 removed outlier: 3.654A pdb=" N SER G 835 " --> pdb=" O VAL G 832 " (cutoff:3.500A) 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 54 through 65 removed outlier: 5.019A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.716A pdb=" N ASN C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.621A pdb=" N LEU C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.832A pdb=" N ILE C 275 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 353 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 422 Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.191A 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 522 Processing helix chain 'C' and resid 564 through 576 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 595 through 598 No H-bonds generated for 'chain 'C' and resid 595 through 598' Processing helix chain 'B' and resid 38 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 107 through 115 Processing helix chain 'B' and resid 127 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: 3.519A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.595A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 removed outlier: 3.936A pdb=" N PHE I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 107 No H-bonds generated for 'chain 'I' and resid 104 through 107' 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 'I' and resid 150 through 153 No H-bonds generated for 'chain 'I' and resid 150 through 153' 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: 4.464A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 3.741A pdb=" N VAL H 127 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU H 131 " --> pdb=" O TYR H 128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE H 132 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP H 135 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 157 Processing helix chain 'H' and resid 160 through 171 removed outlier: 4.230A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 181 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 303 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: 3.717A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.561A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.513A pdb=" N LEU L 18 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 3.628A 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 removed outlier: 4.033A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) 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: 3.762A 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 237 through 244 removed outlier: 4.382A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 261 through 268 Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 300 removed outlier: 4.158A 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 356 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 436 Processing helix chain 'L' and resid 455 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 518 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 548 removed outlier: 6.062A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.004A 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: 3.850A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER L 586 " --> pdb=" O GLY L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 2 through 23 Proline residue: M 10 - end of helix removed outlier: 3.899A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 50 Processing helix chain 'M' and resid 52 through 54 No H-bonds generated for 'chain 'M' and resid 52 through 54' Processing helix chain 'M' and resid 85 through 105 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.582A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.296A 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 200 Processing helix chain 'M' and resid 219 through 233 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 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.695A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 4.035A 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 377 through 379 No H-bonds generated for 'chain 'M' and resid 377 through 379' Processing helix chain 'M' and resid 384 through 396 removed outlier: 3.687A pdb=" N LEU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 444 removed outlier: 4.043A pdb=" N GLY M 428 " --> pdb=" O ILE M 424 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU M 429 " --> pdb=" O SER M 425 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL M 430 " --> pdb=" O THR M 426 " (cutoff:3.500A) 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 502 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: 4.300A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.130A 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: 4.428A 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: 4.426A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 267 through 288 removed outlier: 4.333A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 316 removed outlier: 4.019A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.466A 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 433 removed outlier: 