Starting phenix.real_space_refine on Sun Feb 18 12:12:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwi_34313/02_2024/8gwi_34313_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwi_34313/02_2024/8gwi_34313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwi_34313/02_2024/8gwi_34313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwi_34313/02_2024/8gwi_34313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwi_34313/02_2024/8gwi_34313_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwi_34313/02_2024/8gwi_34313_updated.pdb" } resolution = 3.18 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= -0.000 sd= 0.048 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: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 55 5.49 5 S 158 5.16 5 C 13735 2.51 5 N 3694 2.21 5 O 4305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A GLU 811": "OE1" <-> "OE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "A TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D ASP 143": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "F ASP 450": "OD1" <-> "OD2" Residue "F PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 583": "OD1" <-> "OD2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E ASP 160": "OD1" <-> "OD2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 344": "OD1" <-> "OD2" Residue "E PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 542": "OD1" <-> "OD2" Residue "E TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21955 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7492 Classifications: {'peptide': 931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "D" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1422 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 301 75.578 55.650 121.844 1.00 86.97 S ATOM 2506 SG CYS A 306 75.567 57.180 125.354 1.00 84.94 S ATOM 2538 SG CYS A 310 76.856 53.605 124.773 1.00 84.77 S ATOM 3946 SG CYS A 487 78.264 69.779 106.107 1.00 95.87 S ATOM 5199 SG CYS A 645 77.470 71.834 109.252 1.00 97.77 S ATOM 5205 SG CYS A 646 76.146 68.218 108.904 1.00 89.00 S ATOM 12129 SG CYS F 16 102.478 65.216 50.524 1.00183.45 S ATOM 12144 SG CYS F 19 103.212 62.542 47.852 1.00198.14 S ATOM 12047 SG CYS F 5 114.925 66.378 50.337 1.00183.01 S ATOM 12068 SG CYS F 8 115.808 69.235 47.969 1.00185.13 S ATOM 12206 SG CYS F 26 114.614 70.148 51.170 1.00172.26 S ATOM 12223 SG CYS F 29 112.090 68.304 48.775 1.00175.19 S ATOM 12388 SG CYS F 50 93.154 76.836 65.675 1.00158.72 S ATOM 12418 SG CYS F 55 89.756 76.042 64.216 1.00164.97 S ATOM 12551 SG CYS F 72 91.926 78.390 62.448 1.00168.17 S ATOM 16642 SG CYS E 16 61.349 74.627 65.591 1.00165.58 S ATOM 16657 SG CYS E 19 58.755 72.126 64.275 1.00179.24 S ATOM 16560 SG CYS E 5 70.232 70.535 57.925 1.00188.71 S ATOM 16581 SG CYS E 8 70.961 72.499 54.838 1.00197.10 S ATOM 16719 SG CYS E 26 72.392 73.907 58.159 1.00186.39 S ATOM 16736 SG CYS E 29 68.780 74.086 57.029 1.00167.57 S ATOM 16901 SG CYS E 50 66.240 87.403 79.620 1.00176.08 S ATOM 16931 SG CYS E 55 63.011 88.887 81.055 1.00192.48 S ATOM 17064 SG CYS E 72 65.078 90.922 78.545 1.00187.74 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.42 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.58 residue: pdb=" N AMET E 474 " occ=0.11 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.89 Time building chain proxies: 15.46, per 1000 atoms: 0.70 Number of scatterers: 21955 At special positions: 0 Unit cell: (154.98, 136.94, 186.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 158 16.00 P 55 15.00 O 4305 8.00 N 3694 7.00 C 13735 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: 8.81 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " Number of angles added : 27 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5094 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 20 sheets defined 34.7% alpha, 7.9% beta 21 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 10.09 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.911A pdb=" N PHE A 7 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 8 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 11 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.815A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 177 removed outlier: 3.612A pdb=" N LEU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 177 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 199 Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.325A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.760A pdb=" N LEU A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.645A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.597A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 458 removed outlier: 4.182A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.154A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.610A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 581 removed outlier: 4.033A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 628 through 641 removed outlier: 5.086A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 852 through 854 No H-bonds generated for 'chain 'A' and resid 852 through 854' Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'A' and resid 867 through 871 removed outlier: 3.581A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 901 removed outlier: 3.921A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 916 Processing helix chain 'A' and resid 919 through 925 removed outlier: 3.608A pdb=" N ALA A 923 " --> pdb=" O GLU A 919 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 919 through 925' Processing helix chain 'B' and resid 10 through 27 removed outlier: 4.743A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 97 removed outlier: 4.034A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.763A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.955A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.619A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 176 through 179 Processing helix chain 'C' and resid 4 through 20 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 47 through 60 removed outlier: 3.681A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 32 through 81 removed outlier: 4.449A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'F' and resid 27 through 35 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 117 through 124 Processing helix chain 'F' and resid 128 through 146 Processing helix chain 'F' and resid 266 through 274 Processing helix chain 'F' and resid 291 through 298 Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.684A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 329 No H-bonds generated for 'chain 'F' and resid 327 through 329' Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 426 through 432 removed outlier: 3.999A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 455 removed outlier: 4.410A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 491 through 500 Processing helix chain 'F' and resid 504 through 506 No H-bonds generated for 'chain 'F' and resid 504 through 506' Processing helix chain 'F' and resid 517 through 524 removed outlier: 3.990A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 565 