Starting phenix.real_space_refine on Sun Mar 17 16:53:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/03_2024/6rwo_10044_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/03_2024/6rwo_10044.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/03_2024/6rwo_10044_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/03_2024/6rwo_10044_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/03_2024/6rwo_10044_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/03_2024/6rwo_10044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/03_2024/6rwo_10044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/03_2024/6rwo_10044_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/03_2024/6rwo_10044_updated.pdb" } resolution = 3.05 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= 0.003 sd= 0.465 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 P 84 5.49 5 Mg 4 5.21 5 S 74 5.16 5 Cl 2 4.86 5 C 11364 2.51 5 N 3280 2.21 5 O 3544 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18366 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2140 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain: "Q" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "W" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 378 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 566 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1643 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Chain: "K" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1520 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 2 Chain: "J" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2016 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 2 Chain: "I" Number of atoms: 2140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2140 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain: "S" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "T" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "M" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 378 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 566 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1643 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Chain: "C" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1520 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 2 Chain: "B" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2016 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 2 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {' CL': 1, ' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {' CL': 1, ' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 335 SG CYS A 40 79.872 62.097 31.593 1.00 30.55 S ATOM 357 SG CYS A 43 76.869 64.139 33.032 1.00 29.90 S ATOM 3353 SG CYS E 40 92.806 41.139 54.296 1.00 59.10 S ATOM 3375 SG CYS E 43 95.023 43.160 56.977 1.00 64.54 S ATOM 5909 SG CYS K 40 23.885 48.204 22.080 1.00 82.77 S ATOM 5931 SG CYS K 43 25.815 45.648 24.409 1.00 79.38 S ATOM 7456 SG CYS J 40 58.627 30.323 59.508 1.00 70.60 S ATOM 7478 SG CYS J 43 56.683 31.978 56.543 1.00 77.61 S ATOM 9476 SG CYS I 40 49.826 111.792 31.660 1.00 31.05 S ATOM 9498 SG CYS I 43 52.830 109.752 33.099 1.00 31.06 S ATOM 12494 SG CYS M 40 36.921 132.803 54.254 1.00 58.89 S ATOM 12516 SG CYS M 43 34.698 130.780 56.930 1.00 64.48 S ATOM 15050 SG CYS C 40 105.895 125.664 22.098 1.00 83.13 S ATOM 15072 SG CYS C 43 103.967 128.220 24.427 1.00 78.22 S ATOM 16597 SG CYS B 40 71.141 143.550 59.509 1.00 70.80 S ATOM 16619 SG CYS B 43 73.086 141.895 56.545 1.00 78.44 S Time building chain proxies: 10.04, per 1000 atoms: 0.55 Number of scatterers: 18366 At special positions: 0 Unit cell: (131.1, 175.26, 99.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 Cl 2 17.00 S 74 16.00 P 84 15.00 Mg 4 11.99 F 6 9.00 O 3544 8.00 N 3280 7.00 C 11364 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: 6.75 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 43 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb=" ZN C 500 " pdb="ZN ZN C 500 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 500 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 40 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 43 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 16 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 43 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 40 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 43 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" NE2 HIS J 12 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 16 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 43 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 40 " pdb=" ZN K 500 " pdb="ZN ZN K 500 " - pdb=" NE2 HIS K 12 " pdb="ZN ZN K 500 " - pdb=" ND1 HIS K 16 " pdb="ZN ZN K 500 " - pdb=" SG CYS K 40 " pdb="ZN ZN K 500 " - pdb=" SG CYS K 43 " pdb=" ZN M 500 " pdb="ZN ZN M 500 " - pdb=" ND1 HIS M 16 " pdb="ZN ZN M 500 " - pdb=" NE2 HIS M 12 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 43 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 40 " Number of angles added : 10 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3880 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 82 helices and 24 sheets defined 45.7% alpha, 17.7% beta 30 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 7.52 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 145 through 164 removed outlier: 3.605A pdb=" N HIS A 148 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 149 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 150 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL A 151 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 158 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 196 through 220 removed outlier: 4.459A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 19 through 25 Processing helix chain 'E' and resid 30 through 39 Processing helix chain 'N' and resid 204 through 220 Processing helix chain 'N' and resid 262 through 264 No H-bonds generated for 'chain 'N' and resid 262 through 264' Processing helix chain 'L' and resid 94 through 107 Processing helix chain 'L' and resid 124 through 133 Processing helix chain 'L' and resid 151 through 164 Processing helix chain 'L' and resid 166 through 168 No H-bonds generated for 'chain 'L' and resid 166 through 168' Processing helix