4.076A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) 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 23 Processing helix chain 'K' and resid 28 through 53 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 46 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 113 removed outlier: 5.814A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.752A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) 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: 6.563A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.111A 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 'E' and resid 143 through 145 Processing sheet with id= F, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.469A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= H, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= I, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.286A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 285 through 288 Processing sheet with id= K, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.862A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.403A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= N, first strand: chain 'G' and resid 813 through 816 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 8.006A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER G 861 " --> pdb=" O LYS G 906 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS G 906 " --> pdb=" O SER G 861 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASP G 904 " --> pdb=" O SER G 863 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.175A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.441A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 215 through 219 removed outlier: 3.632A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 532 through 539 removed outlier: 3.721A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 3 through 6 Processing sheet with id= U, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.368A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= W, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.541A pdb=" N GLN I 78 " --> pdb=" O PHE I 91 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= Y, first strand: chain 'L' and resid 60 through 66 removed outlier: 7.113A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.764A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1855 hydrogen bonds defined for protein. 5298 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: 12.51 Time building geometry restraints manager: 16.05 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: 15914 1.42 - 1.64: 21903 1.64 - 1.86: 409 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 38318 Sorted by residual: bond pdb=" C24 HQH H 701 " pdb=" C25 HQH H 701 " ideal model delta sigma weight residual 1.539 1.366 0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" C12 HQH H 701 " pdb=" C19 HQH H 701 " ideal model delta sigma weight residual 1.534 1.362 0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" C24 HQH H 701 " pdb=" N5 HQH H 701 " ideal model delta sigma weight residual 1.498 1.371 0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C12 HQH H 701 " pdb=" N5 HQH H 701 " ideal model delta sigma weight residual 1.494 1.371 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C11 HQH H 701 " pdb=" C18 HQH H 701 " ideal model delta sigma weight residual 1.558 1.466 0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 38313 not shown) Histogram of bond angle deviations from ideal: 69.36 - 82.86: 88 82.86 - 96.35: 0 96.35 - 109.84: 4979 109.84 - 123.33: 45488 123.33 - 136.83: 1428 Bond angle restraints: 51983 Sorted by residual: angle pdb=" C14 HQH H 701 " pdb=" C9 HQH H 701 " pdb=" C7 HQH H 701 " ideal model delta sigma weight residual 68.20 118.40 -50.20 3.00e+00 1.11e-01 2.80e+02 angle pdb=" C18 HQH H 701 " pdb=" C11 HQH H 701 " pdb=" C22 HQH H 701 " ideal model delta sigma weight residual 74.50 118.63 -44.13 3.00e+00 1.11e-01 2.16e+02 angle pdb=" C13 HQH H 701 " pdb=" C20 HQH H 701 " pdb=" C17 HQH H 701 " ideal model delta sigma weight residual 85.93 126.12 -40.19 3.00e+00 1.11e-01 1.80e+02 angle pdb=" C16 HQH H 701 " pdb=" C9 HQH H 701 " pdb=" C7 HQH H 701 " ideal model delta sigma weight residual 85.85 119.62 -33.77 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C14 HQH H 701 " pdb=" C9 HQH H 701 " pdb=" C16 HQH H 701 " ideal model delta sigma weight residual 152.69 121.94 30.75 3.00e+00 1.11e-01 1.05e+02 ... (remaining 51978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 21947 33.91 - 67.83: 565 67.83 - 101.74: 38 101.74 - 135.65: 6 135.65 - 169.57: 1 Dihedral angle restraints: 22557 sinusoidal: 9074 harmonic: 13483 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 180.00 131.51 48.49 0 5.00e+00 4.00e-02 9.40e+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 88.02 169.57 1 2.00e+01 2.50e-03 4.76e+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 180.00 146.34 33.66 0 5.00e+00 4.00e-02 4.53e+01 ... (remaining 22554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.245: 5774 4.245 - 8.491: 0 8.491 - 12.736: 0 12.736 - 16.981: 0 16.981 - 21.226: 28 Chirality restraints: 5802 