No H-bonds generated for 'chain 'F' and resid 562 through 565' Processing helix chain 'E' and resid 27 through 35 Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'E' and resid 117 through 123 Processing helix chain 'E' and resid 128 through 147 Processing helix chain 'E' and resid 265 through 272 Processing helix chain 'E' and resid 291 through 298 removed outlier: 3.748A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 324 removed outlier: 4.509A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ALA E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU E 322 " --> pdb=" O CYS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 424 through 431 removed outlier: 3.864A pdb=" N LYS E 430 " --> pdb=" O CYS E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 455 Processing helix chain 'E' and resid 490 through 493 No H-bonds generated for 'chain 'E' and resid 490 through 493' Processing helix chain 'E' and resid 495 through 499 Processing helix chain 'E' and resid 506 through 508 No H-bonds generated for 'chain 'E' and resid 506 through 508' Processing helix chain 'E' and resid 516 through 525 Processing helix chain 'E' and resid 561 through 566 removed outlier: 4.513A pdb=" N THR E 566 " --> pdb=" O ASN E 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 7.012A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.531A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 330 through 335 removed outlier: 3.551A pdb=" N ILE A 333 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= F, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.800A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= H, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= I, first strand: chain 'B' and resid 127 through 132 removed outlier: 5.943A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.679A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 152 through 154 Processing sheet with id= L, first strand: chain 'F' and resid 370 through 373 removed outlier: 6.351A pdb=" N HIS F 395 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE F 373 " --> pdb=" O HIS F 395 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL F 397 " --> pdb=" O PHE F 373 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= N, first strand: chain 'E' and resid 152 through 154 removed outlier: 3.672A pdb=" N PHE E 225 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 395 through 398 removed outlier: 3.530A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 544 through 546 removed outlier: 3.552A pdb=" N LEU E 573 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 182 through 187 removed outlier: 4.126A pdb=" N GLY E 184 " --> pdb=" O GLY E 196 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 29 through 31 Processing sheet with id= S, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.737A pdb=" N ALA G 54 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE G 56 " --> pdb=" O ILE G 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE G 65 " --> pdb=" O PHE G 56 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 73 through 76 removed outlier: 3.676A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 6.98 Time building geometry restraints manager: 9.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.45 - 0.72: 1 0.72 - 1.00: 0 1.00 - 1.27: 3471 1.27 - 1.54: 18641 1.54 - 1.82: 414 Warning: very small bond lengths. Bond restraints: 22527 Sorted by residual: bond pdb=" CG PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.503 0.448 1.055 3.40e-02 8.65e+02 9.63e+02 bond pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.473 1.632 -0.159 1.40e-02 5.10e+03 1.29e+02 bond pdb=" CG PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.503 1.264 0.239 3.40e-02 8.65e+02 4.94e+01 bond pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.473 1.569 -0.096 1.40e-02 5.10e+03 4.66e+01 bond pdb=" N ALA G 15 " pdb=" CA ALA G 15 " ideal model delta sigma weight residual 1.458 1.541 -0.083 1.27e-02 6.20e+03 4.32e+01 ... (remaining 22522 not shown) Histogram of bond angle deviations from ideal: 68.93 - 82.89: 2 82.89 - 96.85: 6 96.85 - 110.81: 8020 110.81 - 124.77: 22351 124.77 - 138.73: 500 Bond angle restraints: 30879 Sorted by residual: angle pdb=" N PRO F 491 " pdb=" CD PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 103.20 68.93 34.27 1.50e+00 4.44e-01 5.22e+02 angle pdb=" CA PRO E 364 " pdb=" N PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 112.00 89.87 22.13 1.40e+00 5.10e-01 2.50e+02 angle pdb=" CA PRO F 491 " pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 112.00 90.72 21.28 1.40e+00 5.10e-01 2.31e+02 angle pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" C TYR G 32 " ideal model delta sigma weight residual 110.80 138.73 -27.93 2.13e+00 2.20e-01 1.72e+02 angle pdb=" CA PRO F 491 " pdb=" CB PRO F 491 " pdb=" CG PRO F 491 " ideal model delta sigma weight residual 104.50 80.58 23.92 1.90e+00 2.77e-01 1.58e+02 ... (remaining 30874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.29: 12788 33.29 - 66.58: 741 66.58 - 99.87: 35 99.87 - 133.16: 0 133.16 - 166.45: 2 Dihedral angle restraints: 13566 sinusoidal: 5672 harmonic: 7894 Sorted by residual: dihedral pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual 122.80 159.42 -36.62 0 2.50e+00 1.60e-01 2.15e+02 dihedral pdb=" C CYS G 14 " pdb=" N CYS G 14 " pdb=" CA CYS G 14 " pdb=" CB CYS G 14 " ideal model delta harmonic sigma weight residual -122.60 -158.49 35.89 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CA TYR G 32 " pdb=" CB TYR G 32 " ideal model delta harmonic sigma weight residual 122.80 147.41 -24.61 0 2.50e+00 1.60e-01 9.69e+01 ... (remaining 13563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3575 0.321 - 0.642: 2 0.642 - 0.963: 0 0.963 - 1.284: 2 1.284 - 1.605: 2 Chirality restraints: 3581 Sorted by residual: chirality pdb=" CA CYS G 14 " pdb=" N CYS G 14 " pdb=" C CYS G 14 " pdb=" CB CYS G 14 " both_signs ideal model delta sigma weight residual False 2.51 0.91 1.61 2.00e-01 2.50e+01 6.44e+01 chirality pdb=" CA TYR G 32 " pdb=" N TYR G 32 " pdb=" C TYR G 32 " pdb=" CB TYR G 32 " both_signs ideal model delta sigma weight residual False 2.51 1.18 1.33 2.00e-01 2.50e+01 4.42e+01 chirality pdb=" CA GLN G 11 " pdb=" N GLN G 11 " pdb=" C GLN G 11 " pdb=" CB GLN G 11 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 3578 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 72 " -0.030 2.00e-02 2.50e+03 5.97e-02 3.57e+01 pdb=" C VAL A 72 " 0.103 2.00e-02 2.50e+03 pdb=" O VAL A 72 " -0.039 2.00e-02 2.50e+03 pdb=" N LYS A 73 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 363 " 0.106 5.00e-02 4.00e+02 1.40e-01 3.15e+01 pdb=" N PRO E 364 " -0.241 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 490 " 0.092 5.00e-02 4.00e+02 1.20e-01 2.31e+01 pdb=" N PRO F 491 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " 0.062 5.00e-02 4.00e+02 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 310 2.62 - 3.19: 18733 3.19 - 3.76: 34253 3.76 - 4.33: 46531 4.33 - 4.90: 74441 Nonbonded interactions: 174268 Sorted by model distance: nonbonded pdb=" O SER D 173 " pdb=" OG SER D 177 " model vdw 2.045 2.440 nonbonded pdb=" OD1 ASN F 