chain 'L' and resid 172 through 185 Processing helix chain 'L' and resid 196 through 222 removed outlier: 4.524A pdb=" N SER L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 264 No H-bonds generated for 'chain 'L' and resid 262 through 264' Processing helix chain 'K' and resid 5 through 14 Processing helix chain 'K' and resid 19 through 26 Processing helix chain 'K' and resid 30 through 38 Processing helix chain 'K' and resid 94 through 107 Processing helix chain 'K' and resid 124 through 133 Processing helix chain 'K' and resid 151 through 164 Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'K' and resid 172 through 185 Processing helix chain 'K' and resid 196 through 216 Processing helix chain 'J' and resid 2 through 15 Processing helix chain 'J' and resid 19 through 26 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 94 through 107 Processing helix chain 'J' and resid 124 through 133 Processing helix chain 'J' and resid 151 through 164 Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 172 through 185 Processing helix chain 'J' and resid 196 through 222 Processing helix chain 'J' and resid 262 through 264 No H-bonds generated for 'chain 'J' and resid 262 through 264' Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 19 through 25 Processing helix chain 'I' and resid 30 through 38 Processing helix chain 'I' and resid 94 through 107 Processing helix chain 'I' and resid 124 through 133 Processing helix chain 'I' and resid 145 through 164 removed outlier: 3.605A pdb=" N HIS I 148 " --> pdb=" O PRO I 145 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY I 149 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL I 150 " --> pdb=" O SER I 147 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL I 151 " --> pdb=" O HIS I 148 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU I 152 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 158 " --> pdb=" O ASN I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 172 through 185 Processing helix chain 'I' and resid 196 through 220 removed outlier: 4.460A pdb=" N ILE I 220 " --> pdb=" O GLN I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 264 No H-bonds generated for 'chain 'I' and resid 262 through 264' Processing helix chain 'M' and resid 2 through 15 Processing helix chain 'M' and resid 19 through 25 Processing helix chain 'M' and resid 30 through 39 Processing helix chain 'F' and resid 204 through 220 Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'D' and resid 94 through 107 Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 151 through 164 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 172 through 185 Processing helix chain 'D' and resid 196 through 222 removed outlier: 4.524A pdb=" N SER D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'C' and resid 5 through 14 Processing helix chain 'C' and resid 19 through 26 Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 94 through 107 Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 151 through 164 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 172 through 185 Processing helix chain 'C' and resid 196 through 216 Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 19 through 26 Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 94 through 107 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 151 through 164 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 172 through 185 Processing helix chain 'B' and resid 196 through 222 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing sheet with id= A, first strand: chain 'A' and resid 83 through 89 removed outlier: 4.391A pdb=" N VAL A 72 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N HIS A 112 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N MET A 63 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N HIS A 114 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N CYS A 65 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU A 136 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR A 115 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR A 138 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 224 through 227 Processing sheet with id= C, first strand: chain 'A' and resid 257 through 261 removed outlier: 3.541A pdb=" N TRP A 243 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU A 241 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 224 through 227 Processing sheet with id= E, first strand: chain 'N' and resid 257 through 261 removed outlier: 6.183A pdb=" N GLN N 252 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU N 241 " --> pdb=" O GLN N 252 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 83 through 89 removed outlier: 4.435A pdb=" N VAL L 72 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N HIS L 112 " --> pdb=" O TRP L 61 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N MET L 63 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N HIS L 114 " --> pdb=" O MET L 63 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N CYS L 65 " --> pdb=" O HIS L 114 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU L 136 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR L 115 " --> pdb=" O GLU L 136 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR L 138 " --> pdb=" O THR L 115 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 224 through 227 Processing sheet with id= H, first strand: chain 'L' and resid 257 through 261 removed outlier: 5.803A pdb=" N GLN L 252 " --> pdb=" O LEU L 241 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU L 241 " --> pdb=" O GLN L 252 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 83 through 89 removed outlier: 3.823A pdb=" N VAL K 72 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N HIS K 112 " --> pdb=" O TRP K 61 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N MET K 63 " --> pdb=" O HIS K 112 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N HIS K 114 " --> pdb=" O MET K 63 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N CYS K 65 " --> pdb=" O HIS K 114 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU K 136 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR K 115 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR K 138 " --> pdb=" O THR K 115 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 