Starting phenix.real_space_refine on Mon Aug 5 22:07:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt8_37829/08_2024/8wt8_37829.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt8_37829/08_2024/8wt8_37829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt8_37829/08_2024/8wt8_37829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt8_37829/08_2024/8wt8_37829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt8_37829/08_2024/8wt8_37829.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wt8_37829/08_2024/8wt8_37829.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 241 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 8521 2.51 5 N 2759 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 102": "OD1" <-> "OD2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ASP 102": "OD1" <-> "OD2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D ARG 320": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14916 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2429 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 306, 2420 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 bond proxies already assigned to first conformer: 2457 Chain: "B" Number of atoms: 2527 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2507 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Conformer: "B" Number of residues, atoms: 318, 2507 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} bond proxies already assigned to first conformer: 2534 Chain: "C" Number of atoms: 2420 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 305, 2411 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 305, 2411 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 bond proxies already assigned to first conformer: 2448 Chain: "D" Number of atoms: 2513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 317, 2498 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 12, 'TRANS': 304} Conformer: "B" Number of residues, atoms: 317, 2498 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 12, 'TRANS': 304} bond proxies already assigned to first conformer: 2530 Chain: "E" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1249 Classifications: {'RNA': 59} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 11, 'rna3p_pur': 22, 'rna3p_pyr': 22} Link IDs: {'rna2p': 15, 'rna3p': 43} Chain: "F" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1442 Classifications: {'RNA': 68} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 27, 'rna3p_pyr': 27} Link IDs: {'rna2p': 13, 'rna3p': 54} Chain: "G" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 580 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "H" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 557 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "I" Number of atoms: 596 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Conformer: "B" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 bond proxies already assigned to first conformer: 576 Chain: "J" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 602 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AGLN A 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 139 " occ=0.50 residue: pdb=" N AGLN B 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 139 " occ=0.50 residue: pdb=" N AARG B 261 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 261 " occ=0.50 residue: pdb=" N AGLN C 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN C 139 " occ=0.50 residue: pdb=" N AGLN D 139 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN D 139 " occ=0.50 residue: pdb=" N ASER D 241 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 241 " occ=0.50 residue: pdb=" P A DT I 20 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B DT I 20 " occ=0.50 residue: pdb=" P A DA I 21 " occ=0.50 ... (40 atoms not shown) pdb=" C4 B DA I 21 " occ=0.50 residue: pdb="MG B MG I 101 " occ=0.50 Time building chain proxies: 14.05, per 1000 atoms: 0.94 Number of scatterers: 14916 At special positions: 0 Unit cell: (119.52, 123.947, 110.667, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 241 15.00 Mg 1 11.99 O 3346 8.00 N 2759 7.00 C 8521 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: 7.19 Conformation dependent library (CDL) restraints added in 3.4 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 68.6% alpha, 9.9% beta 89 base pairs and 149 stacking pairs defined. Time for finding SS restraints: 6.69 Creating SS restraints... Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 66 through 77 Processing helix chain 'A' and resid 84 through 95 removed outlier: 3.668A pdb=" N GLY A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 125 through 152 Processing helix chain 'A' and resid 153 through 155 No H-bonds generated for 'chain 'A' and resid 153 through 155' Processing helix chain 'A' and resid 159 through 188 removed outlier: 3.640A pdb=" N ASP A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 Processing helix chain 'A' and resid 205 through 217 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.672A pdb=" N PHE A 228 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.576A pdb=" N ALA A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 274 through 288 removed outlier: 3.508A pdb=" N ASN A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 313 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.521A pdb=" N ARG A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 84 through 96 removed outlier: 3.589A pdb=" N GLY B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 125 through 154 removed outlier: 3.861A pdb=" N GLU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 