Starting phenix.real_space_refine on Mon Mar 18 20:27:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwe_34310/03_2024/8gwe_34310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwe_34310/03_2024/8gwe_34310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwe_34310/03_2024/8gwe_34310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwe_34310/03_2024/8gwe_34310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwe_34310/03_2024/8gwe_34310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gwe_34310/03_2024/8gwe_34310_updated.pdb" } resolution = 2.66 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= -0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 59 5.49 5 Mg 1 5.21 5 S 158 5.16 5 C 13773 2.51 5 N 3709 2.21 5 O 4332 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 348": "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-5265/modules/chem_data/mon_lib" Total number of atoms: 22040 Number of models: 1 Model: "" Number of chains: 15 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: "H" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'RNA': 4} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 2} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GNP': 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: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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 74.010 55.944 121.374 1.00 86.97 S ATOM 2506 SG CYS A 306 73.924 57.513 124.866 1.00 84.94 S ATOM 2538 SG CYS A 310 75.252 53.943 124.349 1.00 84.77 S ATOM 3946 SG CYS A 487 76.855 69.911 105.523 1.00 95.87 S ATOM 5199 SG CYS A 645 75.990 71.996 108.628 1.00 97.77 S ATOM 5205 SG CYS A 646 74.701 68.365 108.300 1.00 89.00 S ATOM 12129 SG CYS F 16 102.081 64.912 50.430 1.00183.45 S ATOM 12144 SG CYS F 19 102.885 62.214 47.803 1.00198.14 S ATOM 12047 SG CYS F 5 114.520 66.178 50.446 1.00183.01 S ATOM 12068 SG CYS F 8 115.421 69.014 48.061 1.00185.13 S ATOM 12206 SG CYS F 26 114.163 69.955 51.229 1.00172.26 S ATOM 12223 SG CYS F 29 111.697 68.063 48.813 1.00175.19 S ATOM 12388 SG CYS F 50 92.397 76.627 65.278 1.00158.72 S ATOM 12418 SG CYS F 55 89.031 75.788 63.769 1.00164.97 S ATOM 12551 SG CYS F 72 91.212 78.134 62.012 1.00168.17 S ATOM 16642 SG CYS E 16 60.616 74.147 64.663 1.00165.58 S ATOM 16657 SG CYS E 19 58.067 71.611 63.331 1.00179.24 S ATOM 16560 SG CYS E 5 69.667 70.043 57.202 1.00188.71 S ATOM 16581 SG CYS E 8 70.434 71.978 54.105 1.00197.10 S ATOM 16719 SG CYS E 26 71.793 73.436 57.435 1.00186.39 S ATOM 16736 SG CYS E 29 68.202 73.571 56.240 1.00167.57 S ATOM 16901 SG CYS E 50 65.154 87.126 78.624 1.00176.08 S ATOM 16931 SG CYS E 55 61.889 88.599 79.985 1.00192.48 S ATOM 17064 SG CYS E 72 63.981 90.622 77.488 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: 15.28, per 1000 atoms: 0.69 Number of scatterers: 22040 At special positions: 0 Unit cell: (154.56, 137.28, 187.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 158 16.00 P 59 15.00 Mg 1 11.99 O 4332 8.00 N 3709 7.00 C 13773 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: 7.22 Conformation dependent library (CDL) restraints added in 4.4 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 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " 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 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " 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: 9.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.912A pdb=" N PHE A 7 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 8 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.613A pdb=" N LEU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.563A 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: 4.324A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.864A 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: 3.761A 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: 3.569A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.148A 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: 3.596A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 458 removed outlier: 4.183A 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: 5.578A 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: 4.029A 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: 4.130A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 581 removed outlier: 4.032A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.930A 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: 3.923A 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: 3.606A 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: 4.033A 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: 4.154A 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: 4.961A pdb=" N LYS B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.764A 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: 3.680A 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: 4.475A 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: 3.706A pdb=" N ALA D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.107A 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: 5.523A 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: 3.998A pdb=" N LYS F 430 " --> pdb=" O CYS F 426 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR F 431 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 455 removed outlier: 4.411A 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: 3.991A 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: 4.508A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 3.947A 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: 3.863A 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: 4.515A 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: 7.331A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.492A 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: 6.532A 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: 3.552A 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: 8.072A 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: 9.171A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.693A 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: 3.680A 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: 5.993A 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: 6.352A 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: 6.274A 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: 4.127A pdb=" N GLY E 184 " --> pdb=" O GLY E 196 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 5.075A 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: 3.738A 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: 3.867A 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: 6.94 Time building geometry restraints manager: 7.88 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: 3475 1.27 - 1.54: 18728 1.54 - 1.82: 416 Warning: very small bond lengths. Bond restraints: 22620 Sorted by residual: bond pdb=" CG PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.503 0.446 1.057 3.40e-02 8.65e+02 9.66e+02 bond pdb=" N PRO F 491 " pdb=" CD PRO F 491 " ideal model