83 through 89 removed outlier: 4.181A pdb=" N VAL J 72 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS J 112 " --> pdb=" O TRP J 61 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N MET J 63 " --> pdb=" O HIS J 112 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N HIS J 114 " --> pdb=" O MET J 63 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N CYS J 65 " --> pdb=" O HIS J 114 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLU J 136 " --> pdb=" O LEU J 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR J 115 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR J 138 " --> pdb=" O THR J 115 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 223 through 227 Processing sheet with id= L, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.096A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 83 through 89 removed outlier: 4.391A pdb=" N VAL I 72 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS I 112 " --> pdb=" O TRP I 61 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N MET I 63 " --> pdb=" O HIS I 112 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS I 114 " --> pdb=" O MET I 63 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N CYS I 65 " --> pdb=" O HIS I 114 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU I 136 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR I 115 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR I 138 " --> pdb=" O THR I 115 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 224 through 227 Processing sheet with id= O, first strand: chain 'I' and resid 257 through 261 removed outlier: 3.541A pdb=" N TRP I 243 " --> pdb=" O VAL I 250 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN I 252 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU I 241 " --> pdb=" O GLN I 252 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 224 through 227 Processing sheet with id= Q, first strand: chain 'F' and resid 257 through 261 removed outlier: 6.183A pdb=" N GLN F 252 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU F 241 " --> pdb=" O GLN F 252 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 83 through 89 removed outlier: 4.435A pdb=" N VAL D 72 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N HIS D 112 " --> pdb=" O TRP D 61 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N MET D 63 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N HIS D 114 " --> pdb=" O MET D 63 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N CYS D 65 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU D 136 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR D 115 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR D 138 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 224 through 227 Processing sheet with id= T, first strand: chain 'D' and resid 257 through 261 removed outlier: 5.802A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 83 through 89 removed outlier: 3.823A pdb=" N VAL C 72 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N HIS C 112 " --> pdb=" O TRP C 61 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N MET C 63 " --> pdb=" O HIS C 112 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS C 114 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N CYS C 65 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLU C 136 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR C 115 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C 138 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 83 through 89 removed outlier: 4.181A pdb=" N VAL B 72 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS B 112 " --> pdb=" O TRP B 61 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N MET B 63 " --> pdb=" O HIS B 112 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N HIS B 114 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N CYS B 65 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLU B 136 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR B 115 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR B 138 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 223 through 227 Processing sheet with id= X, first strand: chain 'B' and resid 256 through 261 removed outlier: 6.096A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2334 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4173 1.33 - 1.45: 4539 1.45 - 1.58: 9916 1.58 - 1.70: 166 1.70 - 1.83: 108 Bond restraints: 18902 Sorted by residual: bond pdb=" CAJ KLQ A 303 " pdb=" CAX KLQ A 303 " ideal model delta sigma weight residual 2.011 1.359 0.652 2.00e-02 2.50e+03 1.06e+03 bond pdb=" CAJ KLQ I 303 " pdb=" CAX KLQ I 303 " ideal model delta sigma weight residual 2.011 1.360 0.651 2.00e-02 2.50e+03 1.06e+03 bond pdb=" CAW KLQ A 303 " pdb=" CBA KLQ A 303 " ideal model delta sigma weight residual 0.990 1.454 -0.464 2.00e-02 2.50e+03 5.39e+02 bond pdb=" CAW KLQ I 303 " pdb=" CBA KLQ I 303 " ideal model delta sigma weight residual 0.990 1.449 -0.459 2.00e-02 2.50e+03 5.27e+02 bond pdb=" CAW KLQ I 303 " pdb=" CAZ KLQ I 303 " ideal model delta sigma weight residual 1.723 1.363 0.360 2.00e-02 2.50e+03 3.25e+02 ... (remaining 18897 not shown) Histogram of bond angle deviations from ideal: 97.49 - 104.81: 532 104.81 - 112.14: 9696 112.14 - 119.46: 6428 119.46 - 126.79: 8669 126.79 - 134.11: 591 Bond angle restraints: 25916 Sorted by residual: angle pdb=" CAY KLQ I 303 " pdb=" CAV KLQ I 303 " pdb=" FAG KLQ I 303 " ideal model delta sigma weight residual 142.84 118.58 24.26 3.00e+00 1.11e-01 6.54e+01 angle pdb=" CAY KLQ A 303 " pdb=" CAV KLQ A 303 " pdb=" FAG KLQ A 303 " ideal model delta sigma weight residual 142.84 118.60 24.24 3.00e+00 1.11e-01 6.53e+01 angle pdb=" CAX KLQ A 303 " pdb=" CAJ KLQ A 303 " pdb=" NBF KLQ A 303 " ideal model delta sigma weight residual 106.14 124.06 -17.92 3.00e+00 1.11e-01 3.57e+01 angle pdb=" CAI KLQ I 303 " pdb=" CAV KLQ I 303 " pdb=" FAG KLQ I 303 " ideal model delta sigma weight residual 97.12 114.95 -17.83 3.00e+00 1.11e-01 3.53e+01 angle pdb=" CAI KLQ A 303 " pdb=" CAV KLQ A 303 " pdb=" FAG KLQ A 303 " ideal model delta sigma weight residual 97.12 114.92 -17.80 3.00e+00 1.11e-01 3.52e+01 ... (remaining 25911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 9658 17.41 - 34.83: 846 34.83 - 52.24: 463 52.24 - 69.66: 105 