188 removed outlier: 3.639A pdb=" N ASP B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 200 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.654A pdb=" N ALA B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.766A pdb=" N PHE B 228 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 263 Processing helix chain 'B' and resid 263 through 274 removed outlier: 3.501A pdb=" N SER B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 removed outlier: 3.876A pdb=" N ASN B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 313 removed outlier: 3.503A pdb=" N LEU B 310 " --> pdb=" O ALA B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 321 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 66 through 77 Processing helix chain 'C' and resid 84 through 96 Processing helix chain 'C' and resid 101 through 117 removed outlier: 3.557A pdb=" N ARG C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 154 removed outlier: 3.800A pdb=" N GLU C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 188 removed outlier: 3.620A pdb=" N ASP C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 200 Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.542A pdb=" N ALA C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.746A pdb=" N PHE C 228 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.501A pdb=" N ALA C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 290 through 313 Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.617A pdb=" N ARG C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 50 Processing helix chain 'D' and resid 66 through 77 Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.589A pdb=" N GLY D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 125 through 154 removed outlier: 3.990A pdb=" N GLU D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 188 removed outlier: 3.689A pdb=" N ASP D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 removed outlier: 3.803A pdb=" N ILE D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.557A pdb=" N ALA D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.606A pdb=" N PHE D 228 " --> pdb=" O HIS D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 263 removed outlier: 3.595A pdb=" N LEU D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 274 Processing helix chain 'D' and resid 274 through 288 Processing helix chain 'D' and resid 290 through 313 Processing helix chain 'D' and resid 317 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 34 removed outlier: 6.576A pdb=" N HIS A 6 " --> pdb=" O HIS A 56 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N CYS A 58 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 8 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLU A 60 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ILE A 10 " --> pdb=" O GLU A 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 28 through 34 removed outlier: 6.766A pdb=" N HIS B 6 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N CYS B 58 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE B 8 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N GLU B 60 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ILE B 10 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA B 55 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N SER B 81 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE B 57 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE B 83 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 59 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 236 through 237 removed outlier: 3.853A pdb=" N ARG B 250 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 240 through 241 Processing sheet with id=AA5, first strand: chain 'C' and resid 28 through 34 removed outlier: 6.290A pdb=" N HIS C 6 " --> pdb=" O HIS C 56 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N CYS C 58 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE C 8 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLU C 60 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE C 10 " --> pdb=" O GLU C 60 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 28 through 34 removed outlier: 4.462A pdb=" N GLU D 60 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR D 12 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA D 55 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N SER D 81 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE D 57 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE D 83 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE D 59 " --> pdb=" O ILE D 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 236 through 241 removed outlier: 3.764A pdb=" N ARG D 250 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N TYR D 239 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ALA D 248 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASER D 241 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG D 246 " --> pdb=" O ASER D 241 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 2000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 227 hydrogen bonds 450 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 152 stacking parallelities Total time for adding SS restraints: 5.91 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3712 1.34 - 1.46: 5158 1.46 - 1.58: 6275 1.58 - 1.69: 476 1.69 - 1.81: 84 Bond restraints: 15705 Sorted by residual: bond pdb=" C ILE D 201 " pdb=" N PRO D 202 " ideal model delta sigma weight residual 1.335 1.356 -0.021 8.70e-03 1.32e+04 5.94e+00 bond pdb=" O5' A E 68 " pdb=" C5' A E 68 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.87e+00 