381 " pdb=" OG SER F 424 " model vdw 2.140 2.440 nonbonded pdb=" O PRO E 77 " pdb=" OG SER E 80 " model vdw 2.141 2.440 nonbonded pdb=" N2 G I 12 " pdb=" O2 C J 48 " model vdw 2.148 2.496 nonbonded pdb=" O CYS E 471 " pdb=" OG1 THR E 588 " model vdw 2.171 2.440 ... (remaining 174263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 192)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 192)) } ncs_group { reference = (chain 'E' and (resid 1 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 1 through 473 or resid 475 through 593 or resid 701 throug \ h 703)) } 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=0.11 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: 4.840 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: 0.020 Extract box with map and model: 19.760 Check model and map are aligned: 0.370 Set scattering table: 0.200 Process input model: 72.760 Find NCS groups from input model: 0.890 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: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5008 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 : 0.009 1.055 22527 Z= 0.479 Angle : 0.940 34.266 30879 Z= 0.545 Chirality : 0.063 1.605 3581 Planarity : 0.006 0.140 3748 Dihedral : 18.826 166.450 8472 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.43 % Favored : 91.19 % Rotamer: Outliers : 5.14 % Allowed : 33.58 % Favored : 61.28 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2650 helix: 0.34 (0.18), residues: 947 sheet: -1.60 (0.35), residues: 218 loop : -2.47 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 PHE 0.017 0.001 PHE F 437 TYR 0.022 0.001 TYR F 299 ARG 0.006 0.001 ARG F 303 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 476 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.5122 (tt0) cc_final: 0.4615 (tm-30) REVERT: A 73 LYS cc_start: 0.5142 (OUTLIER) cc_final: 0.4814 (pttp) REVERT: A 76 THR cc_start: 0.2705 (OUTLIER) cc_final: 0.1344 (m) REVERT: A 248 THR cc_start: 0.5941 (p) cc_final: 0.5736 (t) REVERT: A 548 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7936 (tt) REVERT: A 731 LEU cc_start: 0.4636 (OUTLIER) cc_final: 0.4251 (mt) REVERT: A 750 ARG cc_start: 0.6290 (mtp85) cc_final: 0.5789 (ttp-110) REVERT: A 857 GLU cc_start: 0.6351 (pm20) cc_final: 0.5877 (tp30) REVERT: B 58 LYS cc_start: 0.7337 (tppp) cc_final: 0.7127 (tppt) REVERT: B 148 THR cc_start: 0.5665 (p) cc_final: 0.5425 (t) REVERT: D 57 ARG cc_start: 0.5446 (mmt-90) cc_final: 0.5208 (ttp80) REVERT: D 60 GLU cc_start: 0.5644 (tm-30) cc_final: 0.5201 (mm-30) REVERT: D 182 TRP cc_start: 0.5387 (m100) cc_final: 0.4428 (m100) REVERT: F 14 LEU cc_start: 0.5261 (mt) cc_final: 0.4069 (tp) REVERT: F 133 PHE cc_start: 0.3553 (t80) cc_final: 0.3321 (t80) REVERT: F 194 GLN cc_start: 0.3459 (tm-30) cc_final: 0.3070 (tp-100) REVERT: F 396 TYR cc_start: 0.7297 (m-80) cc_final: 0.6932 (m-10) REVERT: F 419 PRO cc_start: 0.6605 (Cg_exo) cc_final: 0.6270 (Cg_endo) REVERT: F 430 LYS cc_start: 0.0919 (mtmm) cc_final: 0.0426 (mmtp) REVERT: F 576 MET cc_start: 0.2990 (mmt) cc_final: 0.2121 (mtp) REVERT: E 48 TYR cc_start: 0.5937 (m-10) cc_final: 0.5510 (m-10) REVERT: E 64 TYR cc_start: 0.6720 (m-80) cc_final: 0.6482 (m-80) REVERT: E 156 GLU cc_start: 0.2354 (pp20) cc_final: 0.1886 (mm-30) REVERT: E 175 PRO cc_start: 0.3467 (Cg_exo) cc_final: 0.2995 (Cg_endo) REVERT: E 180 TYR cc_start: 0.3908 (m-80) cc_final: 0.3699 (m-80) REVERT: E 183 THR cc_start: 0.6263 (OUTLIER) cc_final: 0.5962 (p) REVERT: E 263 SER cc_start: 0.5471 (m) cc_final: 0.5080 (p) REVERT: E 436 MET cc_start: 0.2753 (ttm) cc_final: 0.2447 (ttt) REVERT: E 460 LYS cc_start: 0.0426 (pttp) cc_final: 0.0054 (pttm) REVERT: E 572 ILE cc_start: 0.2184 (mp) cc_final: 0.1960 (mp) REVERT: E 579 ARG cc_start: 0.2913 (mmp80) cc_final: 0.2138 (mmm160) REVERT: G 33 ASN cc_start: 0.1922 (OUTLIER) cc_final: 0.1186 (t0) REVERT: G 36 LYS cc_start: 0.5719 (mppt) cc_final: 0.5078 (mppt) outliers start: 116 outliers final: 19 residues processed: 578 average time/residue: 0.3425 time to fit residues: 299.7766 Evaluate side-chains 287 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 262 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 102 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 20.0000 chunk 202 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 209 optimal weight: 0.6980 chunk 80 optimal weight: 0.0870 chunk 127 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 168 ASN A 381 HIS A 752 HIS B 56 GLN B 100 ASN ** D 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 164 HIS F 354 GLN ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 ASN E 51 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN G 27 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6258 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 22527 Z= 0.285 Angle : 0.769 12.471 30879 Z= 0.396 Chirality : 0.045 0.256 3581 Planarity : 0.006 0.062 3748 Dihedral : 12.667 141.239 3769 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.66 % Favored : 91.07 % Rotamer: Outliers : 5.40 % Allowed : 30.47 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.16), residues: 2650 helix: -0.02 (0.17), residues: 970 sheet: -1.30 (0.33), residues: 254 loop : -2.44 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 216 HIS 0.008 0.001 HIS A 75 PHE 0.022 0.002 PHE B 49 TYR 0.025 0.002 TYR G 89 ARG 0.013 0.001 ARG F 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 306 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.6481 (tt0) cc_final: 0.6060 (tm-30) REVERT: A 138 ASN cc_start: 0.5602 (p0) cc_final: 0.5304 (p0) REVERT: A 273 TYR cc_start: 0.7566 (p90) cc_final: 0.7302 (p90) REVERT: A 601 MET cc_start: 0.7883 (ttm) cc_final: 0.7499 (ttm) REVERT: A 666 MET cc_start: 0.7280 (mmt) cc_final: 0.7075 (mmt) REVERT: A 750 ARG cc_start: 0.7515 (mtp85) cc_final: 0.6574 (ttp80) REVERT: A 757 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7538 (mm) REVERT: A 780 LYS cc_start: 0.5781 (OUTLIER) cc_final: 0.5455 (tptp) REVERT: A 865 ASP cc_start: 0.7572 (t0) cc_final: 0.6892 (m-30) REVERT: B 61 LYS cc_start: 0.7305 (tmmt) cc_final: 0.6953 (tppt) REVERT: B 129 MET cc_start: 0.7313 (mtp) cc_final: 0.7111 (mtm) REVERT: B 136 ASN cc_start: 0.7713 (t0) cc_final: 0.7509 (t0) REVERT: B 143 ASP cc_start: 0.5630 (p0) cc_final: 0.4822 (t0) REVERT: D 31 SER cc_start: 0.7275 (p) cc_final: 0.6968 (t) REVERT: D 60 GLU cc_start: 0.5947 (tm-30) cc_final: 0.5452 (mm-30) REVERT: D 62 MET cc_start: 0.4440 (tmm) cc_final: 0.4203 (tmm) REVERT: D 151 SER cc_start: 0.7796 (t) cc_final: 0.7475 (p) REVERT: F 137 THR cc_start: 0.4403 (OUTLIER) cc_final: 0.3954 (t) REVERT: F 192 LYS cc_start: 0.1258 (OUTLIER) cc_final: 0.0886 (ptpt) REVERT: F 233 MET cc_start: 0.6279 (mpp) cc_final: 0.5209 (ppp) REVERT: F 297 LEU cc_start: 0.6092 (pp) cc_final: 0.5838 (tt) REVERT: F 428 LEU cc_start: -0.0770 (OUTLIER) cc_final: -0.1072 (tt) REVERT: F 429 MET cc_start: -0.0814 (tpt) cc_final: -0.1237 (tpt) REVERT: F 430 LYS cc_start: 0.0933 (mtmm) cc_final: 0.0408 (mmtp) REVERT: F 531 GLN cc_start: -0.0492 (OUTLIER) cc_final: -0.0757 (mt0) REVERT: F 554 HIS cc_start: -0.0821 (OUTLIER) cc_final: -0.1645 (m90) REVERT: F 576 MET