delta sigma weight residual 1.473 1.631 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" CA ASN G 2 " pdb=" C ASN G 2 " ideal model delta sigma weight residual 1.526 1.437 0.089 1.20e-02 6.94e+03 5.50e+01 bond pdb=" CG PRO E 364 " pdb=" CD PRO E 364 " ideal model delta sigma weight residual 1.503 1.265 0.238 3.40e-02 8.65e+02 4.90e+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 4.73e+01 ... (remaining 22615 not shown) Histogram of bond angle deviations from ideal: 69.18 - 83.09: 2 83.09 - 96.99: 7 96.99 - 110.90: 8437 110.90 - 124.81: 22064 124.81 - 138.72: 511 Bond angle restraints: 31021 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 69.18 34.02 1.50e+00 4.44e-01 5.14e+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 89.92 22.08 1.40e+00 5.10e-01 2.49e+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 90.70 21.30 1.40e+00 5.10e-01 2.32e+02 angle pdb=" N TYR G 32 " pdb=" CA TYR G 32 " pdb=" C TYR G 32 " ideal model delta sigma weight residual 110.80 138.72 -27.92 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 80.62 23.88 1.90e+00 2.77e-01 1.58e+02 ... (remaining 31016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.39: 11629 19.39 - 38.79: 1456 38.79 - 58.18: 451 58.18 - 77.57: 86 77.57 - 96.97: 15 Dihedral angle restraints: 13637 sinusoidal: 5743 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 -158.50 35.90 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 122.80 147.55 -24.75 0 2.50e+00 1.60e-01 9.80e+01 ... (remaining 13634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.321: 3593 0.321 - 0.642: 4 0.642 - 0.963: 0 0.963 - 1.283: 2 1.283 - 1.604: 2 Chirality restraints: 3601 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 1.60 2.00e-01 2.50e+01 6.43e+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 4.45e+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 2.61e+01 ... (remaining 3598 not shown) Planarity restraints: 3752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 1 " -0.046 2.00e-02 2.50e+03 8.33e-02 6.93e+01 pdb=" C ASN G 1 " 0.144 2.00e-02 2.50e+03 pdb=" O ASN G 1 " -0.051 2.00e-02 2.50e+03 pdb=" N ASN G 2 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 363 " 0.107 5.00e-02 4.00e+02 1.40e-01 3.16e+01 pdb=" N PRO E 364 " -0.242 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 " 0.091 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO F 491 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " 0.062 5.00e-02 4.00e+02 ... (remaining 3749 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 4 1.83 - 2.60: 274 2.60 - 3.37: 27821 3.37 - 4.13: 53138 4.13 - 4.90: 93970 Nonbonded interactions: 175207 Sorted by model distance: nonbonded pdb=" O2G GNP A1003 " pdb="MG MG H 101 " model vdw 1.065 2.170 nonbonded pdb=" PG GNP A1003 " pdb="MG MG H 101 " model vdw 1.486 2.530 nonbonded pdb=" O1G GNP A1003 " pdb="MG MG H 101 " model vdw 1.591 2.170 nonbonded pdb=" N ASN G 1 " pdb=" P A H 1 " model vdw 1.597 3.480 nonbonded pdb=" O SER D 173 " pdb=" OG SER D 177 " model vdw 2.045 2.440 ... (remaining 175202 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: 3.460 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: 18.850 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 66.010 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0955 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 1.057 22620 Z= 0.499 Angle : 0.973 34.024 31021 Z= 0.554 Chirality : 0.063 1.604 3601 Planarity : 0.006 0.140 3752 Dihedral : 18.803 96.966 8543 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.43 % Favored : 91.23 % Rotamer: Outliers : 5.00 % Allowed : 33.63 % Favored : 61.37 % 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: -1.93 (0.16), residues: 2650 helix: 0.34 (0.18), residues: 946 sheet: -1.48 (0.35), residues: 217 loop : -2.47 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 53 HIS 0.007 0.001 HIS A 928 PHE 0.017 0.001 PHE F 437 TYR 0.021 0.001 TYR F 299 ARG 0.006 0.000 ARG F 22 *********************** 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 392 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 279 time to evaluate : 2.382 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 77 PHE cc_start: 0.1025 (t80) cc_final: 0.0600 (p90) REVERT: A 162 TRP cc_start: 0.0416 (p-90) cc_final: -0.0721 (p-90) REVERT: A 226 THR cc_start: 0.7061 (p) cc_final: 0.6840 (t) REVERT: A 235 ASP cc_start: 0.1665 (OUTLIER) cc_final: 0.0797 (m-30) REVERT: A 566 MET cc_start: 0.3252 (ttm) cc_final: 0.2293 (mmt) REVERT: B 51 ARG cc_start: 0.1916 (mpp-170) cc_final: 0.1536 (tpp80) REVERT: B 114 CYS cc_start: -0.0518 (OUTLIER) cc_final: -0.1070 (m) REVERT: B 155 GLU cc_start: 0.3755 (pt0) cc_final: 0.3224 (mp0) REVERT: D 70 MET cc_start: 0.0397 (ptm) cc_final: -0.0287 (mtt) REVERT: D 139 LYS cc_start: 0.7135 (ttpp) cc_final: 0.6747 (tppt) REVERT: D 140 ASN cc_start: 0.6397 (m-40) cc_final: 0.6004 (t0) REVERT: D 146 THR cc_start: 0.1462 (p) cc_final: 0.1218 (t) REVERT: D 185 ILE cc_start: 0.2302 (OUTLIER) cc_final: 0.2079 (pt) REVERT: F 40 LYS cc_start: 0.6223 (ttmm) cc_final: 0.5728 (tppp) REVERT: F 80 SER cc_start: -0.0327 (OUTLIER) cc_final: -0.2667 (t) REVERT: F 122 LEU cc_start: 0.6175 (tt) cc_final: 0.5678 (mt) REVERT: F 453 SER cc_start: 0.1539 (OUTLIER) cc_final: 0.1137 (p) REVERT: F 495 VAL cc_start: -0.0711 (OUTLIER) cc_final: -0.0940 (p) REVERT: F 532 THR cc_start: 0.1472 (OUTLIER) cc_final: 0.1064 (t) REVERT: F 576 MET cc_start: -0.1261 (mmt) cc_final: -0.1575 (pp-130) REVERT: E 73 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7612 (tmmt) REVERT: E 183 THR cc_start: 0.4608 (OUTLIER) cc_final: 0.4181 (p) REVERT: E 233 MET cc_start: -0.2863 (mpm) cc_final: -0.4470 (tpt) REVERT: E 248 ARG cc_start: 0.6032 (mtt180) cc_final: 0.5662 (mmm-85) REVERT: E 280 LEU cc_start: 0.3714 (mt) cc_final: 0.3462 (tm) REVERT: G 10 ARG cc_start: 0.2455 (OUTLIER) cc_final: 0.1548 (tpm170) REVERT: G 73 CYS cc_start: 0.5910 (OUTLIER) cc_final: 0.5222 (p) outliers start: 113 outliers final: 20 residues processed: 382 average time/residue: 0.9296 time to fit residues: 424.0078 Evaluate side-chains 199 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 453 SER Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 73 CYS 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: 0.2980 chunk 112 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 155 optimal weight: 30.0000 chunk 242 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 213 ASN A 312 ASN A 439 HIS A 492 GLN A 611 ASN A 698 GLN A 705 ASN A 791 ASN A 911 ASN C 19 GLN ** D 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 516 ASN ** F 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 62 GLN ** 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 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1578 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.129 22620 Z= 0.311 Angle : 0.826 16.771 31021 Z= 0.417 Chirality : 0.047 0.377 3601 Planarity : 0.006 0.064 3752 Dihedral : 13.034 87.565 3843 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.04 % Favored : 90.70 % Rotamer: Outliers : 7.24 % Allowed : 30.90 % Favored : 61.