69.66 - 87.07: 10 Dihedral angle restraints: 11082 sinusoidal: 5108 harmonic: 5974 Sorted by residual: dihedral pdb=" CA TYR I 194 " pdb=" C TYR I 194 " pdb=" N SER I 195 " pdb=" CA SER I 195 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TYR A 194 " pdb=" C TYR A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta harmonic sigma weight residual 180.00 159.53 20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LYS L 236 " pdb=" C LYS L 236 " pdb=" N GLY L 237 " pdb=" CA GLY L 237 " ideal model delta harmonic sigma weight residual 180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 11079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2484 0.073 - 0.145: 343 0.145 - 0.218: 29 0.218 - 0.291: 2 0.291 - 0.364: 2 Chirality restraints: 2860 Sorted by residual: chirality pdb=" CBC KLQ A 303 " pdb=" CAM KLQ A 303 " pdb=" CAN KLQ A 303 " pdb=" NBE KLQ A 303 " both_signs ideal model delta sigma weight residual False -2.52 -2.89 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CBC KLQ I 303 " pdb=" CAM KLQ I 303 " pdb=" CAN KLQ I 303 " pdb=" NBE KLQ I 303 " both_signs ideal model delta sigma weight residual False -2.52 -2.88 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CBB KLQ A 303 " pdb=" CAL KLQ A 303 " pdb=" CAN KLQ A 303 " pdb=" OAQ KLQ A 303 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2857 not shown) Planarity restraints: 3010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 28 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO C 29 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 29 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 29 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 260 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO L 261 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 261 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 261 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 28 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO K 29 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO K 29 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO K 29 " 0.029 5.00e-02 4.00e+02 ... (remaining 3007 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 120 2.58 - 3.16: 12968 3.16 - 3.74: 26244 3.74 - 4.32: 38400 4.32 - 4.90: 63554 Nonbonded interactions: 141286 Sorted by model distance: nonbonded pdb=" OAC KLQ A 303 " pdb="MG MG A 305 " model vdw 1.994 2.170 nonbonded pdb=" OAC KLQ I 303 " pdb="MG MG I 305 " model vdw 2.000 2.170 nonbonded pdb="MG MG I 304 " pdb=" O HOH I 401 " model vdw 2.007 2.170 nonbonded pdb="MG MG A 304 " pdb=" O HOH A 401 " model vdw 2.007 2.170 nonbonded pdb="MG MG I 305 " pdb=" O HOH I 403 " model vdw 2.013 2.170 ... (remaining 141281 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 'A' and (resid 1 through 44 or resid 57 through 141 or resid 151 through \ 269)) selection = (chain 'B' and resid 1 through 269) selection = (chain 'I' and (resid 1 through 44 or resid 57 through 141 or resid 151 through \ 269)) selection = (chain 'J' and resid 1 through 269) } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'T' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 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: 0.010 Extract box with map and model: 11.270 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 55.060 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.013 0.652 18902 Z= 0.816 Angle : 0.815 24.264 25916 Z= 0.429 Chirality : 0.051 0.364 2860 Planarity : 0.006 0.053 3010 Dihedral : 17.177 87.074 7202 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.10 % Allowed : 6.49 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.00 (0.14), residues: 2032 helix: -1.79 (0.12), residues: 956 sheet: -0.23 (0.22), residues: 432 loop : -3.35 (0.18), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 19 HIS 0.006 0.001 HIS I 12 PHE 0.016 0.002 PHE I 1 TYR 0.013 0.002 TYR B 83 ARG 0.003 0.000 ARG I 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 323 time to evaluate : 1.908 Fit side-chains revert: symmetry clash REVERT: A 22 MET cc_start: 0.8868 (mtm) cc_final: 0.8330 (mtm) REVERT: A 154 MET cc_start: 0.8976 (mmt) cc_final: 0.8661 (mmt) REVERT: A 264 LYS cc_start: 0.8304 (mttt) cc_final: 0.8035 (mptt) REVERT: E 22 MET cc_start: 0.8469 (mtm) cc_final: 0.8227 (mtm) REVERT: N 229 GLU cc_start: 0.8103 (pt0) cc_final: 0.7747 (pt0) REVERT: N 252 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: L 87 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5975 (mm-30) REVERT: L 207 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7242 (t0) REVERT: L 228 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8601 (mtt180) REVERT: K 27 GLN cc_start: 0.6721 (mt0) cc_final: 0.5751 (tm-30) REVERT: K 104 LEU cc_start: 0.7862 (tp) cc_final: 0.7649 (tp) REVERT: K 151 VAL cc_start: 0.7297 (OUTLIER) cc_final: 0.6999 (m) REVERT: K 155 ASN cc_start: 0.8107 (m-40) cc_final: 0.7907 (m110) REVERT: J 11 GLU cc_start: 0.7327 (tp30) cc_final: 0.7010 (mm-30) REVERT: J 171 LYS cc_start: 0.8117 (mttt) cc_final: 0.7415 (mmmt) REVERT: J 202 ASP cc_start: 0.8161 (t70) cc_final: 0.7876 (t0) REVERT: J 266 LYS cc_start: 0.7617 (mtpp) cc_final: 0.7187 (pttt) REVERT: J 270 ASP cc_start: 0.8372 (t70) cc_final: 0.8161 (t0) REVERT: I 22 MET cc_start: 0.9004 (mtm) cc_final: 0.8583 (mtm) REVERT: I 73 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8208 (mt) REVERT: I 154 MET cc_start: 0.8994 (mmt) cc_final: 0.8722 (mmt) REVERT: I 264 LYS cc_start: 0.8204 (mttt) cc_final: 0.8002 (mptt) REVERT: M 14 LYS cc_start: 0.7080 (mttt) cc_final: 0.5782 (tptp) REVERT: M 26 PHE cc_start: 0.8127 (m-80) cc_final: 0.7865 (m-80) REVERT: F 229 GLU cc_start: 0.8127 (pt0) cc_final: 0.7755 (pt0) REVERT: F 252 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: D 87 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5889 (mm-30) REVERT: D 207 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7029 (t0) REVERT: D 228 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8571 (mtt180) REVERT: C 27 GLN cc_start: 0.6590 (mt0) cc_final: 0.5602 (tm-30) REVERT: C 69 GLU cc_start: 0.5529 (mt-10) cc_final: 0.5315 (mt-10) REVERT: C 151 VAL cc_start: 0.7348 (OUTLIER) cc_final: 0.7089 (m) REVERT: C 155 ASN cc_start: 0.8305 (m-40) cc_final: 0.8105 (m110) REVERT: B 11 GLU cc_start: 