cc_start: 0.3207 (mmt) cc_final: 0.2219 (mtp) REVERT: E 156 GLU cc_start: 0.2326 (pp20) cc_final: 0.1814 (mm-30) REVERT: E 180 TYR cc_start: 0.3949 (m-80) cc_final: 0.3603 (m-10) REVERT: E 183 THR cc_start: 0.5909 (m) cc_final: 0.5527 (p) REVERT: E 437 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.5910 (p90) REVERT: E 460 LYS cc_start: 0.0542 (pttp) cc_final: 0.0194 (pttm) REVERT: E 480 ILE cc_start: 0.3860 (OUTLIER) cc_final: 0.3205 (tp) REVERT: G 78 ASP cc_start: 0.7242 (t0) cc_final: 0.6990 (m-30) outliers start: 122 outliers final: 41 residues processed: 412 average time/residue: 0.3425 time to fit residues: 217.3442 Evaluate side-chains 272 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 157 GLN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 171 LYS Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 216 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 194 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 600 ASN ** A 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN A 898 HIS C 18 GLN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 88 GLN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 22527 Z= 0.384 Angle : 0.812 11.074 30879 Z= 0.420 Chirality : 0.048 0.275 3581 Planarity : 0.005 0.056 3748 Dihedral : 12.415 115.338 3743 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.89 % Favored : 90.85 % Rotamer: Outliers : 4.70 % Allowed : 30.64 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.15), residues: 2650 helix: -0.28 (0.17), residues: 949 sheet: -1.47 (0.34), residues: 225 loop : -2.50 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 268 HIS 0.015 0.002 HIS A 898 PHE 0.037 0.003 PHE A 77 TYR 0.032 0.003 TYR F 396 ARG 0.010 0.001 ARG E 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 275 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.5933 (OUTLIER) cc_final: 0.5704 (tm-30) REVERT: A 58 GLU cc_start: 0.7602 (tt0) cc_final: 0.7210 (tm-30) REVERT: A 158 ASN cc_start: 0.8618 (m-40) cc_final: 0.8366 (m-40) REVERT: A 183 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7737 (ttp-110) REVERT: A 197 ARG cc_start: 0.7000 (ttp-170) cc_final: 0.6294 (tpt170) REVERT: A 258 ASP cc_start: 0.8664 (t0) cc_final: 0.8395 (t0) REVERT: A 277 GLU cc_start: 0.7339 (mm-30) cc_final: 0.6265 (mp0) REVERT: A 281 LYS cc_start: 0.7732 (tptt) cc_final: 0.6650 (mmpt) REVERT: A 284 ASP cc_start: 0.8302 (t70) cc_final: 0.7882 (m-30) REVERT: A 336 ASP cc_start: 0.6803 (m-30) cc_final: 0.6602 (t0) REVERT: A 408 GLN cc_start: 0.8008 (pt0) cc_final: 0.7720 (tt0) REVERT: A 477 ASP cc_start: 0.7675 (t70) cc_final: 0.7288 (t0) REVERT: A 497 ASN cc_start: 0.7707 (t0) cc_final: 0.7127 (t0) REVERT: A 542 MET cc_start: 0.7816 (mtp) cc_final: 0.7525 (ttm) REVERT: A 593 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8164 (pttt) REVERT: A 726 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7406 (mmp-170) REVERT: A 750 ARG cc_start: 0.8640 (mtp85) cc_final: 0.7679 (mtp-110) REVERT: A 757 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8251 (mm) REVERT: A 768 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7789 (p) REVERT: A 778 SER cc_start: 0.7668 (OUTLIER) cc_final: 0.7450 (m) REVERT: A 845 ASP cc_start: 0.5310 (OUTLIER) cc_final: 0.4972 (m-30) REVERT: A 865 ASP cc_start: 0.7819 (t0) cc_final: 0.7578 (m-30) REVERT: A 882 HIS cc_start: 0.8194 (m-70) cc_final: 0.7981 (m-70) REVERT: B 62 MET cc_start: 0.7644 (tpp) cc_final: 0.7281 (ttp) REVERT: B 73 GLN cc_start: 0.6634 (tp40) cc_final: 0.6053 (tt0) REVERT: B 82 LYS cc_start: 0.7998 (tmmt) cc_final: 0.7793 (tttm) REVERT: B 165 LYS cc_start: 0.7826 (mttt) cc_final: 0.6976 (mmtt) REVERT: C 50 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6647 (mm-30) REVERT: C 51 LYS cc_start: 0.7785 (mttm) cc_final: 0.7438 (mttm) REVERT: D 60 GLU cc_start: 0.6584 (tm-30) cc_final: 0.5998 (mm-30) REVERT: D 78 ASP cc_start: 0.6751 (t70) cc_final: 0.6458 (t70) REVERT: D 82 LYS cc_start: 0.7607 (mttp) cc_final: 0.7260 (mptt) REVERT: F 133 PHE cc_start: 0.6372 (m-80) cc_final: 0.6092 (m-80) REVERT: F 145 PHE cc_start: 0.4523 (m-10) cc_final: 0.3855 (t80) REVERT: F 233 MET cc_start: 0.6489 (mpp) cc_final: 0.5534 (ppp) REVERT: F 343 PHE cc_start: 0.2369 (t80) cc_final: 0.2134 (m-80) REVERT: F 378 MET cc_start: 0.2979 (mpp) cc_final: 0.2503 (mpp) REVERT: F 396 TYR cc_start: 0.7446 (m-80) cc_final: 0.7164 (m-10) REVERT: F 430 LYS cc_start: 0.0936 (mtmm) cc_final: 0.0381 (mmtp) REVERT: F 551 GLU cc_start: 0.3664 (pt0) cc_final: 0.3231 (pt0) REVERT: F 576 MET cc_start: 0.3385 (mmt) cc_final: 0.2359 (mtp) REVERT: E 180 TYR cc_start: 0.3956 (m-80) cc_final: 0.3548 (m-10) REVERT: E 183 THR cc_start: 0.5812 (m) cc_final: 0.5407 (p) REVERT: E 460 LYS cc_start: 0.0527 (pttp) cc_final: 0.0081 (pttm) REVERT: E 480 ILE cc_start: 0.3848 (OUTLIER) cc_final: 0.3197 (tp) REVERT: E 579 ARG cc_start: 0.2743 (mmp80) cc_final: 0.2204 (mmp-170) REVERT: G 86 LYS cc_start: 0.0930 (mptt) cc_final: 0.0482 (mptt) outliers start: 106 outliers final: 53 residues processed: 365 average time/residue: 0.3657 time to fit residues: 207.0863 Evaluate side-chains 277 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 214 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 105 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 5.9990 chunk 182 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 231 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 492 GLN B 158 GLN C 63 GLN D 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 265 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.7583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22527 Z= 0.199 Angle : 0.633 14.934 30879 Z= 0.322 Chirality : 0.042 0.208 3581 Planarity : 0.004 0.057 3748 Dihedral : 12.049 83.605 3743 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.72 % Favored : 92.06 % Rotamer: Outliers : 3.47 % Allowed : 31.47 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.16), residues: 2650 helix: 0.18 (0.17), residues: 947 sheet: -1.27 (0.32), residues: 249 loop : -2.40 (0.15), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 182 HIS 0.006 0.001 HIS C 36 PHE 0.018 0.001 PHE E 357 TYR 0.033 0.001 TYR E 421 ARG 0.006 0.001 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 234 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.6017 (OUTLIER) cc_final: 0.5784 (tm-30) REVERT: A 58 GLU cc_start: 0.7647 (tt0) cc_final: 0.7257 (tm-30) REVERT: A 183 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7494 (ttp-110) REVERT: A 197 ARG cc_start: 0.7178 (ttp-170) cc_final: 0.6484 (tpt170) REVERT: A 221 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.7774 (t0) REVERT: A 258 ASP cc_start: 0.8426 (t0) cc_final: 0.7762 (t0) REVERT: A 277 GLU cc_start: 0.7493 (mm-30) cc_final: 0.6416 (mp0) REVERT: A 281 LYS cc_start: 0.7680 (tptt) cc_final: 0.6709 (mmtm) REVERT: A 284 ASP cc_start: 0.8191 (t70) cc_final: 0.7623 (m-30) REVERT: A 408 GLN cc_start: 0.7905 (pt0) cc_final: 0.7592 (tt0) REVERT: A 477 ASP cc_start: 0.7627 (t70) cc_final: 0.7298 (t0) REVERT: A 497 ASN cc_start: 0.7670 (t0) cc_final: 0.7216 (t0) REVERT: A 542 MET cc_start: 0.7686 (mtp) cc_final: 0.7242 (mtm) REVERT: A 726 