Sorted by residual: chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.67 21.23 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.62 21.17 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 -10.61 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5799 not shown) Planarity restraints: 6502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 HQH H 701 " -0.016 2.00e-02 2.50e+03 2.50e-02 1.72e+01 pdb=" C13 HQH H 701 " 0.057 2.00e-02 2.50e+03 pdb=" C19 HQH H 701 " -0.013 2.00e-02 2.50e+03 pdb=" C23 HQH H 701 " -0.007 2.00e-02 2.50e+03 pdb=" C24 HQH H 701 " -0.018 2.00e-02 2.50e+03 pdb=" C25 HQH H 701 " -0.003 2.00e-02 2.50e+03 pdb=" C28 HQH H 701 " -0.010 2.00e-02 2.50e+03 pdb=" N5 HQH H 701 " -0.031 2.00e-02 2.50e+03 pdb=" O2 HQH H 701 " -0.000 2.00e-02 2.50e+03 pdb=" O3 HQH H 701 " 0.042 2.00e-02 2.50e+03 pdb=" O4 HQH H 701 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 792 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" CD GLU G 792 " -0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU G 792 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU G 792 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO N 65 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.043 5.00e-02 4.00e+02 ... (remaining 6499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3878 2.75 - 3.29: 36552 3.29 - 3.83: 67516 3.83 - 4.36: 80550 4.36 - 4.90: 137631 Nonbonded interactions: 326127 Sorted by model distance: nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR H 128 " pdb=" O ALA J 60 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.242 2.440 nonbonded pdb=" O THR M 422 " pdb=" OG1 THR M 426 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR L 594 " pdb=" OD2 ASP N 229 " model vdw 2.273 2.440 ... (remaining 326122 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 3.630 Check model and map are aligned: 0.650 Set scattering table: 0.420 Process input model: 104.220 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.005 0.173 38318 Z= 0.307 Angle : 0.875 50.197 51983 Z= 0.411 Chirality : 1.468 21.226 5802 Planarity : 0.006 0.077 6502 Dihedral : 14.896 169.568 13933 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.63 % Rotamer: Outliers : 0.39 % Allowed : 12.42 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 4680 helix: 0.34 (0.09), residues: 2665 sheet: -1.09 (0.26), residues: 333 loop : -1.24 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP L 143 HIS 0.015 0.001 HIS G 607 PHE 0.039 0.002 PHE L 341 TYR 0.032 0.002 TYR M 435 ARG 0.014 0.000 ARG G 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 375 time to evaluate : 6.178 Fit side-chains REVERT: E 116 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8692 (mmmt) REVERT: G 62 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7406 (mtp85) REVERT: G 312 LYS cc_start: 0.8491 (pttp) cc_final: 0.8051 (tptp) REVERT: H 238 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6219 (t80) REVERT: A 124 ASP cc_start: 0.8428 (m-30) cc_final: 0.7680 (p0) REVERT: M 325 PHE cc_start: 0.8842 (OUTLIER) cc_final: 0.7675 (t80) REVERT: M 370 ASP cc_start: 0.8615 (t0) cc_final: 0.8314 (t70) REVERT: M 466 PHE cc_start: 0.8436 (m-10) cc_final: 0.7461 (t80) REVERT: N 485 MET cc_start: 0.3656 (mmt) cc_final: 0.3309 (mmt) REVERT: K 72 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8953 (mm-30) REVERT: J 3 PHE cc_start: 0.7989 (t80) cc_final: 0.7789 (t80) outliers start: 15 outliers final: 7 residues processed: 382 average time/residue: 0.4840 time to fit residues: 307.7894 Evaluate side-chains 358 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 349 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain N residue 321 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 196 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 238 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 222 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 110 HIS F 237 GLN E 46 GLN E 98 HIS C 359 HIS L 28 ASN ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 406 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.253 38318 Z= 0.764 Angle : 2.191 51.070 51983 Z= 1.435 Chirality : 0.442 6.487 5802 Planarity : 0.004 0.068 6502 Dihedral : 9.424 169.840 5615 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.54 % Favored : 97.44 % Rotamer: Outliers : 1.56 % Allowed : 12.39 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.12), residues: 4680 helix: 1.10 (0.10), residues: 2674 sheet: -1.00 (0.27), residues: 333 loop : -0.99 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 143 HIS 0.006 0.001 HIS C 518 PHE 0.025 0.001 PHE L 341 TYR 0.021 0.001 TYR N 424 ARG 0.005 0.000 ARG G 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 349 time to evaluate : 4.375 Fit side-chains REVERT: G 312 LYS cc_start: 0.8529 (pttp) cc_final: 0.7921 (tptp) REVERT: G 792 GLU cc_start: 0.8183 (pp20) cc_final: 0.7974 (pp20) REVERT: G 793 ASN cc_start: 0.8401 (m-40) cc_final: 0.8083 (m-40) REVERT: B 193 TYR cc_start: 0.8060 (m-80) cc_final: 0.7286 (m-80) REVERT: A 124 ASP cc_start: 0.8401 (m-30) cc_final: 0.7795 (p0) REVERT: M 466 PHE cc_start: 0.8431 (m-10) cc_final: 0.7431 (t80) REVERT: N 183 ASP cc_start: 0.9112 (t0) cc_final: 0.8886 (t0) REVERT: N 430 VAL cc_start: 0.9026 (OUTLIER) cc_final: 0.8784 (p) REVERT: K 97 GLU cc_start: 0.8977 (pt0) cc_final: 0.8720 (pp20) REVERT: J 73 MET cc_start: 0.9003 (mtp) cc_final: 0.8508 (ttt) outliers start: 60 outliers final: 32 residues processed: 388 average time/residue: 0.5176 time to fit residues: 337.6233 Evaluate side-chains 370 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 337 time to evaluate : 4.