0.7269 (tp30) cc_final: 0.7030 (mm-30) REVERT: B 171 LYS cc_start: 0.8124 (mttt) cc_final: 0.7465 (mmmt) REVERT: B 266 LYS cc_start: 0.7527 (mtpp) cc_final: 0.7088 (pttt) REVERT: B 270 ASP cc_start: 0.8432 (t70) cc_final: 0.8191 (t0) outliers start: 72 outliers final: 33 residues processed: 380 average time/residue: 0.3221 time to fit residues: 179.3732 Evaluate side-chains 278 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 234 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 165 ILE Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 228 ARG Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 157 GLN Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 73 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 228 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 165 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN L 134 GLN L 216 GLN L 252 GLN K 18 ASN K 168 GLN J 9 GLN J 157 GLN I 222 ASN D 134 GLN D 216 GLN D 252 GLN C 18 ASN C 117 ASN C 168 GLN C 183 HIS B 9 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18902 Z= 0.170 Angle : 0.520 11.651 25916 Z= 0.281 Chirality : 0.040 0.145 2860 Planarity : 0.004 0.052 3010 Dihedral : 18.919 87.211 3246 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.90 % Allowed : 10.71 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.17), residues: 2032 helix: 0.65 (0.16), residues: 962 sheet: 0.10 (0.22), residues: 440 loop : -3.00 (0.19), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 19 HIS 0.005 0.001 HIS I 51 PHE 0.009 0.001 PHE B 185 TYR 0.010 0.001 TYR D 271 ARG 0.003 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 262 time to evaluate : 1.918 Fit side-chains revert: symmetry clash REVERT: A 18 ASN cc_start: 0.8935 (p0) cc_final: 0.8728 (p0) REVERT: A 154 MET cc_start: 0.8685 (mmt) cc_final: 0.8435 (mmm) REVERT: A 264 LYS cc_start: 0.8259 (mttt) cc_final: 0.8019 (mptt) REVERT: N 229 GLU cc_start: 0.8075 (pt0) cc_final: 0.7766 (pt0) REVERT: N 252 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7986 (tt0) REVERT: K 27 GLN cc_start: 0.6754 (mt0) cc_final: 0.5728 (tm-30) REVERT: K 95 LYS cc_start: 0.6848 (pttm) cc_final: 0.6031 (mmmt) REVERT: J 171 LYS cc_start: 0.7988 (mttt) cc_final: 0.7372 (mmmt) REVERT: J 266 LYS cc_start: 0.7438 (mtpp) cc_final: 0.7005 (pttt) REVERT: I 154 MET cc_start: 0.8671 (mmt) cc_final: 0.8433 (mmm) REVERT: I 264 LYS cc_start: 0.8297 (mttt) cc_final: 0.8026 (mptt) REVERT: F 229 GLU cc_start: 0.8109 (pt0) cc_final: 0.7800 (pt0) REVERT: F 252 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: C 27 GLN cc_start: 0.6660 (mt0) cc_final: 0.5673 (tm-30) REVERT: C 159 LYS cc_start: 0.7759 (mttt) cc_final: 0.7527 (mttm) REVERT: C 191 ILE cc_start: 0.6592 (mt) cc_final: 0.5966 (mt) REVERT: B 171 LYS cc_start: 0.7966 (mttt) cc_final: 0.7532 (mtpt) REVERT: B 266 LYS cc_start: 0.7452 (mtpp) cc_final: 0.7006 (pttt) REVERT: B 270 ASP cc_start: 0.8395 (t70) cc_final: 0.8177 (t0) outliers start: 51 outliers final: 39 residues processed: 296 average time/residue: 0.3050 time to fit residues: 135.5978 Evaluate side-chains 277 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 236 time to evaluate : 1.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 151 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 0.0040 chunk 129 optimal weight: 0.0970 chunk 52 optimal weight: 3.9990 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 155 ASN J 112 HIS I 44 GLN I 99 HIS I 155 ASN D 134 GLN B 112 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18902 Z= 0.181 Angle : 0.513 11.377 25916 Z= 0.275 Chirality : 0.040 0.148 2860 Planarity : 0.004 0.052 3010 Dihedral : 18.716 88.185 3203 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.13 % Allowed : 11.39 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.18), residues: 2032 helix: 1.47 (0.17), residues: 964 sheet: 0.26 (0.22), residues: 444 loop : -2.77 (0.20), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 19 HIS 0.005 0.001 HIS J 78 PHE 0.010 0.001 PHE I 1 TYR 0.009 0.001 TYR B 271 ARG 0.003 0.000 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 246 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8665 (mmt) cc_final: 0.8197 (mmm) REVERT: A 264 LYS cc_start: 0.8283 (mttt) cc_final: 0.8029 (mptt) REVERT: N 229 GLU cc_start: 0.8027 (pt0) cc_final: 0.7735 (pt0) REVERT: K 27 GLN cc_start: 0.6668 (mt0) cc_final: 0.5707 (tm-30) REVERT: K 95 LYS cc_start: 0.6524 (pttm) cc_final: 0.5912 (mmmt) REVERT: J 73 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8420 (mm) REVERT: J 171 LYS cc_start: 0.7926 (mttt) cc_final: 0.7514 (mtpt) REVERT: J 266 LYS cc_start: 0.7336 (mtpp) cc_final: 0.6892 (pttt) REVERT: I 154 MET cc_start: 0.8740 (mmt) cc_final: 0.8325 (mmm) REVERT: I 264 LYS cc_start: 0.8287 (mttt) cc_final: 0.8040 (mptt) REVERT: F 229 GLU cc_start: 0.8111 (pt0) cc_final: 0.7827 (pt0) REVERT: C 27 GLN cc_start: 0.6643 (mt0) cc_final: 0.5696 (tm-30) REVERT: C 159 LYS cc_start: 0.7822 (mttt) cc_final: 0.7525 (mttm) REVERT: C 166 ARG cc_start: 0.8452 (tpt90) cc_final: 0.8137 (tpt90) REVERT: B 73 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8436 (mm) REVERT: B 171 LYS cc_start: 0.7910 (mttt) cc_final: 0.7498 (mtpt) REVERT: B 266 LYS cc_start: 0.7407 (mtpp) cc_final: 0.6976 (pttt) REVERT: B 270 ASP cc_start: 0.8371 (t70) cc_final: 0.8142 (t0) outliers start: 55 outliers final: 40 residues processed: 282 average time/residue: 0.3278 time to fit residues: 135.6428 Evaluate side-chains 273 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 231 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.3980 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18902 Z= 0.195 Angle : 0.518 11.299 25916 Z= 0.277 Chirality : 0.041 0.146 2860 Planarity : 0.004 0.045 3010 Dihedral : 18.686 87.068 3190 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.56 % Allowed : 11.56 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.18), residues: 2032 helix: 1.75 (0.17), residues: 964 sheet: 0.28 (0.22), residues: 442 loop : -2.58 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 19 HIS 0.004 0.001 HIS I 51 PHE 0.010 0.001 PHE I 1 TYR 0.010 0.001 TYR K 83 ARG 0.003 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 245 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8704 (mmt) cc_final: 0.8400 (mmt) REVERT: A 264 LYS cc_start: 0.8278 (mttt) cc_final: 0.8037 (mptt) REVERT: N 229 GLU cc_start: 0.8159 (pt0) cc_final: 0.7891 (pt0) REVERT: L 87 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.6072 (mm-30) REVERT: K 27 GLN cc_start: 0.6674 (mt0) cc_final: 0.5717 (tm-30) REVERT: K 166 ARG cc_start: 0.8433 (tpt90) cc_final: 0.8190 (tpt90) REVERT: J 73 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8411 (mm) REVERT: J 171 LYS cc_start: 0.7926 (mttt) cc_final: 0.7524 (mtpt) REVERT: J 266 LYS cc_start: 0.7499 (mtpp) cc_final: 0.7126 (pttt) REVERT: I 154 MET cc_start: 0.8680 (mmt) cc_final: 0.8429 (mmt) REVERT: I 219 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7702 (ttmm) REVERT: I 264 LYS cc_start: 0.8280 (mttt) cc_final: 0.8042 (mptt) REVERT: F 229 GLU cc_start: 0.8153 (pt0) cc_final: 0.7899 (pt0) REVERT: D 87 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5909 (mm-30) REVERT: C 27 GLN cc_start: 0.6623 (mt0) cc_final: 0.5695 (tm-30) REVERT: C 159 LYS cc_start: 0.7875 (mttt) cc_final: 0.7578 (mttm) REVERT: C 166 ARG cc_start: 0.8380 (tpt90) cc_final: 0.8103 (tpt90) REVERT: B 25 ASP cc_start: 0.7650 (m-30) cc_final: 0.7280 (m-30) REVERT: B 73 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8386 (mm) REVERT: B 171 LYS cc_start: 0.7918 (mttt) cc_final: 0.7512 (mtpt) REVERT: B 266 LYS cc_start: 0.7482 (mtpp) cc_final: 0.6992 (pttt) outliers start: 80 outliers final: 64 residues processed: 305 average time/residue: 0.2919 time to fit residues: 132.1720 Evaluate side-chains 291 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 222 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 134 GLN K 183 HIS J 112 HIS D 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 18902 Z= 0.282 Angle : 0.579 11.170 25916 Z= 0.311 Chirality : 0.043 0.151 2860 Planarity : 0.004 0.044 3010 Dihedral : 18.755 86.662 3186 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.78 % Allowed : 12.24 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.15 (0.18), residues: 2032 helix: 1.66 (0.17), residues: 964 sheet: 0.11 (0.22), residues: 442 loop : -2.47 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 19 HIS 0.005 0.001 HIS K 12 PHE 0.015 0.002 PHE I 1 TYR 0.013 0.002 TYR C 83 ARG 0.003 0.000 ARG F 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 242 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7966 (mmtt) REVERT: A 154 MET cc_start: 0.8719 (mmt) cc_final: 0.8508 (mmt) REVERT: A 264 LYS cc_start: 0.8311 (mttt) cc_final: 0.8074 (mptt) REVERT: N 229 GLU cc_start: 0.8150 (pt0) cc_final: 0.7893 (pt0) REVERT: L 87 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6046 (mm-30) REVERT: K 27 GLN cc_start: 0.6823 (mt0) cc_final: 0.5765 (tm-30) REVERT: K 68 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7754 (tt) REVERT: K 159 LYS cc_start: 0.7852 (mttt) cc_final: 0.7562 (mttm) REVERT: K 166 ARG cc_start: 0.8406 (tpt90) cc_final: 0.8172 (tpt90) REVERT: J 73 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8364 (mm) REVERT: J 171 LYS cc_start: 0.7945 (mttt) cc_final: 0.7328 (mmmt) REVERT: J 266 LYS cc_start: 0.7501 (mtpp) cc_final: 0.7028 (pttt) REVERT: I 111 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7984 (mmtt) REVERT: I 264 LYS cc_start: 0.8314 (mttt) cc_final: 0.8079 (mptt) REVERT: F 229 GLU cc_start: 0.8161 (pt0) cc_final: 0.7908 (pt0) REVERT: D 87 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6047 (mm-30) REVERT: C 27 GLN cc_start: 0.6776 (mt0) cc_final: 0.5738 (tm-30) REVERT: C 68 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7709 (tt) REVERT: C 159 LYS cc_start: 0.7976 (mttt) cc_final: 0.7653 (mttm) REVERT: C 166 ARG cc_start: 0.8393 (tpt90) cc_final: 0.8103 (tpt90) REVERT: B 11 GLU cc_start: 0.7137 (tp30) cc_final: 0.6778 (mm-30) REVERT: B 73 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8335 (mm) REVERT: B 171 LYS cc_start: 0.7939 (mttt) cc_final: 0.7308 (mmmt) REVERT: B 266 LYS cc_start: 0.7502 (mtpp) cc_final: 0.7014 (pttt) outliers start: 84 outliers final: 71 residues processed: 309 average time/residue: 0.3179 time to fit residues: 145.0240 Evaluate side-chains 298 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 221 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 134 GLN J 112 HIS D 134 GLN B 112 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18902 Z= 0.192 Angle : 0.522 11.273 25916 Z= 0.279 Chirality : 0.041 0.146 2860 Planarity : 0.004 0.042 3010 Dihedral : 18.635 85.981 3186 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.33 % Allowed : 13.55 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.35 (0.18), residues: 2032 helix: 1.86 (0.17), residues: 966 sheet: 0.13 (0.22), residues: 442 loop : -2.40 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 19 HIS 0.004 0.001 HIS A 51 PHE 0.009 0.001 PHE A 1 TYR 0.009 0.001 TYR K 83 ARG 0.004 0.000 ARG N 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 243 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8701 (mmt) cc_final: 0.8211 (mmm) REVERT: A 219 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7587 (ttmt) REVERT: A 224 ARG cc_start: 0.6160 (mmt180) cc_final: 0.5645 (mtm-85) REVERT: A 264 LYS cc_start: 0.8285 (mttt) cc_final: 0.8069 (mptt) REVERT: N 229 GLU cc_start: 0.8103 (pt0) cc_final: 0.7847 (pt0) REVERT: L 87 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5952 (mm-30) REVERT: L 213 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.4446 (mp) REVERT: K 27 GLN cc_start: 0.6768 (mt0) cc_final: 0.5689 (tm-30) REVERT: K 68 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7738 (tt) REVERT: K 159 LYS cc_start: 0.7824 (mttt) cc_final: 0.7510 (mttm) REVERT: K 166 ARG cc_start: 0.8400 (tpt90) cc_final: 0.8181 (tpt90) REVERT: J 73 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8424 (mm) REVERT: J 171 LYS cc_start: 0.7906 (mttt) cc_final: 0.7272 (mmmt) REVERT: J 266 LYS cc_start: 0.7562 (mtpp) cc_final: 0.7155 (pttt) REVERT: I 219 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7818 (ttmm) REVERT: I 264 LYS cc_start: 0.8289 (mttt) cc_final: 0.8075 (mptt) REVERT: F 229 GLU cc_start: 0.8048 (pt0) cc_final: 0.7817 (pt0) REVERT: D 87 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5982 (mm-30) REVERT: C 27 GLN cc_start: 0.6732 (mt0) cc_final: 0.5667 (tm-30) REVERT: C 68 