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -2.14 (0.16), residues: 2650 helix: -0.06 (0.17), residues: 930 sheet: -1.29 (0.33), residues: 238 loop : -2.45 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 216 HIS 0.016 0.002 HIS A 752 PHE 0.034 0.003 PHE A 348 TYR 0.039 0.002 TYR A 129 ARG 0.009 0.001 ARG F 497 *********************** 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 351 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 187 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 TRP cc_start: 0.0906 (p-90) cc_final: -0.0700 (p-90) REVERT: A 226 THR cc_start: 0.7736 (p) cc_final: 0.7385 (t) REVERT: A 235 ASP cc_start: 0.2741 (OUTLIER) cc_final: 0.2310 (t70) REVERT: A 438 LYS cc_start: -0.2072 (OUTLIER) cc_final: -0.2540 (ptpt) REVERT: A 566 MET cc_start: 0.3938 (ttm) cc_final: 0.3128 (mmt) REVERT: A 633 MET cc_start: 0.0169 (ttp) cc_final: -0.1932 (mpp) REVERT: A 666 MET cc_start: 0.0124 (OUTLIER) cc_final: -0.0303 (ppp) REVERT: A 871 LYS cc_start: 0.3186 (mmtt) cc_final: 0.2903 (mtpt) REVERT: A 883 LEU cc_start: 0.5079 (OUTLIER) cc_final: 0.4585 (mt) REVERT: B 51 ARG cc_start: 0.2106 (mpp-170) cc_final: 0.1500 (tpp80) REVERT: B 100 ASN cc_start: 0.2354 (OUTLIER) cc_final: 0.1909 (p0) REVERT: C 68 ILE cc_start: -0.3167 (OUTLIER) cc_final: -0.3473 (mm) REVERT: D 42 LEU cc_start: 0.0246 (OUTLIER) cc_final: -0.0023 (mt) REVERT: D 70 MET cc_start: 0.0632 (ptm) cc_final: -0.0618 (mtp) REVERT: D 139 LYS cc_start: 0.7262 (ttpp) cc_final: 0.6846 (tppt) REVERT: D 140 ASN cc_start: 0.6413 (m-40) cc_final: 0.5829 (t0) REVERT: D 182 TRP cc_start: -0.1046 (OUTLIER) cc_final: -0.2007 (m100) REVERT: F 122 LEU cc_start: 0.6180 (tt) cc_final: 0.5689 (mt) REVERT: F 128 GLU cc_start: 0.3463 (tp30) cc_final: 0.3260 (mm-30) REVERT: F 185 TYR cc_start: 0.7565 (p90) cc_final: 0.6935 (t80) REVERT: F 493 ILE cc_start: 0.0333 (OUTLIER) cc_final: 0.0063 (tp) REVERT: E 68 MET cc_start: 0.1031 (OUTLIER) cc_final: -0.0835 (pp-130) REVERT: E 233 MET cc_start: -0.2690 (OUTLIER) cc_final: -0.4325 (tpt) REVERT: E 248 ARG cc_start: 0.5916 (mtt180) cc_final: 0.5701 (mmm-85) REVERT: E 270 GLN cc_start: 0.7122 (tt0) cc_final: 0.6603 (mp10) REVERT: E 280 LEU cc_start: 0.3760 (mt) cc_final: 0.3458 (tm) REVERT: E 315 ASP cc_start: 0.4812 (OUTLIER) cc_final: 0.4464 (t0) REVERT: E 396 TYR cc_start: 0.5405 (OUTLIER) cc_final: 0.5072 (p90) REVERT: E 578 ASP cc_start: 0.2162 (OUTLIER) cc_final: 0.0663 (p0) REVERT: G 10 ARG cc_start: 0.2674 (OUTLIER) cc_final: 0.2144 (mmp80) REVERT: G 73 CYS cc_start: 0.5899 (t) cc_final: 0.5551 (p) REVERT: G 88 LEU cc_start: 0.4103 (OUTLIER) cc_final: 0.2742 (tm) outliers start: 164 outliers final: 50 residues processed: 328 average time/residue: 1.0283 time to fit residues: 398.7290 Evaluate side-chains 232 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 166 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 588 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 263 SER Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 88 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 262 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 82 optimal weight: 0.9980 chunk 194 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 GLN A 650 HIS ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 ASN B 118 ASN C 37 ASN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS F 268 ASN E 116 ASN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2118 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 22620 Z= 0.351 Angle : 0.884 14.952 31021 Z= 0.458 Chirality : 0.050 0.261 3601 Planarity : 0.006 0.068 3752 Dihedral : 13.208 89.471 3823 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.57 % Favored : 90.17 % Rotamer: Outliers : 7.37 % Allowed : 31.47 % Favored : 61.15 % 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: -2.69 (0.15), residues: 2650 helix: -0.90 (0.16), residues: 921 sheet: -1.43 (0.33), residues: 226 loop : -2.53 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP B 182 HIS 0.019 0.003 HIS E 33 PHE 0.049 0.004 PHE A 348 TYR 0.042 0.003 TYR A 129 ARG 0.008 0.001 ARG A 249 *********************** 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 364 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 197 time to evaluate : 2.243 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 113 HIS cc_start: 0.2082 (OUTLIER) cc_final: 0.0539 (m170) REVERT: A 183 ARG cc_start: 0.1915 (OUTLIER) cc_final: 0.1219 (mtp180) REVERT: A 226 THR cc_start: 0.8182 (p) cc_final: 0.7736 (t) REVERT: A 235 ASP cc_start: 0.2320 (OUTLIER) cc_final: 0.1718 (t70) REVERT: A 242 MET cc_start: 0.1843 (OUTLIER) cc_final: 0.0421 (mtp) REVERT: A 332 LYS cc_start: 0.1794 (OUTLIER) cc_final: 0.0746 (ttpp) REVERT: A 380 MET cc_start: 0.2336 (OUTLIER) cc_final: 0.2030 (ptm) REVERT: A 488 ILE cc_start: 0.0760 (OUTLIER) cc_final: 0.0532 (pp) REVERT: A 615 MET cc_start: 0.0362 (OUTLIER) cc_final: 0.0131 (tpt) REVERT: A 633 MET cc_start: 0.0779 (ttp) cc_final: -0.1527 (mpp) REVERT: A 666 MET cc_start: 0.0666 (OUTLIER) cc_final: -0.0467 (pmm) REVERT: A 705 ASN cc_start: 0.7701 (m110) cc_final: 0.7189 (m-40) REVERT: A 871 LYS cc_start: 0.3059 (mmtt) cc_final: 0.2284 (tppt) REVERT: A 879 ASP cc_start: 0.6230 (m-30) cc_final: 0.5940 (m-30) REVERT: A 893 ASP cc_start: 0.5911 (t0) cc_final: 0.5635 (m-30) REVERT: B 51 ARG cc_start: 0.2066 (mpp-170) cc_final: 0.1658 (tpp-160) REVERT: B 55 MET cc_start: 0.0179 (mmp) cc_final: -0.0100 (mmp) REVERT: B 79 LYS cc_start: 0.0410 (pttt) cc_final: -0.0149 (mtmt) REVERT: B 100 ASN cc_start: 0.2012 (OUTLIER) cc_final: 0.1598 (p0) REVERT: D 42 LEU cc_start: -0.0063 (OUTLIER) cc_final: -0.0357 (mt) REVERT: D 55 MET cc_start: 0.1857 (mmp) cc_final: 0.1267 (mmt) REVERT: D 70 MET cc_start: 0.0723 (OUTLIER) cc_final: -0.1115 (mtt) REVERT: D 139 LYS cc_start: 0.7352 (ttpp) cc_final: 0.6876 (tppt) REVERT: D 140 ASN cc_start: 0.6529 (m-40) cc_final: 0.5736 (t0) REVERT: D 182 TRP cc_start: -0.0780 (OUTLIER) cc_final: -0.1789 (m100) REVERT: F 93 TYR cc_start: 0.0167 (m-80) cc_final: -0.2443 (m-80) REVERT: F 122 LEU cc_start: 0.6178 (tt) cc_final: 0.5676 (mt) REVERT: F 128 GLU cc_start: 0.3497 (tp30) cc_final: 0.3142 (pp20) REVERT: F 185 TYR cc_start: 0.7475 (OUTLIER) cc_final: 0.6978 (p90) REVERT: F 493 ILE cc_start: 0.0020 (OUTLIER) cc_final: -0.0266 (tp) REVERT: F 526 LEU cc_start: 0.0560 (OUTLIER) cc_final: 0.0314 (pp) REVERT: F 530 THR cc_start: 0.0948 (OUTLIER) cc_final: 0.0690 (p) REVERT: E 48 TYR cc_start: 0.0235 (OUTLIER) cc_final: -0.0080 (t80) REVERT: E 73 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7884 (ttpp) REVERT: E 155 ARG cc_start: 0.1712 (mmt180) cc_final: 0.1032 (mmm-85) REVERT: E 233 MET cc_start: -0.2474 (OUTLIER) cc_final: -0.4260 (tpt) REVERT: E 248 ARG cc_start: 0.5970 (mtt180) cc_final: 0.5690 (mmm-85) REVERT: E 270 GLN cc_start: 0.7027 (tt0) cc_final: 0.6558 (mp10) REVERT: E 280 LEU cc_start: 0.4071 (mt) cc_final: 0.3632 (tp) REVERT: E 315 ASP cc_start: 0.4706 (OUTLIER) cc_final: 0.4407 (t0) REVERT: E 396 TYR cc_start: 0.5288 (OUTLIER) cc_final: 0.4864 (p90) REVERT: E 497 ARG cc_start: 0.4344 (OUTLIER) cc_final: 0.4107 (mmt90) REVERT: G 3 GLU cc_start: 0.1430 (OUTLIER) cc_final: -0.0059 (mm-30) REVERT: G 10 ARG cc_start: 0.2568 (OUTLIER) cc_final: 0.1792 (tpm170) REVERT: G 73 CYS cc_start: 0.5734 (t) cc_final: 0.5255 (p) REVERT: G 88 LEU cc_start: 0.4266 (OUTLIER) cc_final: 0.2905 (tm) outliers start: 167 outliers final: 71 residues processed: 335 average time/residue: 0.9465 time to fit residues: 378.4271 Evaluate side-chains 273 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 176 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 183 ARG Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 492 GLN Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 788 TYR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 833 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 853 THR Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 43 LEU Chi-restraints excluded: chain F residue 44 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 239 optimal weight: 1.9990 chunk 182 optimal weight: 20.0000 chunk 126 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 115 optimal weight: 0.0570 chunk 163 optimal weight: 0.0670 chunk 243 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 231 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN A 791 ASN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN C 37 ASN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 HIS ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1982 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22620 Z= 0.187 Angle : 0.671 15.437 31021 Z= 0.340 Chirality : 0.043 0.298 3601 Planarity : 0.004 0.048 3752 Dihedral : 12.622 84.701 3818 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.25 % Favored : 91.49 % Rotamer: Outliers : 5.00 % Allowed : 34.20 % Favored : 60.80 % 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: -2.28 (0.16), residues: 2650 helix: -0.33 (0.17), residues: 927 sheet: -1.39 (0.33), residues: 236 loop : -2.42 (0.15), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 182 HIS 0.013 0.001 HIS A 642 PHE 0.022 0.002 PHE A 348 TYR 0.031 0.002 TYR E 299 ARG 0.005 0.001 ARG E 560 *********************** 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 291 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 178 time to evaluate : 2.278 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 226 THR cc_start: 0.8181 (p) cc_final: 0.7745 (t) REVERT: A 235 ASP cc_start: 0.2253 (OUTLIER) cc_final: 0.1614 (t70) REVERT: A 242 MET cc_start: 0.1493 (OUTLIER) cc_final: 0.0011 (mtp) REVERT: A 249 ARG cc_start: -0.0222 (tpt90) cc_final: -0.1404 (tpt90) REVERT: A 332 LYS cc_start: 0.1448 (OUTLIER) cc_final: 0.0425 (ttpp) REVERT: A 380 MET cc_start: 0.2283 (OUTLIER) cc_final: 0.1990 (ptm) REVERT: A 471 PHE cc_start: 0.2431 (t80) cc_final: 0.1755 (p90) REVERT: A 633 MET cc_start: 0.0739 (ttp) cc_final: -0.1573 (mpm) REVERT: A 822 GLN cc_start: -0.2140 (OUTLIER) cc_final: -0.3600 (mm-40) REVERT: A 871 LYS cc_start: 0.2811 (OUTLIER) cc_final: 0.2107 (tptm) REVERT: A 883 LEU cc_start: 0.5323 (OUTLIER) cc_final: 0.4065 (mt) REVERT: A 909 ASN cc_start: 0.4600 (t0) cc_final: 0.2887 (m110) REVERT: B 51 ARG cc_start: 0.2138 (mpp-170) cc_final: 0.1853 (tpp-160) REVERT: D 42 LEU cc_start: 0.0162 (OUTLIER) cc_final: -0.0242 (mt) REVERT: D 55 MET cc_start: 0.2384 (mmp) cc_final: 0.1938 (mmt) REVERT: D 70 MET cc_start: 0.0456 (ptm) cc_final: -0.1141 (mtt) REVERT: D 139 LYS cc_start: 0.7254 (ttpp) cc_final: 0.6826 (tppt) REVERT: D 140 ASN cc_start: 0.6524 (m-40) cc_final: 0.5679 (t0) REVERT: D 182 TRP cc_start: -0.0414 (OUTLIER) cc_final: -0.1445 (m100) REVERT: F 75 HIS cc_start: 0.0080 (OUTLIER) cc_final: -0.2372 (t-90) REVERT: F 93 TYR cc_start: -0.0063 (m-80) cc_final: -0.1318 (m-80) REVERT: F 122 LEU cc_start: 0.6115 (tt) cc_final: 0.5613 (mt) REVERT: F 128 GLU cc_start: 0.3532 (tp30) cc_final: 0.3209 (pp20) REVERT: F 185 TYR cc_start: 0.7460 (p90) cc_final: 0.6923 (p90) REVERT: F 248 ARG cc_start: 0.5264 (OUTLIER) cc_final: 0.4391 (tpm170) REVERT: F 493 ILE cc_start: 0.0322 (OUTLIER) cc_final: 0.0050 (tp) REVERT: E 73 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7583 (ttpp) REVERT: E 155 ARG cc_start: 0.1671 (mmt180) cc_final: 0.0779 (tpp80) REVERT: E 233 MET cc_start: -0.2342 (OUTLIER) cc_final: -0.4226 (tpt) REVERT: E 248 ARG cc_start: 0.6160 (mtt180) cc_final: 0.5794 (mmm-85) REVERT: E 270 GLN cc_start: 0.6993 (tt0) cc_final: 0.6558 (mp10) REVERT: E 280 LEU cc_start: 0.3843 (mt) cc_final: 0.2993 (tp) REVERT: E 315 ASP cc_start: 0.4536 (OUTLIER) cc_final: 0.4296 (t0) REVERT: E 396 TYR cc_start: 0.5674 (OUTLIER) cc_final: 0.5304 (p90) REVERT: E 436 MET cc_start: -0.0417 (pp-130) cc_final: -0.0861 (pp-130) REVERT: E 497 ARG cc_start: 0.4268 (OUTLIER) cc_final: 0.4032 (mmt90) REVERT: G 10 ARG cc_start: 0.2436 (OUTLIER) cc_final: 0.1104 (tpm170) REVERT: G 32 TYR cc_start: 0.0821 (m-80) cc_final: -0.0096 (m-80) REVERT: G 73 CYS cc_start: 0.5451 (t) cc_final: 0.4999 (p) REVERT: G 88 LEU cc_start: 0.3873 (OUTLIER) cc_final: 0.2444 (tm) REVERT: G 106 LEU cc_start: 0.6736 (mt) cc_final: 0.6288 (pt) outliers start: 113 outliers final: 48 residues processed: 265 average time/residue: 1.0285 time to fit residues: 321.2642 Evaluate side-chains 240 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 173 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 432 ILE Chi-restraints excluded: chain E residue 453 SER Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 88 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 214 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 178 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 231 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 HIS E 265 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2222 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22620 Z= 0.247 Angle : 0.729 15.501 31021 Z= 0.373 Chirality : 0.045 0.253 3601 Planarity : 0.005 0.056 3752 Dihedral : 12.611 84.870 3818 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.57 % Favored : 90.24 % Rotamer: Outliers : 5.93 % Allowed : 33.76 % Favored : 60.32 % 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: -2.44 (0.15), residues: 2650 helix: -0.51 (0.17), residues: 924 sheet: -1.39 (0.32), residues: 249 loop : -2.50 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 598 HIS 0.018 0.002 HIS F 33 PHE 0.035 0.003 PHE A 348 TYR 0.027 0.002 TYR A 788 ARG 0.009 0.001 ARG A 889 *********************** 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 309 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 175 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2452 (OUTLIER) cc_final: 0.1087 (m170) REVERT: A 226 THR cc_start: 0.8179 (p) cc_final: 0.7766 (t) REVERT: A 242 MET cc_start: 0.2235 (OUTLIER) cc_final: 0.0891 (mtt) REVERT: A 332 LYS cc_start: 0.1491 (OUTLIER) cc_final: 0.0467 (ttpp) REVERT: A 380 MET cc_start: 0.2293 (OUTLIER) cc_final: 0.2075 (ptm) REVERT: A 633 MET cc_start: 0.0976 (ttp) cc_final: -0.1441 (mpp) REVERT: A 666 MET cc_start: -0.0044 (OUTLIER) cc_final: -0.0714 (ptp) REVERT: A 668 MET