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 461 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 235 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 352 optimal weight: 5.9990 chunk 288 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 424 optimal weight: 0.0970 chunk 458 optimal weight: 20.0000 chunk 378 optimal weight: 8.9990 chunk 421 optimal weight: 5.9990 chunk 144 optimal weight: 40.0000 chunk 340 optimal weight: 9.9990 overall best weight: 3.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 655 HIS H 138 ASN M 117 HIS ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.253 38318 Z= 0.760 Angle : 2.184 50.918 51983 Z= 1.432 Chirality : 0.441 6.452 5802 Planarity : 0.004 0.064 6502 Dihedral : 9.074 169.643 5602 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.08 % Allowed : 12.57 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % 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: 0.68 (0.12), residues: 4680 helix: 1.43 (0.10), residues: 2668 sheet: -0.90 (0.28), residues: 333 loop : -0.80 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 143 HIS 0.006 0.001 HIS G 178 PHE 0.026 0.001 PHE L 341 TYR 0.023 0.001 TYR N 424 ARG 0.005 0.000 ARG G 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 353 time to evaluate : 4.882 Fit side-chains REVERT: F 309 MET cc_start: 0.8619 (mtp) cc_final: 0.8219 (mtp) REVERT: F 327 MET cc_start: 0.9057 (ttp) cc_final: 0.8720 (ttm) REVERT: E 86 ARG cc_start: 0.8994 (mtm-85) cc_final: 0.8156 (mtm-85) REVERT: G 312 LYS cc_start: 0.8552 (pttp) cc_final: 0.7916 (tptp) REVERT: G 792 GLU cc_start: 0.8230 (pp20) cc_final: 0.7950 (pp20) REVERT: G 793 ASN cc_start: 0.8329 (m-40) cc_final: 0.7493 (m-40) REVERT: B 193 TYR cc_start: 0.8150 (m-80) cc_final: 0.7438 (m-80) REVERT: A 124 ASP cc_start: 0.8416 (m-30) cc_final: 0.7716 (p0) REVERT: L 425 THR cc_start: 0.8208 (m) cc_final: 0.7885 (p) REVERT: M 325 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7773 (t80) REVERT: M 466 PHE cc_start: 0.8418 (m-10) cc_final: 0.7486 (t80) REVERT: N 183 ASP cc_start: 0.9165 (t0) cc_final: 0.8840 (t0) REVERT: N 430 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8800 (p) REVERT: N 485 MET cc_start: 0.4464 (mmt) cc_final: 0.3894 (mmt) REVERT: K 72 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8975 (mm-30) REVERT: K 97 GLU cc_start: 0.8917 (pt0) cc_final: 0.8688 (pp20) REVERT: J 73 MET cc_start: 0.9007 (mtp) cc_final: 0.8554 (ttt) outliers start: 80 outliers final: 50 residues processed: 409 average time/residue: 0.4957 time to fit residues: 338.0342 Evaluate side-chains 390 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 338 time to evaluate : 4.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 763 SER Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 419 optimal weight: 9.9990 chunk 319 optimal weight: 20.0000 chunk 220 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 426 optimal weight: 10.0000 chunk 451 optimal weight: 6.9990 chunk 222 optimal weight: 0.0040 chunk 404 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN C 16 GLN L 411 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 38318 Z= 0.775 Angle : 2.192 50.827 51983 Z= 1.436 Chirality : 0.442 6.447 5802 Planarity : 0.004 0.064 6502 Dihedral : 8.972 169.588 5602 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 2.34 % Allowed : 13.17 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % 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: 0.75 (0.12), residues: 4680 helix: 1.49 (0.10), residues: 2668 sheet: -0.93 (0.28), residues: 320 loop : -0.78 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 143 HIS 0.012 0.001 HIS G 178 PHE 0.024 0.001 PHE L 341 TYR 0.021 0.002 TYR N 424 ARG 0.006 0.000 ARG G 288 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 338 time to evaluate : 4.238 Fit side-chains REVERT: F 161 MET cc_start: 0.9016 (mtm) cc_final: 0.8810 (ptp) REVERT: F 309 MET cc_start: 0.8793 (mtp) cc_final: 0.8380 (mtp) REVERT: F 327 MET cc_start: 0.9084 (ttp) cc_final: 0.8756 (ttm) REVERT: G 295 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7803 (mt) REVERT: G 312 LYS cc_start: 0.8557 (pttp) cc_final: 0.8055 (tptp) REVERT: G 792 GLU cc_start: 0.8277 (pp20) cc_final: 0.7945 (pp20) REVERT: G 793 ASN cc_start: 0.8226 (m-40) cc_final: 0.7269 (m-40) REVERT: B 41 LYS cc_start: 0.9117 (mttt) cc_final: 0.8882 (mtmt) REVERT: B 193 TYR cc_start: 0.8134 (m-80) cc_final: 0.7443 (m-80) REVERT: A 124 ASP cc_start: 0.8430 (m-30) cc_final: 0.7718 (p0) REVERT: L 328 TRP cc_start: 0.8538 (OUTLIER) cc_final: 0.7358 (m100) REVERT: L 425 THR cc_start: 0.8236 (m) cc_final: 0.7911 (p) REVERT: M 466 PHE cc_start: 0.8388 (m-10) cc_final: 0.7438 (t80) REVERT: N 183 ASP cc_start: 0.9174 (t0) cc_final: 0.8846 (t0) REVERT: N 192 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7753 (p0) REVERT: N 379 MET cc_start: 0.9101 (mmt) cc_final: 0.8876 (mmt) REVERT: N 430 VAL cc_start: 0.9080 (OUTLIER) cc_final: 0.8836 (p) REVERT: K 97 GLU cc_start: 0.8969 (pt0) cc_final: 0.8746 (pp20) REVERT: J 73 MET cc_start: 0.9004 (mtp) cc_final: 0.8566 (ttt) outliers start: 90 outliers final: 64 residues processed: 405 average time/residue: 0.4817 time to fit residues: 324.6436 Evaluate side-chains 397 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 329 time to evaluate : 4.