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7686 (tt) REVERT: C 159 LYS cc_start: 0.7914 (mttt) cc_final: 0.7591 (mttm) REVERT: B 73 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8427 (mm) REVERT: B 171 LYS cc_start: 0.7909 (mttt) cc_final: 0.7264 (mmmt) REVERT: B 266 LYS cc_start: 0.7557 (mtpp) cc_final: 0.7144 (pttt) outliers start: 76 outliers final: 61 residues processed: 296 average time/residue: 0.3258 time to fit residues: 141.7219 Evaluate side-chains 301 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 231 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain N residue 253 ASP Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 93 THR Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 0.0070 chunk 113 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 112 HIS J 134 GLN B 112 HIS B 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18902 Z= 0.150 Angle : 0.499 11.374 25916 Z= 0.264 Chirality : 0.040 0.143 2860 Planarity : 0.003 0.057 3010 Dihedral : 18.506 85.627 3185 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.59 % Allowed : 14.52 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.60 (0.19), residues: 2032 helix: 2.08 (0.17), residues: 966 sheet: 0.20 (0.22), residues: 444 loop : -2.29 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 19 HIS 0.003 0.001 HIS A 51 PHE 0.008 0.001 PHE A 100 TYR 0.007 0.001 TYR B 83 ARG 0.003 0.000 ARG N 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 241 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ASN cc_start: 0.8776 (p0) cc_final: 0.8530 (p0) REVERT: A 154 MET cc_start: 0.8805 (mmt) cc_final: 0.8322 (mmm) REVERT: A 264 LYS cc_start: 0.8272 (mttt) cc_final: 0.8061 (mptt) REVERT: N 229 GLU cc_start: 0.8074 (pt0) cc_final: 0.7841 (pt0) REVERT: L 87 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6242 (mm-30) REVERT: K 27 GLN cc_start: 0.6594 (mt0) cc_final: 0.5653 (tm-30) REVERT: K 68 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7646 (tt) REVERT: K 159 LYS cc_start: 0.7941 (mttt) cc_final: 0.7601 (mttm) REVERT: K 166 ARG cc_start: 0.8436 (tpt90) cc_final: 0.8236 (tpt90) REVERT: J 73 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8392 (mm) REVERT: J 171 LYS cc_start: 0.7879 (mttt) cc_final: 0.7253 (mmmt) REVERT: J 266 LYS cc_start: 0.7492 (mtpp) cc_final: 0.7044 (pttt) REVERT: I 219 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7560 (ttmt) REVERT: I 224 ARG cc_start: 0.6105 (mmt180) cc_final: 0.5613 (mtm-85) REVERT: I 264 LYS cc_start: 0.8292 (mttt) cc_final: 0.8064 (mptt) REVERT: F 229 GLU cc_start: 0.8045 (pt0) cc_final: 0.7817 (pt0) REVERT: D 87 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6187 (mm-30) REVERT: C 27 GLN cc_start: 0.6569 (mt0) cc_final: 0.5636 (tm-30) REVERT: C 68 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7661 (tt) REVERT: C 159 LYS cc_start: 0.7908 (mttt) cc_final: 0.7607 (mttm) REVERT: B 171 LYS cc_start: 0.7891 (mttt) cc_final: 0.7244 (mmmt) REVERT: B 266 LYS cc_start: 0.7485 (mtpp) cc_final: 0.7034 (pttt) outliers start: 63 outliers final: 50 residues processed: 288 average time/residue: 0.3179 time to fit residues: 134.9445 Evaluate side-chains 290 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 234 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 60 optimal weight: 0.0010 chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 112 HIS J 134 GLN B 112 HIS B 134 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18902 Z= 0.148 Angle : 0.495 11.341 25916 Z= 0.262 Chirality : 0.040 0.142 2860 Planarity : 0.003 0.059 3010 Dihedral : 18.415 84.976 3184 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.82 % Allowed : 14.52 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.19), residues: 2032 helix: 2.24 (0.17), residues: 958 sheet: 0.26 (0.22), residues: 444 loop : -2.27 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 19 HIS 0.003 0.001 HIS I 51 PHE 0.007 0.001 PHE I 100 TYR 0.008 0.001 TYR I 194 ARG 0.004 0.000 ARG L 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 240 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ASN cc_start: 0.8768 (p0) cc_final: 0.8513 (p0) REVERT: A 154 MET cc_start: 0.8794 (mmt) cc_final: 0.8318 (mmm) REVERT: A 224 ARG cc_start: 0.6080 (mmt180) cc_final: 0.5656 (mtm-85) REVERT: N 229 GLU cc_start: 0.7979 (pt0) cc_final: 0.7769 (pt0) REVERT: L 87 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6238 (mm-30) REVERT: K 27 GLN cc_start: 0.6571 (mt0) cc_final: 0.5659 (tm-30) REVERT: K 68 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7692 (tt) REVERT: K 159 LYS cc_start: 0.7936 (mttt) cc_final: 0.7599 (mttm) REVERT: J 25 ASP cc_start: 0.7498 (m-30) cc_final: 0.7168 (m-30) REVERT: J 73 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8384 (mm) REVERT: J 171 LYS cc_start: 0.7871 (mttt) cc_final: 0.7248 (mmmt) REVERT: J 266 LYS cc_start: 0.7446 (mtpp) cc_final: 0.7017 (pttt) REVERT: I 18 ASN cc_start: 0.8747 (p0) cc_final: 0.8513 (p0) REVERT: I 264 LYS cc_start: 0.8276 (mttt) cc_final: 0.8049 (mptt) REVERT: D 87 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6116 (mm-30) REVERT: C 27 GLN cc_start: 0.6545 (mt0) cc_final: 0.5639 (tm-30) REVERT: C 68 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7647 (tt) REVERT: C 159 LYS cc_start: 0.7911 (mttt) cc_final: 0.7604 (mttm) REVERT: B 7 LYS cc_start: 0.7857 (mttt) cc_final: 0.7645 (mttt) REVERT: B 73 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8395 (mm) REVERT: B 171 LYS cc_start: 0.7875 (mttt) cc_final: 0.7238 (mmmt) REVERT: B 266 LYS cc_start: 0.7440 (mtpp) cc_final: 0.7008 (pttt) outliers start: 67 outliers final: 53 residues processed: 290 average time/residue: 0.3108 time to fit residues: 133.4085 Evaluate side-chains 291 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 232 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 1.9990 chunk 176 optimal weight: 5.9990 chunk 188 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 112 HIS B 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18902 Z= 0.168 Angle : 0.510 11.376 25916 Z= 0.270 Chirality : 0.040 0.143 2860 Planarity : 0.003 0.055 3010 Dihedral : 18.433 83.480 3182 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.82 % Allowed : 14.58 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.19), residues: 2032 