bond pdb=" O5' G F 133 " pdb=" C5' G F 133 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.63e+00 bond pdb=" O5' G F 169 " pdb=" C5' G F 169 " ideal model delta sigma weight residual 1.420 1.456 -0.036 1.50e-02 4.44e+03 5.60e+00 bond pdb=" P DT G 10 " pdb=" OP1 DT G 10 " ideal model delta sigma weight residual 1.480 1.527 -0.047 2.00e-02 2.50e+03 5.57e+00 ... (remaining 15700 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.21: 957 104.21 - 111.77: 7283 111.77 - 119.34: 6566 119.34 - 126.91: 6756 126.91 - 134.47: 728 Bond angle restraints: 22290 Sorted by residual: angle pdb=" O3' DA G 32 " pdb=" P DT G 33 " pdb=" O5' DT G 33 " ideal model delta sigma weight residual 104.00 96.64 7.36 1.50e+00 4.44e-01 2.41e+01 angle pdb=" O3' DT G 31 " pdb=" P DA G 32 " pdb=" O5' DA G 32 " ideal model delta sigma weight residual 104.00 97.25 6.75 1.50e+00 4.44e-01 2.03e+01 angle pdb=" CA ASP C 25 " pdb=" CB ASP C 25 " pdb=" CG ASP C 25 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" O3' DT G 33 " pdb=" P DC G 34 " pdb=" O5' DC G 34 " ideal model delta sigma weight residual 104.00 97.41 6.59 1.50e+00 4.44e-01 1.93e+01 angle pdb=" O3' G F 138 " pdb=" P G F 139 " pdb=" O5' G F 139 " ideal model delta sigma weight residual 104.00 97.44 6.56 1.50e+00 4.44e-01 1.91e+01 ... (remaining 22285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 8697 35.61 - 71.21: 678 71.21 - 106.82: 49 106.82 - 142.42: 0 142.42 - 178.03: 2 Dihedral angle restraints: 9426 sinusoidal: 5800 harmonic: 3626 Sorted by residual: dihedral pdb=" O4' U F 159 " pdb=" C1' U F 159 " pdb=" N1 U F 159 " pdb=" C2 U F 159 " ideal model delta sinusoidal sigma weight residual 232.00 53.97 178.03 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C5' U F 168 " pdb=" C4' U F 168 " pdb=" C3' U F 168 " pdb=" O3' U F 168 " ideal model delta sinusoidal sigma weight residual 147.00 98.77 48.23 1 8.00e+00 1.56e-02 5.01e+01 dihedral pdb=" O4' U F 168 " pdb=" C4' U F 168 " pdb=" C3' U F 168 " pdb=" C2' U F 168 " ideal model delta sinusoidal sigma weight residual 24.00 -14.47 38.47 1 8.00e+00 1.56e-02 3.26e+01 ... (remaining 9423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 2309 0.135 - 0.271: 265 0.271 - 0.406: 1 0.406 - 0.542: 0 0.542 - 0.677: 6 Chirality restraints: 2581 Sorted by residual: chirality pdb=" P DT G 10 " pdb=" OP1 DT G 10 " pdb=" OP2 DT G 10 " pdb=" O5' DT G 10 " both_signs ideal model delta sigma weight residual True 2.35 -3.02 -0.68 2.00e-01 2.50e+01 1.15e+01 chirality pdb=" P DA H 3 " pdb=" OP1 DA H 3 " pdb=" OP2 DA H 3 " pdb=" O5' DA H 3 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DG J 12 " pdb=" OP1 DG J 12 " pdb=" OP2 DG J 12 " pdb=" O5' DG J 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 2578 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A F 157 " -0.024 2.00e-02 2.50e+03 9.85e-03 2.67e+00 pdb=" N9 A F 157 " 0.015 2.00e-02 2.50e+03 pdb=" C8 A F 157 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A F 157 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A F 157 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A F 157 " -0.006 2.00e-02 2.50e+03 pdb=" N6 A F 157 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A F 157 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A F 157 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A F 157 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A F 157 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA G 29 " 0.020 2.00e-02 2.50e+03 8.85e-03 2.15e+00 pdb=" N9 DA G 29 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA G 29 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA G 29 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA G 29 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA G 29 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA G 29 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA G 29 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA G 29 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA G 29 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA G 29 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U E 74 " -0.021 2.00e-02 2.50e+03 9.59e-03 2.07e+00 pdb=" N1 U E 74 " 0.013 2.00e-02 2.50e+03 pdb=" C2 U E 74 " 0.005 2.00e-02 2.50e+03 pdb=" O2 U E 74 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U E 74 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U E 74 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U E 74 " -0.005 2.00e-02 2.50e+03 pdb=" C5 U E 74 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U E 74 " 0.010 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 5 2.27 - 2.93: 5256 2.93 - 3.58: 22124 3.58 - 4.24: 40380 4.24 - 4.90: 61660 Nonbonded interactions: 129425 Sorted by model distance: nonbonded pdb=" OG BSER D 241 " pdb=" P B DA I 21 " model vdw 1.611 3.400 nonbonded pdb=" OE2 GLU A 60 " pdb="MG B MG I 101 " model vdw 2.078 2.170 nonbonded pdb=" O3'B DT I 20 " pdb="MG B MG I 101 " model vdw 2.085 2.170 nonbonded pdb=" OP1B DA I 21 " pdb="MG B MG I 101 " model vdw 2.091 2.170 nonbonded pdb=" OD1 ASP A 11 " pdb="MG B MG I 101 " model vdw 2.103 2.170 ... (remaining 129420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 138 or resid 140 through 260 or resid 262 throug \ h 321)) selection = (chain 'B' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ h 260 or resid 262 through 321)) selection = (chain 'C' and (resid 5 through 138 or resid 140 through 260 or resid 262 throug \ h 321)) selection = (chain 'D' and (resid 5 through 138 or resid 140 through 238 or resid 251 throug \ h 260 or resid 262 through 