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 763 SER Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 378 ARG 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 B residue 4 THR Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 375 optimal weight: 8.9990 chunk 256 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 336 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 385 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 230 optimal weight: 8.9990 chunk 405 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN H 138 ASN H 208 HIS ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 38318 Z= 0.788 Angle : 2.198 50.866 51983 Z= 1.438 Chirality : 0.442 6.468 5802 Planarity : 0.004 0.065 6502 Dihedral : 8.971 170.119 5602 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.01 % Favored : 96.97 % Rotamer: Outliers : 2.78 % Allowed : 13.74 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.75 (0.12), residues: 4680 helix: 1.48 (0.10), residues: 2673 sheet: -0.97 (0.28), residues: 318 loop : -0.74 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP L 143 HIS 0.011 0.001 HIS G 178 PHE 0.023 0.002 PHE L 341 TYR 0.021 0.002 TYR N 424 ARG 0.006 0.000 ARG G 288 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 340 time to evaluate : 4.298 Fit side-chains revert: symmetry clash REVERT: F 327 MET cc_start: 0.9076 (ttp) cc_final: 0.8755 (ttm) REVERT: G 295 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7926 (mt) REVERT: G 312 LYS cc_start: 0.8505 (pttp) cc_final: 0.8008 (tptp) REVERT: G 870 THR cc_start: 0.6492 (OUTLIER) cc_final: 0.6236 (t) REVERT: G 906 LYS cc_start: 0.8302 (mmtm) cc_final: 0.8035 (mmtm) REVERT: H 36 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8656 (tp30) REVERT: H 242 TYR cc_start: 0.8900 (m-80) cc_final: 0.8644 (m-80) REVERT: A 124 ASP cc_start: 0.8452 (m-30) cc_final: 0.7752 (p0) REVERT: L 328 TRP cc_start: 0.8535 (OUTLIER) cc_final: 0.7427 (m100) REVERT: L 425 THR cc_start: 0.8331 (m) cc_final: 0.8031 (p) REVERT: M 466 PHE cc_start: 0.8454 (m-10) cc_final: 0.7455 (t80) REVERT: N 183 ASP cc_start: 0.9178 (t0) cc_final: 0.8842 (t0) REVERT: N 192 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7788 (p0) REVERT: N 430 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8906 (p) REVERT: K 72 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8975 (mm-30) REVERT: J 73 MET cc_start: 0.9016 (mtp) cc_final: 0.8584 (ttt) outliers start: 107 outliers final: 72 residues processed: 420 average time/residue: 0.4885 time to fit residues: 341.9655 Evaluate side-chains 409 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 331 time to evaluate : 3.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 94 SER Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 209 THR Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 763 SER Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain G residue 870 THR Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 273 ASP 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 B residue 4 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 275 MET Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 393 VAL Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 89 LYS Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 151 optimal weight: 0.5980 chunk 406 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 451 optimal weight: 5.9990 chunk 375 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.248 38318 Z= 0.759 Angle : 2.189 51.015 51983 Z= 1.434 Chirality : 0.441 6.427 5802 Planarity : 0.004 0.064 6502 Dihedral : 8.837 169.975 5600 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.49 % Allowed : 14.57 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % 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: 0.88 (0.12), residues: 4680 helix: 1.58 (0.10), residues: 2669 sheet: -0.89 (0.28), residues: 325 loop : -0.69 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 143 HIS 0.010 0.001 HIS G 178 PHE 0.024 0.001 PHE L 341 TYR 0.023 0.001 TYR N 424 ARG 0.007 0.000 ARG G 288 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 345 time to evaluate : 4.386 Fit side-chains REVERT: F 161 MET cc_start: 0.9062 (mtm) cc_final: 0.8851 (ptp) REVERT: G 295 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7904 (mt) REVERT: G 312 LYS cc_start: 0.8535 (pttp) cc_final: 0.8050 (tptp) REVERT: G 792 GLU cc_start: 0.8365 (pp20) cc_final: 0.7992 (pp20) REVERT: G 793 ASN cc_start: 0.8342 (m-40) cc_final: 