cc_start: 0.3776 (mpt) cc_final: 0.3421 (mmt) REVERT: A 780 LYS cc_start: -0.0936 (OUTLIER) cc_final: -0.1841 (tptp) REVERT: A 822 GLN cc_start: -0.0698 (OUTLIER) cc_final: -0.2651 (mm-40) REVERT: A 871 LYS cc_start: 0.3015 (OUTLIER) cc_final: 0.1968 (tptp) REVERT: A 889 ARG cc_start: 0.7166 (ttp80) cc_final: 0.6535 (ttm110) REVERT: B 51 ARG cc_start: 0.1981 (mpp-170) cc_final: 0.1545 (tpp-160) REVERT: B 100 ASN cc_start: 0.2347 (OUTLIER) cc_final: 0.1690 (p0) REVERT: D 42 LEU cc_start: 0.0289 (OUTLIER) cc_final: -0.0208 (mt) REVERT: D 55 MET cc_start: 0.2200 (mmp) cc_final: 0.1624 (mmt) REVERT: D 67 MET cc_start: -0.0392 (OUTLIER) cc_final: -0.0601 (pp-130) REVERT: D 70 MET cc_start: 0.0351 (ptm) cc_final: -0.1261 (mtt) REVERT: D 139 LYS cc_start: 0.7170 (ttpp) cc_final: 0.6867 (tppt) REVERT: D 182 TRP cc_start: -0.0336 (OUTLIER) cc_final: -0.1566 (m100) REVERT: F 75 HIS cc_start: -0.0298 (OUTLIER) cc_final: -0.2550 (t-90) REVERT: F 93 TYR cc_start: -0.0268 (m-80) cc_final: -0.1998 (m-80) REVERT: F 122 LEU cc_start: 0.6101 (tt) cc_final: 0.5590 (mt) REVERT: F 128 GLU cc_start: 0.3542 (tp30) cc_final: 0.3037 (tm-30) REVERT: F 185 TYR cc_start: 0.7499 (p90) cc_final: 0.6977 (p90) REVERT: F 248 ARG cc_start: 0.5191 (tmm160) cc_final: 0.4341 (tpm170) REVERT: F 493 ILE cc_start: 0.0299 (OUTLIER) cc_final: -0.0042 (tp) REVERT: F 526 LEU cc_start: 0.0459 (OUTLIER) cc_final: 0.0188 (pp) REVERT: E 21 ARG cc_start: -0.1443 (OUTLIER) cc_final: -0.2482 (ppp80) REVERT: E 73 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7911 (ttpp) REVERT: E 155 ARG cc_start: 0.1578 (mmt180) cc_final: 0.0988 (mmm-85) REVERT: E 233 MET cc_start: -0.2447 (OUTLIER) cc_final: -0.4238 (tpt) REVERT: E 270 GLN cc_start: 0.7100 (tt0) cc_final: 0.6684 (mp10) REVERT: E 280 LEU cc_start: 0.3672 (mt) cc_final: 0.2769 (tp) REVERT: E 315 ASP cc_start: 0.4483 (OUTLIER) cc_final: 0.4255 (t0) REVERT: E 396 TYR cc_start: 0.5699 (OUTLIER) cc_final: 0.5328 (p90) REVERT: E 436 MET cc_start: 0.0983 (OUTLIER) cc_final: -0.0579 (pp-130) REVERT: E 497 ARG cc_start: 0.4207 (OUTLIER) cc_final: 0.3973 (mmt90) REVERT: G 3 GLU cc_start: 0.1172 (OUTLIER) cc_final: -0.0479 (mm-30) REVERT: G 10 ARG cc_start: 0.2312 (OUTLIER) cc_final: 0.1126 (tpm170) REVERT: G 73 CYS cc_start: 0.5373 (t) cc_final: 0.5092 (p) REVERT: G 88 LEU cc_start: 0.3582 (OUTLIER) cc_final: 0.2768 (tm) outliers start: 134 outliers final: 64 residues processed: 280 average time/residue: 0.9764 time to fit residues: 325.0185 Evaluate side-chains 251 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 162 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 816 HIS Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 453 SER Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.8980 chunk 232 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 258 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN ** A 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN A 541 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 886 GLN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2266 moved from start: 0.6415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22620 Z= 0.228 Angle : 0.724 14.652 31021 Z= 0.361 Chirality : 0.044 0.278 3601 Planarity : 0.005 0.049 3752 Dihedral : 12.462 84.567 3816 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.00 % Favored : 90.81 % Rotamer: Outliers : 6.10 % Allowed : 33.76 % Favored : 60.14 % 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: -2.44 (0.15), residues: 2650 helix: -0.49 (0.17), residues: 921 sheet: -1.58 (0.32), residues: 238 loop : -2.46 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 598 HIS 0.010 0.001 HIS A 642 PHE 0.028 0.002 PHE A 348 TYR 0.026 0.002 TYR A 788 ARG 0.006 0.001 ARG A 889 *********************** 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 307 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 169 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: -0.1444 (OUTLIER) cc_final: -0.2457 (ppt170) REVERT: A 113 HIS cc_start: 0.2396 (OUTLIER) cc_final: 0.1210 (m170) REVERT: A 226 THR cc_start: 0.8254 (p) cc_final: 0.7832 (t) REVERT: A 242 MET cc_start: 0.2569 (OUTLIER) cc_final: 0.1315 (mtt) REVERT: A 332 LYS cc_start: 0.1435 (OUTLIER) cc_final: 0.0421 (ttpp) REVERT: A 633 MET cc_start: 0.1047 (ttp) cc_final: -0.1346 (mpm) REVERT: A 666 MET cc_start: -0.0153 (OUTLIER) cc_final: -0.0770 (ptp) REVERT: A 668 MET cc_start: 0.3785 (mpt) cc_final: 0.3545 (mmt) REVERT: A 754 SER cc_start: 0.6883 (OUTLIER) cc_final: 0.6619 (m) REVERT: A 770 TYR cc_start: -0.0385 (OUTLIER) cc_final: -0.2037 (m-10) REVERT: A 780 LYS cc_start: -0.0850 (OUTLIER) cc_final: -0.1722 (tptp) REVERT: A 871 LYS cc_start: 0.3374 (OUTLIER) cc_final: 0.3103 (mttt) REVERT: A 889 ARG cc_start: 0.7233 (ttp80) cc_final: 0.6739 (ttm110) REVERT: B 51 ARG cc_start: 0.1889 (mpp-170) cc_final: 0.1607 (tpp-160) REVERT: B 176 ASN cc_start: 0.5333 (t0) cc_final: 0.4609 (m-40) REVERT: C 20 LEU cc_start: 0.5431 (tt) cc_final: 0.4613 (mp) REVERT: D 42 LEU cc_start: 0.0359 (OUTLIER) cc_final: -0.0123 (mt) REVERT: D 55 MET cc_start: 0.2102 (mmp) cc_final: 0.1586 (mmt) REVERT: D 70 MET cc_start: 0.0490 (ptm) cc_final: -0.1190 (mtt) REVERT: D 182 TRP cc_start: -0.0124 (OUTLIER) cc_final: -0.1424 (m100) REVERT: F 75 HIS cc_start: -0.0347 (OUTLIER) cc_final: -0.2643 (t-90) REVERT: F 93 TYR cc_start: -0.0192 (m-80) cc_final: -0.2070 (m-80) REVERT: F 122 LEU cc_start: 0.6105 (tt) cc_final: 0.5593 (mt) REVERT: F 128 GLU cc_start: 0.3500 (tp30) cc_final: 0.3040 (tm-30) REVERT: F 176 LEU cc_start: 0.3612 (OUTLIER) cc_final: 0.3263 (tp) REVERT: F 185 TYR cc_start: 0.7527 (p90) cc_final: 0.6993 (p90) REVERT: F 248 ARG cc_start: 0.5238 (OUTLIER) cc_final: 0.4398 (tpm170) REVERT: F 493 ILE cc_start: 0.0381 (OUTLIER) cc_final: 0.0033 (tp) REVERT: F 526 LEU cc_start: 0.0197 (OUTLIER) cc_final: -0.0074 (pp) REVERT: E 21 ARG cc_start: -0.1465 (OUTLIER) cc_final: -0.2445 (ppp80) REVERT: E 73 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7955 (ttpp) REVERT: E 233 MET cc_start: -0.2354 (mpm) cc_final: -0.4108 (tpt) REVERT: E 236 SER cc_start: 0.4272 (OUTLIER) cc_final: 0.3613 (m) REVERT: E 271 LYS cc_start: -0.0307 (pptt) cc_final: -0.0719 (pptt) REVERT: E 280 LEU cc_start: 0.3734 (mt) cc_final: 0.2745 (tp) REVERT: E 306 TYR cc_start: 0.3452 (m-80) cc_final: 0.3094 (m-80) REVERT: E 315 ASP cc_start: 0.4480 (OUTLIER) cc_final: 0.4263 (t0) REVERT: E 396 TYR cc_start: 0.5726 (OUTLIER) cc_final: 0.5384 (p90) REVERT: E 436 MET cc_start: 0.0365 (OUTLIER) cc_final: -0.0851 (pp-130) REVERT: E 497 ARG cc_start: 0.4078 (OUTLIER) cc_final: 0.3847 (mmt90) REVERT: G 3 GLU cc_start: 0.1000 (OUTLIER) cc_final: -0.0445 (mm-30) REVERT: G 10 ARG cc_start: 0.2337 (OUTLIER) cc_final: 0.0881 (tpm170) REVERT: G 73 CYS cc_start: 0.5285 (t) cc_final: 0.4999 (p) REVERT: G 88 LEU cc_start: 0.3182 (OUTLIER) cc_final: 0.2428 (tm) REVERT: G 92 LYS cc_start: 0.0867 (OUTLIER) cc_final: -0.0291 (mppt) outliers start: 138 outliers final: 78 residues processed: 273 average time/residue: 0.9837 time to fit residues: 321.3773 Evaluate side-chains 267 