Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 19:07:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/04_2023/6rwo_10044_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/04_2023/6rwo_10044.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/04_2023/6rwo_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_10044/04_2023/6rwo_10044_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/04_2023/6rwo_10044_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/04_2023/6rwo_10044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/04_2023/6rwo_10044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/04_2023/6rwo_10044_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwo_10044/04_2023/6rwo_10044_updated.pdb" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 9.78, per 1000 atoms: 0.53 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: 7.04 Conformation dependent library (CDL) restraints added in 2.6 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: 6.02 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: 5.98 Time building geometry restraints manager: 7.55 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: 9590 17.41 - 34.83: 790 34.83 - 52.24: 455 52.24 - 69.66: 105 69.66 - 87.07: 10 Dihedral angle restraints: 10950 sinusoidal: 4976 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 10947 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: 2.730 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: 12.110 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 53.360 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.870 ------------------------------------------------------------------------------- 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 : 17.068 87.074 7070 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 % 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 *********************** 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 : 2.131 Fit side-chains revert: symmetry clash outliers start: 72 outliers final: 33 residues processed: 380 average time/residue: 0.3235 time to fit residues: 179.6780 Evaluate side-chains 264 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 time to evaluate : 1.920 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1589 time to fit residues: 12.5027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 190 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 155 ASN K 168 GLN J 9 GLN I 222 ASN D 134 GLN D 216 GLN D 252 GLN C 18 ASN C 117 ASN C 155 ASN C 168 GLN C 183 HIS B 9 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 18902 Z= 0.181 Angle : 0.532 11.259 25916 Z= 0.288 Chirality : 0.041 0.146 2860 Planarity : 0.004 0.052 3010 Dihedral : 18.495 88.448 3034 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.37 % 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: -0.82 (0.17), residues: 2032 helix: 0.66 (0.16), residues: 962 sheet: 0.10 (0.22), residues: 444 loop : -2.98 (0.20), residues: 626 *********************** 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 281 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 257 time to evaluate : 2.156 Fit side-chains outliers start: 24 outliers final: 16 residues processed: 269 average time/residue: 0.3228 time to fit residues: 128.8274 Evaluate side-chains 249 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 233 time to evaluate : 2.159 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1662 time to fit residues: 7.7048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 158 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 B 112 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 18902 Z= 0.386 Angle : 0.650 11.251 25916 Z= 0.350 Chirality : 0.046 0.155 2860 Planarity : 0.005 0.056 3010 Dihedral : 18.626 88.655 3034 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 2.90 % 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: -0.54 (0.18), residues: 2032 helix: 0.97 (0.16), residues: 972 sheet: 0.05 (0.22), residues: 440 loop : -2.87 (0.20), residues: 620 *********************** 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 294 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 243 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 274 average time/residue: 0.3368 time to fit residues: 134.9849 Evaluate side-chains 247 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1909 time to fit residues: 12.2446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 18902 Z= 0.142 Angle : 0.493 11.301 25916 Z= 0.264 Chirality : 0.040 0.143 2860 Planarity : 0.003 0.049 3010 Dihedral : 18.460 89.651 3034 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.91 % 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: 0.19 (0.18), residues: 2032 helix: 1.73 (0.17), residues: 966 sheet: 0.20 (0.22), residues: 432 loop : -2.56 (0.21), residues: 634 *********************** 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 257 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 241 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 249 average time/residue: 0.3434 time to fit residues: 125.5019 Evaluate side-chains 230 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 221 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1708 time to fit residues: 5.7881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 chunk 140 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS I 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 18902 Z= 0.296 Angle : 0.587 11.167 25916 Z= 0.315 Chirality : 0.044 0.148 2860 Planarity : 0.004 0.053 3010 Dihedral : 18.600 89.936 3034 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 1.14 % 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: 0.11 (0.18), residues: 2032 helix: 1.66 (0.17), residues: 964 sheet: 0.06 (0.22), residues: 442 loop : -2.53 (0.21), residues: 626 *********************** 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 245 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 2.130 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 238 average time/residue: 0.3417 time to fit residues: 120.1806 Evaluate side-chains 240 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 222 time to evaluate : 