0.8108 (m-40) REVERT: G 906 LYS cc_start: 0.8304 (mmtm) cc_final: 0.7996 (mmtm) REVERT: B 41 LYS cc_start: 0.9093 (mttt) cc_final: 0.8868 (mtmt) REVERT: H 36 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8670 (tp30) REVERT: A 124 ASP cc_start: 0.8433 (m-30) cc_final: 0.7666 (p0) REVERT: L 243 MET cc_start: 0.8687 (mmm) cc_final: 0.8388 (mmm) REVERT: L 328 TRP cc_start: 0.8476 (OUTLIER) cc_final: 0.7383 (m100) REVERT: L 425 THR cc_start: 0.8255 (m) cc_final: 0.7960 (p) REVERT: M 325 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.7782 (t80) REVERT: M 466 PHE cc_start: 0.8444 (m-10) cc_final: 0.7443 (t80) REVERT: N 183 ASP cc_start: 0.9167 (t0) cc_final: 0.8793 (t0) REVERT: N 192 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7790 (p0) REVERT: N 430 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8878 (p) REVERT: K 72 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8977 (mm-30) REVERT: K 98 MET cc_start: 0.8599 (mtm) cc_final: 0.8228 (mtm) REVERT: J 73 MET cc_start: 0.8998 (mtp) cc_final: 0.8557 (ttt) outliers start: 96 outliers final: 66 residues processed: 414 average time/residue: 0.4956 time to fit residues: 341.1394 Evaluate side-chains 403 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 331 time to evaluate : 4.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 763 SER Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 THR 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 B residue 94 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 65 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 351 SER Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 415 MET Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 192 ASN Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 435 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 257 optimal weight: 4.9990 chunk 329 optimal weight: 0.2980 chunk 255 optimal weight: 0.8980 chunk 380 optimal weight: 20.0000 chunk 252 optimal weight: 9.9990 chunk 450 optimal weight: 2.9990 chunk 281 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 513 GLN C 568 HIS H 323 GLN ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.254 38318 Z= 0.745 Angle : 2.180 51.019 51983 Z= 1.431 Chirality : 0.439 6.449 5802 Planarity : 0.004 0.066 6502 Dihedral : 8.566 168.734 5600 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.08 % Allowed : 15.01 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.13), residues: 4680 helix: 1.77 (0.10), residues: 2662 sheet: -0.80 (0.28), residues: 334 loop : -0.55 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.011 0.001 HIS G 178 PHE 0.026 0.001 PHE L 341 TYR 0.025 0.001 TYR N 424 ARG 0.008 0.000 ARG G 288 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 358 time to evaluate : 4.623 Fit side-chains revert: symmetry clash REVERT: F 94 MET cc_start: 0.8133 (mmm) cc_final: 0.7243 (tpt) REVERT: F 237 GLN cc_start: 0.9007 (mt0) cc_final: 0.8575 (mp10) REVERT: F 391 LEU cc_start: 0.8197 (mp) cc_final: 0.7965 (mp) REVERT: E 60 ASP cc_start: 0.8790 (p0) cc_final: 0.8386 (p0) REVERT: E 112 LYS cc_start: 0.8584 (mtpt) cc_final: 0.8338 (ttmm) REVERT: G 312 LYS cc_start: 0.8528 (pttp) cc_final: 0.7911 (tptp) REVERT: G 593 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7688 (ttt) REVERT: G 792 GLU cc_start: 0.8337 (pp20) cc_final: 0.7859 (pp20) REVERT: G 793 ASN cc_start: 0.8168 (m-40) cc_final: 0.7562 (m-40) REVERT: C 204 TRP cc_start: 0.7782 (m100) cc_final: 0.7242 (m100) REVERT: H 36 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8612 (tp30) REVERT: A 124 ASP cc_start: 0.8407 (m-30) cc_final: 0.7639 (p0) REVERT: L 328 TRP cc_start: 0.8392 (OUTLIER) cc_final: 0.6981 (m100) REVERT: M 224 MET cc_start: 0.8983 (tmm) cc_final: 0.8756 (tmm) REVERT: M 325 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.7826 (t80) REVERT: M 466 PHE cc_start: 0.8429 (m-10) cc_final: 0.7474 (t80) REVERT: N 183 ASP cc_start: 0.9085 (t0) cc_final: 0.8737 (t0) REVERT: K 72 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8972 (mm-30) REVERT: J 73 MET cc_start: 0.8940 (mtp) cc_final: 0.8452 (ttt) outliers start: 80 outliers final: 53 residues processed: 413 average time/residue: 0.5209 time to fit residues: 359.6181 Evaluate side-chains 396 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 339 time to evaluate : 4.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 439 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 362 TRP Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 238 PHE Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 99 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 278 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 268 optimal weight: 7.9990 chunk 135 optimal weight: 0.0270 chunk 88 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 286 optimal weight: 20.0000 chunk 306 optimal weight: 7.9990 chunk 222 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 353 optimal weight: 5.9990 overall best weight: 4.