helix: 2.23 (0.17), residues: 958 sheet: 0.29 (0.22), residues: 442 loop : -2.27 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 19 HIS 0.003 0.001 HIS A 51 PHE 0.008 0.001 PHE I 1 TYR 0.009 0.001 TYR C 83 ARG 0.004 0.000 ARG D 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 240 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8694 (mmt) cc_final: 0.8200 (mmm) REVERT: A 219 LYS cc_start: 0.7978 (OUTLIER) cc_final: 0.7437 (ttmt) REVERT: A 224 ARG cc_start: 0.6218 (mmt180) cc_final: 0.5721 (ttm-80) REVERT: A 264 LYS cc_start: 0.8289 (mttp) cc_final: 0.7979 (mptt) REVERT: L 87 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.6087 (mm-30) REVERT: K 27 GLN cc_start: 0.6570 (mt0) cc_final: 0.5671 (tm-30) REVERT: K 68 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7623 (tt) REVERT: K 159 LYS cc_start: 0.7949 (mttt) cc_final: 0.7605 (mttm) REVERT: J 25 ASP cc_start: 0.7492 (m-30) cc_final: 0.7140 (m-30) REVERT: J 73 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8391 (mm) REVERT: J 171 LYS cc_start: 0.7876 (mttt) cc_final: 0.7249 (mmmt) REVERT: J 266 LYS cc_start: 0.7323 (mtpp) cc_final: 0.6965 (pttt) REVERT: I 18 ASN cc_start: 0.8807 (p0) cc_final: 0.8561 (p0) REVERT: I 224 ARG cc_start: 0.6125 (mmt180) cc_final: 0.5646 (mtm-85) REVERT: D 87 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6122 (mm-30) REVERT: C 27 GLN cc_start: 0.6549 (mt0) cc_final: 0.5652 (tm-30) REVERT: C 68 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7647 (tt) REVERT: C 159 LYS cc_start: 0.7916 (mttt) cc_final: 0.7610 (mttm) REVERT: B 73 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8398 (mm) REVERT: B 171 LYS cc_start: 0.7886 (mttt) cc_final: 0.7245 (mmmt) REVERT: B 266 LYS cc_start: 0.7327 (mtpp) cc_final: 0.6964 (pttt) outliers start: 67 outliers final: 56 residues processed: 288 average time/residue: 0.3468 time to fit residues: 148.3350 Evaluate side-chains 295 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 232 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 13 GLU Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 112 HIS B 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18902 Z= 0.157 Angle : 0.501 11.346 25916 Z= 0.265 Chirality : 0.040 0.142 2860 Planarity : 0.003 0.054 3010 Dihedral : 18.386 81.619 3182 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.59 % Allowed : 14.98 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.19), residues: 2032 helix: 2.27 (0.17), residues: 958 sheet: 0.33 (0.23), residues: 442 loop : -2.22 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 19 HIS 0.003 0.001 HIS A 51 PHE 0.007 0.001 PHE I 100 TYR 0.008 0.001 TYR C 83 ARG 0.004 0.000 ARG D 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 236 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 ASN cc_start: 0.8782 (p0) cc_final: 0.8562 (p0) REVERT: A 154 MET cc_start: 0.8798 (mmt) cc_final: 0.8316 (mmm) REVERT: A 219 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7406 (ttmt) REVERT: A 264 LYS cc_start: 0.8243 (mttp) cc_final: 0.7965 (mptt) REVERT: L 87 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6230 (mm-30) REVERT: K 27 GLN cc_start: 0.6551 (mt0) cc_final: 0.5668 (tm-30) REVERT: K 68 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7621 (tt) REVERT: K 159 LYS cc_start: 0.7906 (mttt) cc_final: 0.7570 (mttm) REVERT: J 25 ASP cc_start: 0.7461 (m-30) cc_final: 0.7112 (m-30) REVERT: J 73 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8376 (mm) REVERT: J 171 LYS cc_start: 0.7872 (mttt) cc_final: 0.7244 (mmmt) REVERT: J 266 LYS cc_start: 0.7353 (mtpp) cc_final: 0.7005 (pttt) REVERT: I 18 ASN cc_start: 0.8777 (p0) cc_final: 0.8525 (p0) REVERT: I 224 ARG cc_start: 0.6199 (mmt180) cc_final: 0.5674 (ttm-80) REVERT: I 264 LYS cc_start: 0.8247 (mttp) cc_final: 0.7977 (mptt) REVERT: D 87 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.6110 (mm-30) REVERT: C 27 GLN cc_start: 0.6526 (mt0) cc_final: 0.5651 (tm-30) REVERT: C 68 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7665 (tt) REVERT: C 159 LYS cc_start: 0.7914 (mttt) cc_final: 0.7609 (mttm) REVERT: B 25 ASP cc_start: 0.7497 (m-30) cc_final: 0.7149 (m-30) REVERT: B 73 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8387 (mm) REVERT: B 171 LYS cc_start: 0.7873 (mttt) cc_final: 0.7234 (mmmt) REVERT: B 266 LYS cc_start: 0.7352 (mtpp) cc_final: 0.7003 (pttt) outliers start: 63 outliers final: 55 residues processed: 283 average time/residue: 0.3178 time to fit residues: 131.7876 Evaluate side-chains 295 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 233 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 156 HIS Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 207 ASP Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain J residue 17 ASN Chi-restraints excluded: chain J residue 73 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain I residue 3 ASP Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 167 ASP Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 256 ASP Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 251 ILE Chi-restraints excluded: chain F residue 253 ASP Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 171 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 HIS I 39 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.165232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.151656 restraints weight = 19653.585| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 0.70 r_work: 0.3382 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work: 0.3117 rms_B_bonded: 4.79 restraints_weight: 0.1250 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 18902 Z= 0.428 Angle : 0.674 11.368 25916 Z= 0.362 Chirality : 0.048 0.164 2860 Planarity : 0.005 0.051 3010 Dihedral : 18.698 78.257 3182 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.87 % Allowed : 14.98 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.07 (0.18), residues: 2032 helix: 1.49 (0.16), residues: 958 sheet: -0.08 (0.22), residues: 446 loop : -2.51 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 19 HIS 0.006 0.002 HIS C 12 PHE 0.022 0.002 PHE I 1 TYR 0.017 0.002 TYR C 83 ARG 0.005 0.001 ARG L 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3903.53 seconds wall clock time: 72 minutes 51.66 seconds (4371.66 seconds total)