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7328 (mmp-170) REVERT: A 757 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8198 (mm) REVERT: A 768 SER cc_start: 0.8140 (OUTLIER) cc_final: 0.7708 (p) REVERT: A 794 MET cc_start: 0.8938 (ttp) cc_final: 0.8672 (ttt) REVERT: A 894 GLU cc_start: 0.8071 (tt0) cc_final: 0.7839 (tt0) REVERT: B 56 GLN cc_start: 0.5200 (OUTLIER) cc_final: 0.4304 (tm130) REVERT: B 73 GLN cc_start: 0.6637 (tp40) cc_final: 0.5999 (tt0) REVERT: B 158 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6597 (tt0) REVERT: B 165 LYS cc_start: 0.7795 (mttt) cc_final: 0.7138 (mmpt) REVERT: C 50 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6641 (mm-30) REVERT: C 51 LYS cc_start: 0.7771 (mttm) cc_final: 0.7554 (mttt) REVERT: C 75 MET cc_start: 0.5250 (tpt) cc_final: 0.5030 (tpt) REVERT: D 78 ASP cc_start: 0.6842 (t70) cc_final: 0.6608 (t70) REVERT: D 82 LYS cc_start: 0.7621 (mttp) cc_final: 0.7103 (mtmt) REVERT: D 165 LYS cc_start: 0.6574 (mtmm) cc_final: 0.6329 (ptpt) REVERT: F 42 VAL cc_start: 0.7079 (t) cc_final: 0.6798 (t) REVERT: F 133 PHE cc_start: 0.6497 (m-80) cc_final: 0.6215 (m-80) REVERT: F 192 LYS cc_start: 0.0697 (OUTLIER) cc_final: 0.0237 (ptpt) REVERT: F 233 MET cc_start: 0.6528 (mpp) cc_final: 0.5565 (ppp) REVERT: F 297 LEU cc_start: 0.5746 (pp) cc_final: 0.5371 (tt) REVERT: F 343 PHE cc_start: 0.2426 (t80) cc_final: 0.2140 (m-80) REVERT: F 429 MET cc_start: -0.1010 (tpt) cc_final: -0.1465 (tpt) REVERT: F 430 LYS cc_start: 0.1921 (mtmm) cc_final: 0.1021 (mmtt) REVERT: F 508 LYS cc_start: 0.3846 (OUTLIER) cc_final: 0.3509 (pttt) REVERT: F 551 GLU cc_start: 0.3527 (pt0) cc_final: 0.3135 (pt0) REVERT: F 554 HIS cc_start: -0.0627 (OUTLIER) cc_final: -0.1473 (m-70) REVERT: F 576 MET cc_start: 0.3290 (mmt) cc_final: 0.2142 (mtp) REVERT: E 180 TYR cc_start: 0.3942 (m-80) cc_final: 0.3549 (m-10) REVERT: E 183 THR cc_start: 0.5766 (m) cc_final: 0.5345 (p) REVERT: E 357 PHE cc_start: 0.5879 (m-80) cc_final: 0.5477 (m-80) REVERT: E 405 LEU cc_start: -0.1026 (OUTLIER) cc_final: -0.1354 (mt) REVERT: E 437 PHE cc_start: 0.6385 (OUTLIER) cc_final: 0.5996 (p90) REVERT: E 460 LYS cc_start: 0.0389 (pttp) cc_final: -0.0172 (pttm) REVERT: E 579 ARG cc_start: 0.2732 (mmp80) cc_final: 0.2163 (mmp-170) outliers start: 78 outliers final: 43 residues processed: 296 average time/residue: 0.3536 time to fit residues: 159.7886 Evaluate side-chains 277 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 220 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLN Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 726 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 19 CYS Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 220 optimal weight: 40.0000 chunk 178 optimal weight: 30.0000 chunk 0 optimal weight: 5.9990 chunk 131 optimal weight: 0.8980 chunk 231 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 600 ASN B 88 GLN B 108 ASN B 109 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.9035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 22527 Z= 0.561 Angle : 0.837 14.610 30879 Z= 0.433 Chirality : 0.052 0.348 3581 Planarity : 0.006 0.045 3748 Dihedral : 12.212 73.691 3742 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.53 % Favored : 90.24 % Rotamer: Outliers : 5.36 % Allowed : 29.68 % Favored : 64.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.15), residues: 2650 helix: -0.37 (0.16), residues: 948 sheet: -1.52 (0.31), residues: 262 loop : -2.57 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 268 HIS 0.015 0.002 HIS C 36 PHE 0.024 0.003 PHE A 102 TYR 0.026 0.003 TYR E 421 ARG 0.016 0.001 ARG F 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 215 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.7372 (OUTLIER) cc_final: 0.6809 (p) REVERT: A 183 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7910 (ttp-110) REVERT: A 221 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8169 (t0) REVERT: A 258 ASP cc_start: 0.8371 (t0) cc_final: 0.7971 (t0) REVERT: A 269 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8293 (p0) REVERT: A 277 GLU cc_start: 0.7891 (mm-30) cc_final: 0.6784 (mp0) REVERT: A 281 LYS cc_start: 0.7893 (tptt) cc_final: 0.7007 (mmtt) REVERT: A 284 ASP cc_start: 0.8181 (t70) cc_final: 0.7868 (m-30) REVERT: A 350 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: A 408 GLN cc_start: 0.8289 (pt0) cc_final: 0.8066 (tt0) REVERT: A 477 ASP cc_start: 0.8292 (t70) cc_final: 0.8007 (t0) REVERT: A 768 SER cc_start: 0.8318 (OUTLIER) cc_final: 0.7865 (p) REVERT: A 796 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7985 (mp0) REVERT: B 56 GLN cc_start: 0.5142 (OUTLIER) cc_final: 0.4258 (tm130) REVERT: B 71 TYR cc_start: 0.7435 (t80) cc_final: 0.7049 (t80) REVERT: C 44 ASP cc_start: 0.8610 (p0) cc_final: 0.8264 (p0) REVERT: C 51 LYS cc_start: 0.8100 (mttm) cc_final: 0.7822 (mttm) REVERT: C 75 MET cc_start: 0.5232 (tpt) cc_final: 0.4998 (tpt) REVERT: D 65 GLN cc_start: 0.6846 (tm-30) cc_final: 0.6080 (mm110) REVERT: D 75 ARG cc_start: 0.7247 (tpp-160) cc_final: 0.6997 (tpt90) REVERT: D 77 GLU cc_start: 0.8123 (tp30) cc_final: 0.7439 (mt-10) REVERT: D 82 LYS cc_start: 0.8054 (mttp) cc_final: 0.7530 (mtpt) REVERT: D 165 LYS cc_start: 0.6764 (mtmm) cc_final: 0.6544 (ptpt) REVERT: D 182 TRP cc_start: 0.7144 (m100) cc_final: 0.6234 (m100) REVERT: F 233 MET cc_start: 0.6803 (mpp) cc_final: 0.6075 (pmm) REVERT: F 343 PHE cc_start: 0.2540 (t80) cc_final: 0.2231 (m-80) REVERT: F 430 LYS cc_start: 0.1654 (mtmm) cc_final: 0.0942 (ttmt) REVERT: F 508 LYS cc_start: 0.3623 (OUTLIER) cc_final: 0.3347 (pttt) REVERT: F 551 GLU cc_start: 0.3803 (pt0) cc_final: 0.3516 (pt0) REVERT: F 554 HIS cc_start: -0.0262 (OUTLIER) cc_final: -0.1035 (m90) REVERT: F 576 MET cc_start: 0.3381 (mmt) cc_final: 0.2443 (mtp) REVERT: E 180 TYR cc_start: 0.3837 (m-80) cc_final: 0.3448 (m-10) REVERT: E 183 THR cc_start: 0.5891 (m) cc_final: 0.5477 (p) REVERT: E 290 HIS cc_start: 0.3294 (m-70) cc_final: 0.3039 (m170) REVERT: E 437 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.6108 (p90) REVERT: E 485 SER cc_start: 0.0942 (OUTLIER) cc_final: 0.0449 (t) REVERT: E 579 ARG cc_start: 0.3592 (mmp80) cc_final: 0.2749 (mmp-170) outliers start: 121 outliers final: 62 residues processed: 322 average time/residue: 0.3469 time to fit residues: 172.7176 Evaluate side-chains 267 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 194 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 41 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.7980 chunk 232 optimal weight: 30.0000 chunk 51 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 258 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 168 ASN B 109 ASN C 19 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.9165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22527 Z= 0.197 Angle : 0.613 14.537 30879 Z= 0.315 Chirality : 0.042 0.217 3581 Planarity : 0.004 0.045 3748 Dihedral : 11.817 73.702 3741 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.60 % Favored : 92.17 % Rotamer: Outliers : 3.34 % Allowed : 31.52 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.16), residues: 2650 helix: 0.12 (0.17), residues: 957 sheet: -1.29 (0.33), residues: 252 loop : -2.33 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.036 0.001 PHE A 77 TYR 0.021 0.001 TYR F 31 ARG 0.004 0.000 ARG E 497 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 209 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 THR cc_start: 0.7506 (m) cc_final: 0.7275 (p) REVERT: A 183 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6806 (ttp-110) REVERT: A 258 ASP cc_start: 0.8216 (t0) cc_final: 0.7791 (t0) REVERT: A 281 LYS cc_start: 0.7839 (tptt) cc_final: 0.7019 (mmtt) REVERT: A 284 ASP cc_start: 0.8193 (t70) cc_final: 0.7768 (m-30) REVERT: A 408 GLN cc_start: 0.8043 (pt0) cc_final: 0.7837 (tt0) REVERT: A 497 ASN cc_start: 0.8031 (t0) cc_final: 0.7700 (t0) REVERT: A 499 ASP cc_start: 0.7830 (p0) cc_final: 0.7569 (p0) REVERT: A 796 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7788 (mp0) REVERT: B 56 GLN cc_start: 0.4956 (OUTLIER) cc_final: 0.4125 (tm130) REVERT: B 67 MET cc_start: 0.7035 (tpt) cc_final: 0.6661 (tpt) REVERT: C 44 ASP cc_start: 0.8505 (p0) cc_final: 0.8199 (p0) REVERT: C 50 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6868 (mm-30) REVERT: C 51 LYS cc_start: 0.8005 (mttm) cc_final: 0.7494 (mttt) REVERT: C 75 MET cc_start: 0.5447 (tpt) cc_final: 0.5141 (tpt) REVERT: D 65 GLN cc_start: 0.6958 (tm-30) cc_final: 0.6332 (mm110) REVERT: D 75 ARG cc_start: 0.7155 (tpp-160) cc_final: 0.6903 (tpt90) REVERT: D 77 GLU cc_start: 0.7964 (tp30) cc_final: 0.7242 (mt-10) REVERT: D 78 ASP cc_start: 0.7259 (t70) cc_final: 0.6931 (t70) REVERT: D 82 LYS cc_start: 0.7928 (mttp) cc_final: 0.7400 (mtpt) REVERT: D 101 ASP cc_start: 0.7902 (p0) cc_final: 0.7352 (t0) REVERT: D 165 LYS cc_start: 0.6777 (mtmm) cc_final: 0.6565 (ptpt) REVERT: D 168 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7384 (mm-40) REVERT: D 182 TRP cc_start: 0.7130 (m100) cc_final: 0.6143 (m100) REVERT: D 185 ILE cc_start: 0.7348 (mt) cc_final: 0.7083 (mm) REVERT: F 233 MET cc_start: 0.6661 (mpp) cc_final: 0.5955 (ppp) REVERT: F 297 LEU cc_start: 0.5737 (pp) cc_final: 0.5362 (tt) REVERT: F 343 PHE cc_start: 0.2509 (t80) cc_final: 0.2213 (m-80) REVERT: F 430 LYS cc_start: 0.1941 (mtmm) cc_final: 0.1254 (ttmt) REVERT: F 508 LYS cc_start: 0.3630 (OUTLIER) cc_final: 0.3380 (pttt) REVERT: F 551 GLU cc_start: 0.3653 (pt0) cc_final: 0.3303 (pt0) REVERT: F 554 HIS cc_start: -0.0581 (OUTLIER) cc_final: -0.1331 (m-70) REVERT: F 576 MET cc_start: 0.3314 (mmt) cc_final: 0.2200 (mtp) REVERT: E 180 TYR cc_start: 0.3813 (m-80) cc_final: 0.3418 (m-10) REVERT: E 183 THR cc_start: 0.5737 (m) cc_final: 0.5291 (p) REVERT: E 290 HIS cc_start: 0.3242 (m-70) cc_final: 0.2983 (m170) REVERT: E 437 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.6044 (p90) REVERT: E 485 SER cc_start: 0.0808 (OUTLIER) cc_final: 0.0339 (t) REVERT: E 579 ARG cc_start: 0.3495 (mmp80) cc_final: 0.2680 (mmp-170) outliers start: 75 outliers final: 45 residues processed: 275 average time/residue: 0.3625 time to fit residues: 152.0645 Evaluate side-chains 245 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 168 GLN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 533 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 147 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 217 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 161 optimal weight: 40.0000 chunk 156 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.9716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 22527 Z= 0.440 Angle : 0.742 13.657 30879 Z= 0.381 Chirality : 0.047 0.290 3581 Planarity : 0.005 0.044 3748 Dihedral : 11.994 73.716 3741 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.49 % Favored : 90.28 % Rotamer: Outliers : 4.21 % Allowed : 30.60 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.16), residues: 2650 helix: -0.07 (0.17), residues: 947 sheet: -1.35 (0.33), residues: 247 loop : -2.43 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 916 HIS 0.014 0.001 HIS C 36 PHE 0.021 0.002 PHE F 472 TYR 0.022 0.002 TYR F 31 ARG 0.005 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 200 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.6817 (p) REVERT: A 76 THR cc_start: 0.7997 (m) cc_final: 0.7753 (p) REVERT: A 183 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7602 (ttp-110) REVERT: A 221 ASP cc_start: 0.8372 (t0) cc_final: 0.7720 (p0) REVERT: A 258 ASP cc_start: 0.8326 (t0) cc_final: 0.7927 (t0) REVERT: A 277 GLU cc_start: 0.7875 (mm-30) cc_final: 0.6794 (mp0) REVERT: A 281 LYS cc_start: 0.7878 (tptt) cc_final: 0.6996 (mmtt) REVERT: A 284 ASP cc_start: 0.8263 (t70) cc_final: 0.7855 (m-30) REVERT: A 350 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6842 (mt-10) REVERT: A 408 GLN cc_start: 0.8204 (pt0) cc_final: 0.8002 (tt0) REVERT: A 499 ASP cc_start: 0.7791 (p0) cc_final: 0.7588 (p0) REVERT: A 545 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8497 (mtmt) REVERT: A 555 ARG cc_start: 0.7590 (mmm-85) cc_final: 0.7259 (mmm160) REVERT: A 796 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7882 (mp0) REVERT: A 889 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7105 (ttm170) REVERT: B 56 GLN cc_start: 0.4992 (OUTLIER) cc_final: 0.4195 (tm130) REVERT: B 67 MET cc_start: 0.7042 (tpt) cc_final: 0.6716 (tpt) REVERT: B 71 TYR cc_start: 0.7340 (t80) cc_final: 0.7055 (t80) REVERT: C 44 ASP cc_start: 0.8594 (p0) cc_final: 0.8226 (p0) REVERT: C 51 LYS cc_start: 0.8053 (mttm) cc_final: 0.7765 (mttm) REVERT: C 75 MET cc_start: 0.5250 (tpt) cc_final: 0.4952 (tpt) REVERT: D 65 GLN cc_start: 0.6939 (tm-30) cc_final: 0.6354 (mm110) REVERT: D 77 GLU cc_start: 0.8057 (tp30) cc_final: 0.7419 (mt-10) REVERT: D 82 LYS cc_start: 0.8097 (mttp) cc_final: 0.7532 (mtpt) REVERT: D 101 ASP cc_start: 0.7974 (p0) cc_final: 0.7604 (t0) REVERT: D 185 ILE cc_start: 0.7560 (mt) cc_final: 0.7331 (mm) REVERT: F 233 MET cc_start: 0.6688 (mpp) cc_final: 0.6465 (pmm) REVERT: F 343 PHE cc_start: 0.2525 (t80) cc_final: 0.2217 (m-80) REVERT: F 414 LYS cc_start: 0.4181 (OUTLIER) cc_final: 0.3710 (mttm) REVERT: F 430 LYS cc_start: 0.2059 (mtmm) cc_final: 0.1292 (ttmt) REVERT: F 508 LYS cc_start: 0.3549 (OUTLIER) cc_final: 0.3338 (pttt) REVERT: F 551 GLU cc_start: 0.3720 (pt0) cc_final: 0.3357 (pt0) REVERT: F 554 HIS cc_start: -0.0376 (OUTLIER) cc_final: -0.1134 (m-70) REVERT: F 576 MET cc_start: 0.3331 (mmt) cc_final: 0.2234 (mtp) REVERT: E 180 TYR cc_start: 0.3921 (m-80) cc_final: 0.3434 (m-10) REVERT: E 183 THR cc_start: 0.5827 (m) cc_final: 0.5407 (p) REVERT: E 233 MET cc_start: 0.5132 (mpm) cc_final: 0.4381 (mtt) REVERT: E 290 HIS cc_start: 0.3296 (m-70) cc_final: 0.3011 (m170) REVERT: E 437 PHE cc_start: 0.6377 (OUTLIER) cc_final: 0.6111 (p90) REVERT: E 485 SER cc_start: 0.0899 (OUTLIER) cc_final: 0.0416 (t) REVERT: E 579 ARG cc_start: 0.3841 (mmp80) cc_final: 0.2979 (mmp-170) outliers start: 95 outliers final: 64 residues processed: 289 average time/residue: 0.3489 time to fit residues: 154.7966 Evaluate side-chains 262 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 187 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 59 LYS Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 350 GLU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 88 