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 513 GLN C 568 HIS ** L 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.253 38318 Z= 0.768 Angle : 2.192 51.005 51983 Z= 1.436 Chirality : 0.441 6.491 5802 Planarity : 0.004 0.066 6502 Dihedral : 8.573 169.232 5600 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.08 % Allowed : 15.14 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.12), residues: 4680 helix: 1.70 (0.10), residues: 2671 sheet: -0.84 (0.28), residues: 324 loop : -0.58 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.023 0.001 PHE L 341 TYR 0.025 0.001 TYR L 428 ARG 0.009 0.000 ARG G 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 348 time to evaluate : 4.888 Fit side-chains REVERT: E 60 ASP cc_start: 0.8818 (p0) cc_final: 0.8355 (p0) REVERT: E 112 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8359 (ttmm) REVERT: E 116 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8614 (mmmt) REVERT: G 312 LYS cc_start: 0.8510 (pttp) cc_final: 0.7901 (tptp) REVERT: G 593 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7846 (ttt) REVERT: G 792 GLU cc_start: 0.8352 (pp20) cc_final: 0.7854 (pp20) REVERT: G 793 ASN cc_start: 0.8159 (m-40) cc_final: 0.7403 (m-40) REVERT: G 906 LYS cc_start: 0.8316 (mmtm) cc_final: 0.8041 (mmtm) REVERT: C 204 TRP cc_start: 0.7949 (m100) cc_final: 0.7403 (m100) REVERT: B 39 MET cc_start: 0.6788 (ttm) cc_final: 0.6569 (ttm) REVERT: B 41 LYS cc_start: 0.9091 (mttt) cc_final: 0.8853 (mtmt) REVERT: H 36 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8605 (tp30) REVERT: A 124 ASP cc_start: 0.8397 (m-30) cc_final: 0.7594 (p0) REVERT: L 328 TRP cc_start: 0.8444 (OUTLIER) cc_final: 0.7200 (m100) REVERT: M 466 PHE cc_start: 0.8434 (m-10) cc_final: 0.7443 (t80) REVERT: N 183 ASP cc_start: 0.9148 (t0) cc_final: 0.8811 (t0) REVERT: N 430 VAL cc_start: 0.9093 (OUTLIER) cc_final: 0.8848 (p) REVERT: J 73 MET cc_start: 0.8851 (mtp) cc_final: 0.8375 (ttt) outliers start: 80 outliers final: 65 residues processed: 409 average time/residue: 0.4964 time to fit residues: 337.5376 Evaluate side-chains 410 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 341 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 593 MET Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 178 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 B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain L residue 163 ASN Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 137 LEU Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 430 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain J residue 69 PHE Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 409 optimal weight: 2.9990 chunk 431 optimal weight: 9.9990 chunk 393 optimal weight: 0.0670 chunk 419 optimal weight: 1.9990 chunk 252 optimal weight: 0.4980 chunk 182 optimal weight: 0.8980 chunk 329 optimal weight: 0.0030 chunk 128 optimal weight: 0.5980 chunk 379 optimal weight: 10.0000 chunk 396 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 overall best weight: 0.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 238 ASN F 386 GLN G 261 HIS C 319 HIS C 568 HIS L 360 GLN N 37 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.257 38318 Z= 0.744 Angle : 2.181 50.786 51983 Z= 1.431 Chirality : 0.439 6.416 5802 Planarity : 0.004 0.070 6502 Dihedral : 8.279 167.905 5600 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.64 % Allowed : 15.61 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4680 helix: 1.84 (0.10), residues: 2655 sheet: -0.65 (0.28), residues: 328 loop : -0.49 (0.15), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.011 0.001 HIS G 178 PHE 0.027 0.001 PHE L 341 TYR 0.027 0.001 TYR N 424 ARG 0.009 0.000 ARG G 288 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 363 time to evaluate : 4.725 Fit side-chains REVERT: F 237 GLN cc_start: 0.8967 (mt0) cc_final: 0.8440 (mp10) REVERT: E 60 ASP cc_start: 0.8870 (p0) cc_final: 0.8599 (p0) REVERT: G 312 LYS cc_start: 0.8545 (pttp) cc_final: 0.7964 (tptp) REVERT: G 792 GLU cc_start: 0.8340 (pp20) cc_final: 0.7831 (pp20) REVERT: G 793 ASN cc_start: 0.8148 (m-40) cc_final: 0.7484 (m-40) REVERT: G 906 LYS cc_start: 0.8345 (mmtm) cc_final: 0.8094 (mmtm) REVERT: C 204 TRP cc_start: 0.7766 (m100) cc_final: 0.7214 (m100) REVERT: C 546 TYR cc_start: 0.9333 (m-80) cc_final: 0.9129 (m-80) REVERT: B 94 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: H 36 GLU cc_start: 0.9282 (OUTLIER) cc_final: 0.8671 (tp30) REVERT: H 165 MET cc_start: 0.8505 (mmp) cc_final: 0.8232 (mmm) REVERT: A 124 ASP cc_start: 0.8364 (m-30) cc_final: 0.7561 (p0) REVERT: L 258 MET cc_start: 0.8862 (ttt) cc_final: 0.8628 (ttt) REVERT: L 328 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.6698 (m100) REVERT: L 415 MET cc_start: 0.7464 (ptp) cc_final: 0.7235 (ptm) REVERT: M 325 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.7830 (t80) REVERT: M 466 PHE cc_start: 0.8441 (m-10) cc_final: 0.7457 (t80) REVERT: N 183 ASP cc_start: 0.9036 (t0) cc_final: 0.8654 (t0) REVERT: J 3 PHE cc_start: 0.8010 (t80) cc_final: 0.7764 (t80) REVERT: J 73 MET cc_start: 0.8753 (mtp) cc_final: 0.8315 (ttt) outliers start: 63 outliers final: 47 residues processed: 410 average time/residue: 0.4886 time to fit residues: 335.0096 Evaluate side-chains 396 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 