2.083 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1841 time to fit residues: 8.6500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 203 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 18902 Z= 0.149 Angle : 0.503 11.280 25916 Z= 0.267 Chirality : 0.040 0.142 2860 Planarity : 0.003 0.057 3010 Dihedral : 18.466 89.767 3034 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 0.57 % 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: 0.48 (0.19), residues: 2032 helix: 2.02 (0.17), residues: 966 sheet: 0.16 (0.22), residues: 444 loop : -2.42 (0.22), residues: 622 *********************** 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 249 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 239 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 241 average time/residue: 0.3545 time to fit residues: 126.5684 Evaluate side-chains 226 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1665 time to fit residues: 4.6029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 171 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 123 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 18902 Z= 0.174 Angle : 0.516 11.313 25916 Z= 0.275 Chirality : 0.041 0.198 2860 Planarity : 0.004 0.053 3010 Dihedral : 18.466 89.955 3034 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.63 % 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: 0.55 (0.19), residues: 2032 helix: 2.11 (0.17), residues: 958 sheet: 0.20 (0.22), residues: 444 loop : -2.39 (0.22), residues: 630 *********************** 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 238 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 227 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 229 average time/residue: 0.3547 time to fit residues: 119.0959 Evaluate side-chains 223 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 216 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1709 time to fit residues: 5.0622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 HIS B 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 18902 Z= 0.131 Angle : 0.488 11.341 25916 Z= 0.256 Chirality : 0.039 0.153 2860 Planarity : 0.003 0.060 3010 Dihedral : 18.287 89.110 3034 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.51 % 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: 0.82 (0.19), residues: 2032 helix: 2.35 (0.17), residues: 952 sheet: 0.35 (0.23), residues: 444 loop : -2.27 (0.22), residues: 636 *********************** 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 238 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 229 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 231 average time/residue: 0.3480 time to fit residues: 117.8714 Evaluate side-chains 219 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 212 time to evaluate : 1.992 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1618 time to fit residues: 4.9783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 7.9990 chunk 176 optimal weight: 30.0000 chunk 188 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS B 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2604 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= 0.206 Angle : 0.534 11.284 25916 Z= 0.283 Chirality : 0.041 0.149 2860 Planarity : 0.004 0.050 3010 Dihedral : 18.417 88.121 3034 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.28 % 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: 0.61 (0.19), residues: 2032 helix: 2.14 (0.17), residues: 958 sheet: 0.21 (0.22), residues: 444 loop : -2.31 (0.22), residues: 630 *********************** 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 224 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 219 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 220 average time/residue: 0.3476 time to fit residues: 112.3159 Evaluate side-chains 218 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 2.033 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1615 time to fit residues: 4.0339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 8.9990 chunk 121 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 166 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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** D 134 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 18902 Z= 0.305 Angle : 0.607 11.456 25916 Z= 0.325 Chirality : 0.044 0.180 2860 Planarity : 0.004 0.058 3010 Dihedral : 18.535 83.394 3034 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.40 % 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: 0.23 (0.18), residues: 2032 helix: 1.73 (0.17), residues: 966 sheet: 0.05 (0.22), residues: 444 loop : -2.39 (0.22), residues: 622 ********************** 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 227 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 220 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 223 average time/residue: 0.3555 time to fit residues: 116.2351 Evaluate side-chains 218 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 212 time to evaluate : 2.212 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1746 time to fit residues: 4.9066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 166 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN D 134 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.167331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.151069 restraints weight = 19586.546| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 0.84 r_work: 0.3374 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work: 0.3197 rms_B_bonded: 4.05 restraints_weight: 0.1250 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 18902 Z= 0.304 Angle : 0.604 11.276 25916 Z= 0.322 Chirality : 0.044 0.178 2860 Planarity : 0.004 0.051 3010 Dihedral : 18.517 82.661 3034 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.40 % 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: 0.08 (0.18), residues: 2032 helix: 1.61 (0.16), residues: 968 sheet: -0.09 (0.22), residues: 444 loop : -2.43 (0.22), residues: 620 =============================================================================== Job complete usr+sys time: 3692.90 seconds wall clock time: 68 minutes 4.68 seconds (4084.68 seconds total)