GLN Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 163 optimal weight: 0.0270 chunk 175 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.9772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 22527 Z= 0.171 Angle : 0.600 13.789 30879 Z= 0.307 Chirality : 0.041 0.204 3581 Planarity : 0.004 0.045 3748 Dihedral : 11.747 73.719 3741 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.60 % Favored : 92.21 % Rotamer: Outliers : 2.85 % Allowed : 32.05 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.16), residues: 2650 helix: 0.33 (0.17), residues: 952 sheet: -1.13 (0.33), residues: 245 loop : -2.21 (0.15), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 182 HIS 0.005 0.001 HIS C 36 PHE 0.018 0.001 PHE F 472 TYR 0.021 0.001 TYR F 31 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 200 time to evaluate : 2.418 Fit side-chains revert: symmetry clash REVERT: A 158 ASN cc_start: 0.8727 (m-40) cc_final: 0.8492 (m-40) REVERT: A 183 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6859 (ttp-110) REVERT: A 221 ASP cc_start: 0.8428 (t0) cc_final: 0.7587 (p0) REVERT: A 258 ASP cc_start: 0.8204 (t0) cc_final: 0.7822 (t0) REVERT: A 281 LYS cc_start: 0.7821 (tptt) cc_final: 0.7007 (mmtt) REVERT: A 284 ASP cc_start: 0.8202 (t70) cc_final: 0.7766 (m-30) REVERT: A 408 GLN cc_start: 0.8130 (pt0) cc_final: 0.7890 (tt0) REVERT: A 497 ASN cc_start: 0.8002 (t0) cc_final: 0.7800 (t0) REVERT: A 545 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8289 (mtmt) REVERT: A 555 ARG cc_start: 0.7580 (mmm-85) cc_final: 0.6668 (mtm-85) REVERT: A 796 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7891 (mp0) REVERT: A 889 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7225 (ttm170) REVERT: B 67 MET cc_start: 0.7070 (tpt) cc_final: 0.6825 (tpt) REVERT: B 139 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8272 (ttmm) REVERT: B 171 GLU cc_start: 0.7238 (pt0) cc_final: 0.6875 (pt0) REVERT: C 44 ASP cc_start: 0.8505 (p0) cc_final: 0.8180 (p0) REVERT: C 51 LYS cc_start: 0.7971 (mttm) cc_final: 0.7656 (mttm) REVERT: D 65 GLN cc_start: 0.6972 (tm-30) cc_final: 0.6413 (mm110) REVERT: D 77 GLU cc_start: 0.8009 (tp30) cc_final: 0.7354 (mt-10) REVERT: D 82 LYS cc_start: 0.8054 (mttp) cc_final: 0.7503 (mtpt) REVERT: D 101 ASP cc_start: 0.7953 (p0) cc_final: 0.7520 (t0) REVERT: D 185 ILE cc_start: 0.7557 (mt) cc_final: 0.7337 (mm) REVERT: F 297 LEU cc_start: 0.5861 (pp) cc_final: 0.4876 (tt) REVERT: F 324 TYR cc_start: 0.3776 (m-10) cc_final: 0.2976 (t80) REVERT: F 343 PHE cc_start: 0.2345 (t80) cc_final: 0.2048 (m-80) REVERT: F 414 LYS cc_start: 0.4543 (OUTLIER) cc_final: 0.4093 (mttm) REVERT: F 430 LYS cc_start: 0.1989 (mtmm) cc_final: 0.1349 (ttmt) REVERT: F 508 LYS cc_start: 0.3573 (OUTLIER) cc_final: 0.3343 (pttt) REVERT: F 551 GLU cc_start: 0.3594 (pt0) cc_final: 0.3273 (pt0) REVERT: F 554 HIS cc_start: -0.0518 (OUTLIER) cc_final: -0.1161 (m-70) REVERT: F 576 MET cc_start: 0.3223 (mmt) cc_final: 0.2132 (mtp) REVERT: E 180 TYR cc_start: 0.3806 (m-80) cc_final: 0.3433 (m-10) REVERT: E 233 MET cc_start: 0.5006 (mpm) cc_final: 0.4305 (mtt) REVERT: E 274 MET cc_start: 0.3826 (mmp) cc_final: 0.3455 (mtp) REVERT: E 290 HIS cc_start: 0.3359 (m-70) cc_final: 0.3089 (m170) REVERT: E 437 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.6116 (p90) REVERT: E 485 SER cc_start: 0.0772 (OUTLIER) cc_final: 0.0294 (t) REVERT: E 579 ARG cc_start: 0.3727 (mmp80) cc_final: 0.2908 (mmp-170) REVERT: G 86 LYS cc_start: 0.1943 (OUTLIER) cc_final: 0.0838 (mptt) outliers start: 64 outliers final: 43 residues processed: 258 average time/residue: 0.3728 time to fit residues: 146.0441 Evaluate side-chains 237 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 185 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 0.9990 chunk 246 optimal weight: 30.0000 chunk 224 optimal weight: 20.0000 chunk 239 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 188 optimal weight: 40.0000 chunk 73 optimal weight: 0.0270 chunk 216 optimal weight: 0.0170 chunk 226 optimal weight: 50.0000 chunk 238 optimal weight: 0.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.9913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22527 Z= 0.216 Angle : 0.609 14.128 30879 Z= 0.311 Chirality : 0.042 0.222 3581 Planarity : 0.004 0.103 3748 Dihedral : 11.690 73.776 3740 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.17 % Favored : 91.68 % Rotamer: Outliers : 3.20 % Allowed : 31.21 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.16), residues: 2650 helix: 0.46 (0.17), residues: 949 sheet: -1.04 (0.33), residues: 238 loop : -2.15 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 182 HIS 0.008 0.001 HIS C 36 PHE 0.026 0.002 PHE F 145 TYR 0.036 0.001 TYR E 421 ARG 0.005 0.000 ARG A 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 189 time to evaluate : 2.294 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7001 (tpp80) cc_final: 0.6779 (tpp80) REVERT: A 20 THR cc_start: 0.7197 (OUTLIER) cc_final: 0.6831 (p) REVERT: A 76 THR cc_start: 0.7747 (m) cc_final: 0.7428 (p) REVERT: A 183 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7084 (ttp-110) REVERT: A 258 ASP cc_start: 0.8208 (t0) cc_final: 0.7834 (t0) REVERT: A 281 LYS cc_start: 0.7817 (tptt) cc_final: 0.6984 (mmtt) REVERT: A 284 ASP cc_start: 0.8244 (t70) cc_final: 0.7825 (m-30) REVERT: A 408 GLN cc_start: 0.8117 (pt0) cc_final: 0.7887 (tt0) REVERT: A 545 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8468 (mtmt) REVERT: A 555 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.7226 (mmm160) REVERT: A 794 MET cc_start: 0.8920 (ttp) cc_final: 0.8619 (ttt) REVERT: A 796 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7923 (mp0) REVERT: A 857 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6098 (tp30) REVERT: A 889 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7224 (ttm170) REVERT: B 56 GLN cc_start: 0.4835 (OUTLIER) cc_final: 0.4097 (tm130) REVERT: B 67 MET cc_start: 0.7088 (tpt) cc_final: 0.6881 (tpt) REVERT: B 139 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8169 (ttmm) REVERT: B 171 GLU cc_start: 0.7211 (pt0) cc_final: 0.6850 (pt0) REVERT: C 44 ASP cc_start: 0.8475 (p0) cc_final: 0.8148 (p0) REVERT: C 51 LYS cc_start: 0.8010 (mttm) cc_final: 0.7665 (mttm) REVERT: D 65 GLN cc_start: 0.6977 (tm-30) cc_final: 0.6474 (mm110) REVERT: D 77 GLU cc_start: 0.8043 (tp30) cc_final: 0.7384 (mt-10) REVERT: D 82 LYS cc_start: 0.8057 (mttp) cc_final: 0.7530 (mtpt) REVERT: D 101 ASP cc_start: 0.7969 (p0) cc_final: 0.7573 (t0) REVERT: F 297 LEU cc_start: 0.5888 (pp) cc_final: 0.4885 (tt) REVERT: F 324 TYR cc_start: 0.3778 (m-10) cc_final: 0.2986 (t80) REVERT: F 343 PHE cc_start: 0.2385 (t80) cc_final: 0.2115 (m-80) REVERT: F 414 LYS cc_start: 0.4500 (OUTLIER) cc_final: 0.4042 (mttm) REVERT: F 430 LYS cc_start: 0.2257 (mtmm) cc_final: 0.1621 (ttmt) REVERT: F 508 LYS cc_start: 0.3454 (OUTLIER) cc_final: 0.3248 (pttt) REVERT: F 551 GLU cc_start: 0.3637 (pt0) cc_final: 0.3330 (pt0) REVERT: F 554 HIS cc_start: -0.0436 (OUTLIER) cc_final: -0.0946 (m-70) REVERT: F 576 MET cc_start: 0.3251 (mmt) cc_final: 0.2109 (mtp) REVERT: E 180 TYR cc_start: 0.3753 (m-80) cc_final: 0.3360 (m-10) REVERT: E 233 MET cc_start: 0.5066 (mpm) cc_final: 0.4388 (mtt) REVERT: E 274 MET cc_start: 0.3861 (mmp) cc_final: 0.3468 (mtp) REVERT: E 290 HIS cc_start: 0.3399 (m-70) cc_final: 0.3124 (m170) REVERT: E 373 PHE cc_start: 0.7549 (t80) cc_final: 0.6586 (t80) REVERT: E 437 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.6171 (p90) REVERT: E 485 SER cc_start: 0.0900 (OUTLIER) cc_final: 0.0379 (t) REVERT: E 576 MET cc_start: 0.2531 (ppp) cc_final: 0.2147 (pmm) REVERT: E 579 ARG cc_start: 0.3704 (mmp80) cc_final: 0.2854 (mmp-170) REVERT: G 52 LYS cc_start: 0.7930 (mppt) cc_final: 0.7649 (mmtt) REVERT: G 86 LYS cc_start: 0.2189 (OUTLIER) cc_final: 0.1012 (mptt) outliers start: 72 outliers final: 54 residues processed: 252 average time/residue: 0.3718 time to fit residues: 142.9383 Evaluate side-chains 247 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 181 time to evaluate : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 756 MET Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 458 ASP Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 421 TYR Chi-restraints excluded: chain E residue 437 PHE Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 120 optimal weight: 0.0570 chunk 176 optimal weight: 3.9990 chunk 266 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 1.0163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22527 Z= 0.265 Angle : 0.637 13.735 30879 Z= 0.325 Chirality : 0.043 0.240 3581 Planarity : 0.005 0.181 3748 Dihedral : 11.693 73.797 3738 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.59 % Favored : 91.30 % Rotamer: Outliers : 3.12 % Allowed : 31.34 % Favored : 65.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.16), residues: 2650 helix: 0.41 (0.17), residues: 949 sheet: -0.93 (0.34), residues: 227 loop : -2.15 (0.15), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 916 HIS 0.010 0.001 HIS C 36 PHE 0.022 0.002 PHE F 145 TYR 0.019 0.002 TYR A 80 ARG 0.018 0.001 ARG D 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5300 Ramachandran restraints generated. 2650 Oldfield, 0 Emsley, 2650 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 193 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7161 (tpp80) cc_final: 0.6945 (tpp80) REVERT: A 20 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6832 (p) REVERT: A 76 THR cc_start: 0.7896 (m) cc_final: 0.7583 (p) REVERT: A 183 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7250 (ttp-110) REVERT: A 221 ASP cc_start: 0.8394 (t0) cc_final: 0.7718 (p0) REVERT: A 258 ASP cc_start: 0.8255 (t0) cc_final: 0.7886 (t0) REVERT: A 281 LYS cc_start: 0.7838 (tptt) cc_final: 0.6974 (mmtt) REVERT: A 284 ASP cc_start: 0.8212 (t70) cc_final: 0.7794 (m-30) REVERT: A 408 GLN cc_start: 0.8122 (pt0) cc_final: 0.7913 (tt0) REVERT: A 545 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8444 (mtmt) REVERT: A 555 ARG cc_start: 0.7580 (mmm-85) cc_final: 0.7213 (mmm160) REVERT: A 794 MET cc_start: 0.8927 (ttp) cc_final: 0.8609 (ttt) REVERT: A 889 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7155 (ttm170) REVERT: B 56 GLN cc_start: 0.4871 (OUTLIER) cc_final: 0.4230 (tm130) REVERT: B 67 MET cc_start: 0.7098 (tpt) cc_final: 0.6889 (tpt) REVERT: B 171 GLU cc_start: 0.7191 (pt0) cc_final: 0.6872 (pt0) REVERT: C 44 ASP cc_start: 0.8504 (p0) cc_final: 0.8147 (p0) REVERT: C 51 LYS cc_start: 0.8051 (mttm) cc_final: 0.7711 (mttm) REVERT: D 65 GLN cc_start: 0.6947 (tm-30) cc_final: 0.6474 (mm110) REVERT: D 77 GLU cc_start: 0.8033 (tp30) cc_final: 0.7396 (mt-10) REVERT: D 82 LYS cc_start: 0.8085 (mttp) cc_final: 0.7550 (mtpt) REVERT: D 94 MET cc_start: 0.8043 (mtp) cc_final: 0.7812 (mtp) REVERT: D 101 ASP cc_start: 0.7967 (p0) cc_final: 0.7657 (t0) REVERT: F 9 ASN cc_start: 0.5213 (t0) cc_final: 0.4966 (m-40) REVERT: F 297 LEU cc_start: 0.5876 (pp) cc_final: 0.4832 (tt) REVERT: F 324 TYR cc_start: 0.3924 (m-10) cc_final: 0.3159 (t80) REVERT: F 343 PHE cc_start: 0.2474 (t80) cc_final: 0.2201 (m-80) REVERT: F 414 LYS cc_start: 0.4478 (OUTLIER) cc_final: 0.3971 (mttm) REVERT: F 430 LYS cc_start: 0.2447 (mtmm) cc_final: 0.1984 (ttmt) REVERT: F 508 LYS cc_start: 0.3570 (OUTLIER) cc_final: 0.3340 (pttt) REVERT: F 551 GLU cc_start: 0.3666 (pt0) cc_final: 0.3262 (pt0) REVERT: F 554 HIS cc_start: -0.0520 (OUTLIER) cc_final: -0.0895 (m90) REVERT: F 576 MET cc_start: 0.3149 (mmt) cc_final: 0.1976 (mtp) REVERT: E 180 TYR cc_start: 0.3943 (m-80) cc_final: 0.3399 (m-10) REVERT: E 233 MET cc_start: 0.5119 (mpm) cc_final: 0.4487 (mtt) REVERT: E 274 MET cc_start: 0.3649 (mmp) cc_final: 0.3182 (mtp) REVERT: E 290 HIS cc_start: 0.3483 (m-70) cc_final: 0.3204 (m170) REVERT: E 373 PHE cc_start: 0.7536 (t80) cc_final: 0.6564 (t80) REVERT: E 396 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7404 (p90) REVERT: E 485 SER cc_start: 0.1128 (OUTLIER) cc_final: 0.0541 (t) REVERT: E 579 ARG cc_start: 0.3675 (mmp80) cc_final: 0.2837 (mmp-170) REVERT: G 52 LYS cc_start: 0.7964 (mppt) cc_final: 0.7707 (mmtt) REVERT: G 86 LYS cc_start: 0.2575 (OUTLIER) cc_final: 0.1333 (mptt) outliers start: 70 outliers final: 54 residues processed: 254 average time/residue: 0.3706 time to fit residues: 145.5755 Evaluate side-chains 251 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 186 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 8 CYS Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 458 ASP Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 508 LYS Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 421 TYR Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 101 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 0.0870 chunk 225 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 195 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 58 optimal weight: 0.0020 chunk 212 optimal weight: 0.2980 chunk 88 optimal weight: 0.5980 chunk 217 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.2766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 600 ASN A 743 ASN ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 ASN E 51 ASN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.207349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.161021 restraints weight = 59214.876| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 3.94 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4072 r_free = 0.4072 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4072 r_free = 0.4072 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 1.0244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 22527 Z= 0.148 Angle : 0.570 14.458 30879 Z= 0.290 Chirality : 0.040 0.172 3581 Planarity : 0.004 0.144 3748 Dihedral : 11.543 73.630 3738 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.13 % Rotamer: Outliers : 2.59 % Allowed : 31.91 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.16), residues: 2650 helix: 0.70 (0.18), residues: 932 sheet: -0.91 (0.34), residues: 224 loop : -2.02 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 182 HIS 0.004 0.001 HIS A 113 PHE 0.025 0.001 PHE F 145 TYR 0.015 0.001 TYR F 31 ARG 0.016 0.000 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5550.38 seconds wall clock time: 101 minutes 46.06 seconds (6106.06 seconds total)