345 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 362 TRP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 325 PHE Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain M residue 470 LEU Chi-restraints excluded: chain M residue 493 ILE Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 275 optimal weight: 20.0000 chunk 443 optimal weight: 7.9990 chunk 270 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 308 optimal weight: 3.9990 chunk 465 optimal weight: 9.9990 chunk 428 optimal weight: 20.0000 chunk 370 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 286 optimal weight: 20.0000 chunk 227 optimal weight: 0.1980 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 GLN F 386 GLN E 46 GLN E 119 GLN C 568 HIS H 138 ASN H 170 GLN M 308 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.256 38318 Z= 0.752 Angle : 2.186 50.821 51983 Z= 1.433 Chirality : 0.440 6.443 5802 Planarity : 0.004 0.070 6502 Dihedral : 8.261 168.039 5600 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.32 % Allowed : 15.92 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.13), residues: 4680 helix: 1.85 (0.10), residues: 2656 sheet: -0.67 (0.28), residues: 330 loop : -0.46 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.026 0.001 PHE L 341 TYR 0.025 0.001 TYR M 435 ARG 0.008 0.000 ARG G 288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 349 time to evaluate : 4.322 Fit side-chains REVERT: F 237 GLN cc_start: 0.9010 (mt0) cc_final: 0.8487 (mp10) REVERT: F 391 LEU cc_start: 0.8178 (mp) cc_final: 0.7957 (mp) REVERT: E 60 ASP cc_start: 0.8888 (p0) cc_final: 0.8592 (p0) REVERT: G 312 LYS cc_start: 0.8537 (pttp) cc_final: 0.7953 (tptp) REVERT: G 792 GLU cc_start: 0.8348 (pp20) cc_final: 0.7827 (pp20) REVERT: G 793 ASN cc_start: 0.8107 (m-40) cc_final: 0.7314 (m-40) REVERT: G 906 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8117 (mmtt) REVERT: C 204 TRP cc_start: 0.7823 (m100) cc_final: 0.7231 (m100) REVERT: C 546 TYR cc_start: 0.9333 (m-80) cc_final: 0.9072 (m-80) REVERT: H 36 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8624 (tp30) REVERT: H 165 MET cc_start: 0.8481 (mmp) cc_final: 0.8206 (mmm) REVERT: A 124 ASP cc_start: 0.8368 (m-30) cc_final: 0.7570 (p0) REVERT: L 328 TRP cc_start: 0.8375 (OUTLIER) cc_final: 0.6874 (m100) REVERT: M 466 PHE cc_start: 0.8426 (m-10) cc_final: 0.7486 (t80) REVERT: N 183 ASP cc_start: 0.9097 (t0) cc_final: 0.8685 (t0) outliers start: 51 outliers final: 47 residues processed: 387 average time/residue: 0.4829 time to fit residues: 311.6477 Evaluate side-chains 394 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 345 time to evaluate : 4.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 330 ASP Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 409 GLN Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain G residue 159 CYS Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 732 ILE Chi-restraints excluded: chain G residue 785 VAL Chi-restraints excluded: chain G residue 799 THR Chi-restraints excluded: chain G residue 852 LEU Chi-restraints excluded: chain G residue 854 VAL Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain I residue 66 CYS Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 64 MET Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 138 ASN Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain L residue 179 VAL Chi-restraints excluded: chain L residue 291 LEU Chi-restraints excluded: chain L residue 328 TRP Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 483 THR Chi-restraints excluded: chain L residue 516 ARG Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 146 MET Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 246 ASP Chi-restraints excluded: chain M residue 374 MET Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain J residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 294 optimal weight: 8.9990 chunk 394 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 341 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 102 optimal weight: 4.9990 chunk 371 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 381 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 238 ASN F 386 GLN H 138 ASN H 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.074627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.058239 restraints weight = 87633.810| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.71 r_work: 0.2853 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.251 38318 Z= 0.775 Angle : 2.199 50.880 51983 Z= 1.438 Chirality : 0.441 6.474 5802 Planarity : 0.004 0.069 6502 Dihedral : 8.407 169.514 5600 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.56 % Allowed : 15.82 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.12), residues: 4680 helix: 1.73 (0.10), residues: 2666 sheet: -0.69 (0.28), residues: 318 loop : -0.52 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 143 HIS 0.009 0.001 HIS G 178 PHE 0.023 0.001 PHE L 341 TYR 0.021 0.002 TYR L 428 ARG 0.008 0.000 ARG G 664 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8422.69 seconds wall clock time: 155 minutes 23.40 seconds (9323.40 seconds total)