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 162 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 816 HIS Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 466 ASP Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 453 SER Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 249 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 chunk 188 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 217 optimal weight: 0.9980 chunk 144 optimal weight: 0.1980 chunk 257 optimal weight: 6.9990 chunk 161 optimal weight: 0.3980 chunk 156 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 447 ASN A 459 ASN A 507 ASN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 GLN ** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2229 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22620 Z= 0.182 Angle : 0.664 14.599 31021 Z= 0.330 Chirality : 0.042 0.240 3601 Planarity : 0.004 0.052 3752 Dihedral : 12.270 82.945 3815 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.47 % Favored : 91.30 % Rotamer: Outliers : 5.75 % Allowed : 33.93 % Favored : 60.32 % 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: -2.28 (0.15), residues: 2650 helix: -0.35 (0.17), residues: 913 sheet: -1.52 (0.32), residues: 255 loop : -2.37 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 182 HIS 0.008 0.001 HIS A 642 PHE 0.022 0.002 PHE A 348 TYR 0.021 0.001 TYR A 788 ARG 0.009 0.001 ARG E 560 *********************** 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 304 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 174 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 HIS cc_start: 0.2318 (OUTLIER) cc_final: 0.1390 (m170) REVERT: A 226 THR cc_start: 0.8129 (p) cc_final: 0.7747 (t) REVERT: A 242 MET cc_start: 0.2505 (OUTLIER) cc_final: 0.1318 (mtt) REVERT: A 332 LYS cc_start: 0.1790 (OUTLIER) cc_final: 0.0769 (ttpp) REVERT: A 633 MET cc_start: 0.1094 (ttp) cc_final: -0.1275 (mpm) REVERT: A 666 MET cc_start: -0.0113 (OUTLIER) cc_final: -0.0883 (ptp) REVERT: A 770 TYR cc_start: -0.0345 (OUTLIER) cc_final: -0.1958 (m-10) REVERT: A 780 LYS cc_start: -0.0804 (OUTLIER) cc_final: -0.1419 (tptp) REVERT: A 822 GLN cc_start: -0.1546 (OUTLIER) cc_final: -0.3907 (mm-40) REVERT: A 875 GLN cc_start: 0.2768 (mp10) cc_final: 0.2513 (mt0) REVERT: A 883 LEU cc_start: 0.5841 (tp) cc_final: 0.4521 (mm) REVERT: A 889 ARG cc_start: 0.7184 (ttp80) cc_final: 0.6764 (ttm110) REVERT: A 899 MET cc_start: 0.5711 (OUTLIER) cc_final: 0.3791 (mpm) REVERT: A 924 MET cc_start: 0.2080 (tpt) cc_final: 0.0938 (tpt) REVERT: B 94 MET cc_start: 0.1283 (ppp) cc_final: 0.0712 (tmm) REVERT: B 114 CYS cc_start: -0.0760 (OUTLIER) cc_final: -0.1458 (t) REVERT: C 20 LEU cc_start: 0.5706 (tt) cc_final: 0.4796 (mp) REVERT: D 42 LEU cc_start: 0.0365 (OUTLIER) cc_final: -0.0139 (mt) REVERT: D 55 MET cc_start: 0.2021 (mmp) cc_final: 0.1551 (mmt) REVERT: D 70 MET cc_start: 0.0459 (OUTLIER) cc_final: -0.1093 (mtt) REVERT: F 75 HIS cc_start: -0.0149 (OUTLIER) cc_final: -0.2465 (t-90) REVERT: F 93 TYR cc_start: -0.0212 (m-80) cc_final: -0.1815 (m-80) REVERT: F 122 LEU cc_start: 0.6071 (tt) cc_final: 0.5562 (mt) REVERT: F 128 GLU cc_start: 0.3426 (tp30) cc_final: 0.2924 (tm-30) REVERT: F 176 LEU cc_start: 0.3443 (OUTLIER) cc_final: 0.3068 (tp) REVERT: F 185 TYR cc_start: 0.7512 (p90) cc_final: 0.6972 (p90) REVERT: F 248 ARG cc_start: 0.5198 (OUTLIER) cc_final: 0.4291 (tpm170) REVERT: F 254 PRO cc_start: 0.4810 (Cg_exo) cc_final: 0.4515 (Cg_endo) REVERT: F 391 LEU cc_start: 0.4585 (OUTLIER) cc_final: 0.4385 (mm) REVERT: F 493 ILE cc_start: 0.0359 (OUTLIER) cc_final: 0.0013 (tp) REVERT: F 526 LEU cc_start: 0.0156 (OUTLIER) cc_final: -0.0116 (pp) REVERT: E 21 ARG cc_start: -0.1498 (OUTLIER) cc_final: -0.2412 (ppp80) REVERT: E 73 LYS cc_start: 0.8368 (mppt) cc_final: 0.8007 (ttpp) REVERT: E 226 VAL cc_start: 0.4540 (OUTLIER) cc_final: 0.4304 (t) REVERT: E 233 MET cc_start: -0.2277 (mpm) cc_final: -0.4009 (tpt) REVERT: E 236 SER cc_start: 0.4371 (OUTLIER) cc_final: 0.3699 (m) REVERT: E 270 GLN cc_start: 0.7219 (pt0) cc_final: 0.6759 (mp10) REVERT: E 280 LEU cc_start: 0.3984 (mt) cc_final: 0.2992 (tp) REVERT: E 306 TYR cc_start: 0.3728 (m-80) cc_final: 0.3521 (m-80) REVERT: E 315 ASP cc_start: 0.4361 (OUTLIER) cc_final: 0.4160 (t0) REVERT: E 396 TYR cc_start: 0.5693 (OUTLIER) cc_final: 0.5389 (p90) REVERT: E 436 MET cc_start: 0.0822 (OUTLIER) cc_final: -0.0486 (pp-130) REVERT: E 497 ARG cc_start: 0.4194 (OUTLIER) cc_final: 0.3957 (mmt90) REVERT: G 3 GLU cc_start: 0.1006 (OUTLIER) cc_final: -0.0640 (mm-30) REVERT: G 10 ARG cc_start: 0.2321 (OUTLIER) cc_final: 0.0803 (tpm170) REVERT: G 73 CYS cc_start: 0.5344 (t) cc_final: 0.4878 (p) REVERT: G 88 LEU cc_start: 0.3313 (OUTLIER) cc_final: 0.2472 (tm) REVERT: G 92 LYS cc_start: 0.0953 (OUTLIER) cc_final: -0.0160 (mppt) outliers start: 130 outliers final: 69 residues processed: 273 average time/residue: 1.0040 time to fit residues: 324.8789 Evaluate side-chains 257 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 160 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 816 HIS Chi-restraints excluded: chain A residue 821 LYS Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 492 GLN Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 453 SER Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 159 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.0770 chunk 49 optimal weight: 0.0980 chunk 163 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 202 optimal weight: 0.6980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 ASN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 HIS ** A 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN E 124 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2334 moved from start: 0.7128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22620 Z= 0.208 Angle : 0.701 14.728 31021 Z= 0.348 Chirality : 0.043 0.272 3601 Planarity : 0.005 0.051 3752 Dihedral : 12.299 81.982 3814 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.23 % Favored : 90.51 % Rotamer: Outliers : 5.49 % Allowed : 34.37 % Favored : 60.14 % 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: -2.38 (0.15), residues: 2650 helix: -0.46 (0.17), residues: 926 sheet: -1.51 (0.32), residues: 247 loop : -2.43 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 916 HIS 0.010 0.001 HIS A 816 PHE 0.026 0.002 PHE A 348 TYR 0.024 0.002 TYR A 788 ARG 0.009 0.001 ARG A 889 *********************** 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 286 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 162 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: -0.1975 (OUTLIER) cc_final: -0.2532 (ppt170) REVERT: A 107 ASP cc_start: 0.1600 (m-30) cc_final: 0.1166 (m-30) REVERT: A 113 HIS cc_start: 0.2321 (OUTLIER) cc_final: 0.1419 (m170) REVERT: A 226 THR cc_start: 0.8057 (p) cc_final: 0.7684 (t) REVERT: A 242 MET cc_start: 0.2849 (OUTLIER) cc_final: 0.1654 (mtt) REVERT: A 332 LYS cc_start: 0.1899 (OUTLIER) cc_final: 0.0853 (ttpp) REVERT: A 633 MET cc_start: 0.1201 (ttp) cc_final: -0.1243 (mpm) REVERT: A 666 MET cc_start: -0.0032 (OUTLIER) cc_final: -0.0903 (ptp) REVERT: A 780 LYS cc_start: -0.0800 (OUTLIER) cc_final: -0.1439 (tptp) REVERT: A 825 ASP cc_start: 0.3621 (p0) cc_final: 0.3365 (t0) REVERT: A 889 ARG cc_start: 0.7132 (ttp80) cc_final: 0.6631 (ttm110) REVERT: A 924 MET cc_start: 0.2393 (tpt) cc_final: 0.1374 (tpt) REVERT: B 100 ASN cc_start: 0.2535 (OUTLIER) cc_final: 0.1551 (p0) REVERT: B 176 ASN cc_start: 0.5225 (m110) cc_final: 0.4646 (m-40) REVERT: D 55 MET cc_start: 0.2220 (mmp) cc_final: 0.1714 (mmt) REVERT: D 70 MET cc_start: 0.0566 (ptm) cc_final: -0.1092 (mtt) REVERT: F 93 TYR cc_start: -0.0230 (m-80) cc_final: -0.1787 (m-80) REVERT: F 122 LEU cc_start: 0.6090 (tt) cc_final: 0.5577 (mt) REVERT: F 128 GLU cc_start: 0.3377 (tp30) cc_final: 0.2945 (tm-30) REVERT: F 176 LEU cc_start: 0.3267 (OUTLIER) cc_final: 0.2868 (tp) REVERT: F 185 TYR cc_start: 0.7538 (p90) cc_final: 0.6997 (p90) REVERT: F 248 ARG cc_start: 0.5263 (OUTLIER) cc_final: 0.4264 (tpm170) REVERT: F 391 LEU cc_start: 0.4388 (OUTLIER) cc_final: 0.4183 (mm) REVERT: F 493 ILE cc_start: 0.0332 (OUTLIER) cc_final: -0.0016 (tp) REVERT: F 526 LEU cc_start: 0.0230 (OUTLIER) cc_final: -0.0028 (pp) REVERT: E 21 ARG cc_start: -0.1585 (OUTLIER) cc_final: -0.2323 (ppp80) REVERT: E 73 LYS cc_start: 0.8355 (mppt) cc_final: 0.8041 (ttpp) REVERT: E 130 LEU cc_start: 0.4467 (tp) cc_final: 0.3757 (mm) REVERT: E 226 VAL cc_start: 0.4504 (OUTLIER) cc_final: 0.4259 (t) REVERT: E 233 MET cc_start: -0.2287 (mpm) cc_final: -0.3861 (tpt) REVERT: E 271 LYS cc_start: 0.0601 (pptt) cc_final: -0.0048 (pptt) REVERT: E 280 LEU cc_start: 0.4015 (mt) cc_final: 0.2940 (tp) REVERT: E 306 TYR cc_start: 0.3720 (m-80) cc_final: 0.3389 (m-80) REVERT: E 396 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.5390 (p90) REVERT: E 436 MET cc_start: 0.0947 (OUTLIER) cc_final: -0.0457 (pp-130) REVERT: E 497 ARG cc_start: 0.4158 (OUTLIER) cc_final: 0.3922 (mmt90) REVERT: G 3 GLU cc_start: 0.0704 (OUTLIER) cc_final: -0.0819 (mm-30) REVERT: G 10 ARG cc_start: 0.2415 (OUTLIER) cc_final: 0.0894 (tpm170) REVERT: G 73 CYS cc_start: 0.5468 (t) cc_final: 0.4891 (p) REVERT: G 88 LEU cc_start: 0.2893 (OUTLIER) cc_final: 0.1996 (tm) REVERT: G 92 LYS cc_start: 0.0810 (OUTLIER) cc_final: -0.0257 (mppt) outliers start: 124 outliers final: 73 residues processed: 263 average time/residue: 1.0026 time to fit residues: 314.6730 Evaluate side-chains 251 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 157 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 816 HIS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 453 SER Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 234 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 216 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 chunk 238 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS A 507 ASN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 GLN B 73 GLN B 179 ASN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2320 moved from start: 0.7407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22620 Z= 0.188 Angle : 0.671 14.693 31021 Z= 0.332 Chirality : 0.042 0.235 3601 Planarity : 0.004 0.051 3752 Dihedral : 12.221 80.100 3814 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.47 % Favored : 91.30 % Rotamer: Outliers : 4.96 % Allowed : 35.16 % Favored : 59.88 % 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: -2.28 (0.15), residues: 2650 helix: -0.39 (0.17), residues: 920 sheet: -1.33 (0.33), residues: 238 loop : -2.37 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 916 HIS 0.009 0.001 HIS E 164 PHE 0.022 0.002 PHE A 348 TYR 0.021 0.001 TYR A 788 ARG 0.006 0.000 ARG E 560 *********************** 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 280 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 168 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: -0.2531 (OUTLIER) cc_final: -0.2760 (ppt170) REVERT: A 107 ASP cc_start: 0.1624 (m-30) cc_final: 0.1205 (m-30) REVERT: A 113 HIS cc_start: 0.2381 (OUTLIER) cc_final: 0.1523 (m170) REVERT: A 226 THR cc_start: 0.8035 (p) cc_final: 0.7677 (t) REVERT: A 242 MET cc_start: 0.2878 (OUTLIER) cc_final: 0.1755 (mtt) REVERT: A 294 TYR cc_start: 0.4957 (OUTLIER) cc_final: 0.4369 (t80) REVERT: A 332 LYS cc_start: 0.1890 (OUTLIER) cc_final: 0.0792 (ttpp) REVERT: A 633 MET cc_start: 0.1275 (ttp) cc_final: -0.1179 (mpp) REVERT: A 666 MET cc_start: -0.0021 (OUTLIER) cc_final: -0.0942 (ptp) REVERT: A 770 TYR cc_start: -0.0221 (OUTLIER) cc_final: -0.1914 (m-10) REVERT: A 780 LYS cc_start: -0.0719 (OUTLIER) cc_final: -0.1211 (tptp) REVERT: A 875 GLN cc_start: 0.2541 (mp10) cc_final: 0.2217 (mt0) REVERT: A 889 ARG cc_start: 0.7333 (ttp80) cc_final: 0.6159 (ttm170) REVERT: A 924 MET cc_start: 0.2247 (tpt) cc_final: 0.1203 (tpt) REVERT: B 94 MET cc_start: 0.1371 (ppp) cc_final: 0.0836 (tmm) REVERT: B 100 ASN cc_start: 0.2456 (OUTLIER) cc_final: 0.1314 (p0) REVERT: D 42 LEU cc_start: -0.0230 (OUTLIER) cc_final: -0.0768 (mt) REVERT: D 55 MET cc_start: 0.2181 (mmp) cc_final: 0.1737 (mmt) REVERT: D 70 MET cc_start: 0.0471 (ptm) cc_final: -0.1221 (mtt) REVERT: F 93 TYR cc_start: -0.0223 (m-80) cc_final: -0.1900 (m-80) REVERT: F 122 LEU cc_start: 0.6079 (tt) cc_final: 0.5567 (mt) REVERT: F 128 GLU cc_start: 0.3419 (tp30) cc_final: 0.3030 (tm-30) REVERT: F 176 LEU cc_start: 0.3193 (OUTLIER) cc_final: 0.2777 (tp) REVERT: F 185 TYR cc_start: 0.7565 (p90) cc_final: 0.7021 (p90) REVERT: F 248 ARG cc_start: 0.5284 (OUTLIER) cc_final: 0.4282 (tpm170) REVERT: F 391 LEU cc_start: 0.4309 (OUTLIER) cc_final: 0.4059 (mm) REVERT: F 493 ILE cc_start: 0.0262 (OUTLIER) cc_final: -0.0090 (tp) REVERT: F 526 LEU cc_start: 0.0216 (OUTLIER) cc_final: -0.0047 (pp) REVERT: F 576 MET cc_start: -0.3565 (OUTLIER) cc_final: -0.3771 (pp-130) REVERT: E 73 LYS cc_start: 0.8382 (mppt) cc_final: 0.8069 (ttpp) REVERT: E 130 LEU cc_start: 0.4483 (tp) cc_final: 0.3826 (mm) REVERT: E 226 VAL cc_start: 0.4435 (OUTLIER) cc_final: 0.4170 (t) REVERT: E 233 MET cc_start: -0.1931 (mpm) cc_final: -0.3779 (tpt) REVERT: E 270 GLN cc_start: 0.6410 (pp30) cc_final: 0.5944 (mm-40) REVERT: E 280 LEU cc_start: 0.4207 (mt) cc_final: 0.3073 (tp) REVERT: E 306 TYR cc_start: 0.3903 (m-80) cc_final: 0.3637 (m-80) REVERT: E 396 TYR cc_start: 0.5643 (OUTLIER) cc_final: 0.5385 (p90) REVERT: E 436 MET cc_start: 0.1229 (OUTLIER) cc_final: -0.0184 (pp-130) REVERT: E 460 LYS cc_start: -0.0972 (pttp) cc_final: -0.1980 (pttt) REVERT: E 497 ARG cc_start: 0.4161 (OUTLIER) cc_final: 0.3926 (mmt90) REVERT: G 3 GLU cc_start: 0.0996 (OUTLIER) cc_final: -0.0431 (mm-30) REVERT: G 10 ARG cc_start: 0.2304 (OUTLIER) cc_final: 0.0843 (tpm170) REVERT: G 92 LYS cc_start: 0.0747 (OUTLIER) cc_final: -0.0207 (mppt) outliers start: 112 outliers final: 75 residues processed: 260 average time/residue: 0.9808 time to fit residues: 303.2951 Evaluate side-chains 258 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 160 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 770 TYR Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 816 HIS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 453 SER Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain E residue 557 ASN Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 12 MET Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 157 optimal weight: 0.0670 chunk 253 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 244 optimal weight: 0.0030 chunk 211 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 562 ASN E 270 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2326 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22620 Z= 0.184 Angle : 0.672 14.466 31021 Z= 0.332 Chirality : 0.042 0.240 3601 Planarity : 0.004 0.055 3752 Dihedral : 12.197 79.002 3813 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.08 % Favored : 90.70 % Rotamer: Outliers : 4.83 % Allowed : 35.34 % Favored : 59.83 % 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: -2.23 (0.15), residues: 2650 helix: -0.36 (0.17), residues: 922 sheet: -1.24 (0.33), residues: 238 loop : -2.35 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.009 0.001 HIS A 642 PHE 0.023 0.002 PHE A 348 TYR 0.033 0.001 TYR G 89 ARG 0.004 0.000 ARG A 889 ********************** 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 275 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 166 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: -0.2462 (OUTLIER) cc_final: -0.2696 (ppt170) REVERT: A 107 ASP cc_start: 0.1736 (m-30) cc_final: 0.1346 (m-30) REVERT: A 113 HIS cc_start: 0.2267 (OUTLIER) cc_final: 0.1574 (m170) REVERT: A 226 THR cc_start: 0.8026 (p) cc_final: 0.7663 (t) REVERT: A 242 MET cc_start: 0.2859 (OUTLIER) cc_final: 0.1729 (mtt) REVERT: A 294 TYR cc_start: 0.4944 (OUTLIER) cc_final: 0.4398 (t80) REVERT: A 332 LYS cc_start: 0.1883 (OUTLIER) cc_final: 0.0778 (ttpp) REVERT: A 411 LYS cc_start: 0.2378 (mtmt) cc_final: 0.1662 (mmmt) REVERT: A 519 MET cc_start: -0.0261 (OUTLIER) cc_final: -0.4000 (mmt) REVERT: A 633 MET cc_start: 0.1430 (ttp) cc_final: -0.1014 (mpp) REVERT: A 666 MET cc_start: 0.0055 (OUTLIER) cc_final: -0.0910 (ptp) REVERT: A 780 LYS cc_start: -0.0670 (OUTLIER) cc_final: -0.1208 (tptp) REVERT: A 875 GLN cc_start: 0.2520 (mp10) cc_final: 0.2190 (mt0) REVERT: A 889 ARG cc_start: 0.7315 (ttp80) cc_final: 0.6157 (ttm170) REVERT: A 924 MET cc_start: 0.2150 (tpt) cc_final: 0.1080 (tpt) REVERT: B 100 ASN cc_start: 0.2578 (OUTLIER) cc_final: 0.1397 (p0) REVERT: B 176 ASN cc_start: 0.5180 (m110) cc_final: 0.4677 (m-40) REVERT: D 42 LEU cc_start: -0.0228 (OUTLIER) cc_final: -0.0775 (mt) REVERT: D 55 MET cc_start: 0.2184 (mmp) cc_final: 0.1747 (mmt) REVERT: D 70 MET cc_start: 0.0466 (ptm) cc_final: -0.1189 (mtt) REVERT: D 127 LYS cc_start: 0.5134 (ttpp) cc_final: 0.4791 (tptp) REVERT: F 93 TYR cc_start: -0.0251 (m-80) cc_final: -0.1939 (m-80) REVERT: F 122 LEU cc_start: 0.6071 (tt) cc_final: 0.5560 (mt) REVERT: F 128 GLU cc_start: 0.3415 (tp30) cc_final: 0.3041 (tm-30) REVERT: F 185 TYR cc_start: 0.7582 (p90) cc_final: 0.7040 (p90) REVERT: F 248 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.4675 (tpm170) REVERT: F 253 TYR cc_start: 0.3982 (OUTLIER) cc_final: 0.3515 (t80) REVERT: F 274 MET cc_start: 0.7245 (ptp) cc_final: 0.6872 (mpp) REVERT: F 391 LEU cc_start: 0.4305 (OUTLIER) cc_final: 0.4048 (mm) REVERT: F 493 ILE cc_start: 0.0252 (OUTLIER) cc_final: -0.0100 (tp) REVERT: F 526 LEU cc_start: 0.0073 (OUTLIER) cc_final: -0.0182 (pp) REVERT: F 576 MET cc_start: -0.3592 (OUTLIER) cc_final: -0.3856 (pp-130) REVERT: E 73 LYS cc_start: 0.8383 (mppt) cc_final: 0.8050 (ttpp) REVERT: E 130 LEU cc_start: 0.4371 (tp) cc_final: 0.3738 (mm) REVERT: E 226 VAL cc_start: 0.4381 (OUTLIER) cc_final: 0.4085 (t) REVERT: E 233 MET cc_start: -0.1690 (mpm) cc_final: -0.3590 (tpt) REVERT: E 270 GLN cc_start: 0.6378 (OUTLIER) cc_final: 0.5970 (mm-40) REVERT: E 280 LEU cc_start: 0.4053 (mt) cc_final: 0.2988 (tp) REVERT: E 396 TYR cc_start: 0.5606 (OUTLIER) cc_final: 0.5363 (p90) REVERT: E 436 MET cc_start: 0.0963 (OUTLIER) cc_final: -0.0510 (pp-130) REVERT: E 460 LYS cc_start: -0.0918 (pttp) cc_final: -0.1934 (pttt) REVERT: E 497 ARG cc_start: 0.4181 (OUTLIER) cc_final: 0.3938 (mmt90) REVERT: G 3 GLU cc_start: 0.0894 (OUTLIER) cc_final: -0.0554 (mm-30) REVERT: G 10 ARG cc_start: 0.2183 (OUTLIER) cc_final: 0.0830 (tpm170) REVERT: G 92 LYS cc_start: 0.0852 (OUTLIER) cc_final: -0.0067 (mppt) outliers start: 109 outliers final: 72 residues processed: 251 average time/residue: 1.0237 time to fit residues: 305.9242 Evaluate side-chains 259 residues out of total 2327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 163 time to evaluate : 2.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 534 ASN Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 598 TRP Chi-restraints excluded: chain A residue 603 LYS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 698 GLN Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 816 HIS Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 879 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 248 ARG Chi-restraints excluded: chain F residue 249 ILE Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 422 PHE Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 539 SER Chi-restraints excluded: chain F residue 555 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 270 GLN Chi-restraints excluded: chain E residue 374 ASP Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 453 SER Chi-restraints excluded: chain E residue 497 ARG Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 101 MET Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 168 optimal weight: 6.9990 chunk 225 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 31 optimal weight: 0.0770 chunk 58 optimal weight: 0.5980 chunk 212 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 217 optimal weight: 0.3980 chunk 26 optimal weight: 0.3980 chunk 39 optimal weight: 0.0980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.246063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.202589 restraints weight = 74353.344| |-----------------------------------------------------------------------------| r_work (start): 0.4600 rms_B_bonded: 3.51 r_work: 0.4496 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4488 r_free = 0.4488 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4488 r_free = 0.4488 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2483 moved from start: 0.7610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.213 22620 Z= 0.259 Angle : 0.852 59.123 31021 Z= 0.459 Chirality : 0.048 1.301 3601 Planarity : 0.004 0.055 3752 Dihedral : 12.200 78.998 3813 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.15 % Favored : 90.62 % Rotamer: Outliers : 4.65 % Allowed : 35.47 % Favored : 59.88 % Cbeta Deviations : 0.04 % 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: -2.22 (0.15), residues: 2650 helix: -0.36 (0.17), residues: 922 sheet: -1.23 (0.33), residues: 238 loop : -2.34 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS A 642 PHE 0.023 0.002 PHE A 348 TYR 0.028 0.001 TYR G 89 ARG 0.007 0.000 ARG E 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8000.55 seconds wall clock time: 143 minutes 18.08 seconds (8598.08 seconds total)