321)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 56.490 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 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 : 0.008 0.047 15705 Z= 0.495 Angle : 1.330 7.360 22290 Z= 0.862 Chirality : 0.079 0.677 2581 Planarity : 0.003 0.026 1996 Dihedral : 20.482 178.027 7082 Min Nonbonded Distance : 1.611 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.59 % Allowed : 2.46 % Favored : 96.95 % 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: -2.17 (0.19), residues: 1252 helix: -1.14 (0.14), residues: 807 sheet: -1.67 (0.35), residues: 150 loop : -1.49 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP C 169 HIS 0.006 0.002 HIS D 256 PHE 0.015 0.002 PHE A 231 TYR 0.017 0.002 TYR D 78 ARG 0.013 0.002 ARG D 300 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.367 Fit side-chains REVERT: A 268 MET cc_start: 0.8145 (mtm) cc_final: 0.7889 (mtp) outliers start: 5 outliers final: 0 residues processed: 120 average time/residue: 1.8895 time to fit residues: 243.3867 Evaluate side-chains 78 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 0.0030 chunk 57 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 28 HIS C 54 HIS C 115 GLN D 54 HIS D 93 GLN D 287 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15705 Z= 0.250 Angle : 0.616 7.518 22290 Z= 0.344 Chirality : 0.040 0.236 2581 Planarity : 0.004 0.037 1996 Dihedral : 22.581 168.070 4635 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.08 % Allowed : 7.17 % Favored : 91.75 % 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: 1.25 (0.23), residues: 1252 helix: 1.82 (0.17), residues: 814 sheet: -0.99 (0.36), residues: 138 loop : -0.96 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 46 HIS 0.007 0.001 HIS B 256 PHE 0.012 0.002 PHE B 112 TYR 0.020 0.002 TYR D 215 ARG 0.008 0.001 ARG D 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.285 Fit side-chains REVERT: B 191 MET cc_start: 0.8381 (mtm) cc_final: 0.8127 (mtm) REVERT: D 265 MET cc_start: 0.8169 (mmm) cc_final: 0.7687 (mmm) outliers start: 10 outliers final: 1 residues processed: 83 average time/residue: 1.5862 time to fit residues: 143.2147 Evaluate side-chains 71 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 0.0570 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 6 HIS C 115 GLN D 54 HIS D 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15705 Z= 0.278 Angle : 0.566 7.618 22290 Z= 0.317 Chirality : 0.039 0.196 2581 Planarity : 0.005 0.100 1996 Dihedral : 22.649 173.071 4635 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.08 % Allowed : 7.76 % Favored : 91.16 % 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: 1.87 (0.24), residues: 1252 helix: 2.29 (0.18), residues: 817 sheet: -0.67 (0.36), residues: 142 loop : -0.78 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 46 HIS 0.006 0.001 HIS C 54 PHE 0.011 0.002 PHE B 112 TYR 0.015 0.002 TYR D 307 ARG 0.017 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.266 Fit side-chains REVERT: B 238 ARG cc_start: 0.7350 (mtp180) cc_final: 0.7038 (tpt90) outliers start: 10 outliers final: 0 residues processed: 80 average time/residue: 1.5069 time to fit residues: 131.7301 Evaluate side-chains 71 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 304 GLN D 54 HIS D 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15705 Z= 0.211 Angle : 0.517 8.469 22290 Z= 0.288 Chirality : 0.036 0.185 2581 Planarity : 0.004 0.073 1996 Dihedral : 22.696 174.888 4635 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.08 % Allowed : 7.86 % Favored : 91.06 % 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: 2.22 (0.24), residues: 1252 helix: 2.53 (0.18), residues: 818 sheet: -0.34 (0.35), residues: 143 loop : -0.69 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 46 HIS 0.004 0.001 HIS D 166 PHE 0.009 0.001 PHE B 112 TYR 0.016 0.001 TYR C 307 ARG 0.009 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.523 Fit side-chains REVERT: B 27 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7614 (mtm180) REVERT: B 215 TYR cc_start: 0.8847 (m-80) cc_final: 0.8600 (m-80) REVERT: B 238 ARG cc_start: 0.7339 (mtp180) cc_final: 0.7028 (tpt90) REVERT: D 265 MET cc_start: 0.8000 (mmm) cc_final: 0.7567 (mmm) outliers start: 10 outliers final: 1 residues processed: 82 average time/residue: 1.6746 time to fit residues: 149.5593 Evaluate side-chains 75 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain D residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 99 ASN D 54 HIS D 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15705 Z= 0.178 Angle : 0.505 8.394 22290 Z= 0.280 Chirality : 0.034 0.180 2581 Planarity : 0.004 0.040 1996 Dihedral : 22.615 176.154 4635 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.98 % Allowed : 8.74 % Favored : 90.28 % 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: 2.43 (0.24), residues: 1252 helix: 2.69 (0.18), residues: 819 sheet: -0.18 (0.35), residues: 137 loop : -0.69 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 46 HIS 0.007 0.001 HIS C 54 PHE 0.010 0.001 PHE B 112 TYR 0.018 0.001 TYR C 307 ARG 0.023 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 78 time to evaluate : 1.327 Fit side-chains REVERT: B 27 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7540 (mtm180) REVERT: B 215 TYR cc_start: 0.8788 (m-80) cc_final: 0.8559 (m-80) REVERT: B 238 ARG cc_start: 0.7374 (mtp180) cc_final: 0.7045 (tpt90) REVERT: D 265 MET cc_start: 0.8054 (mmm) cc_final: 0.7849 (mmm) outliers start: 9 outliers final: 1 residues processed: 79 average time/residue: 1.6534 time to fit residues: 143.3553 Evaluate side-chains 74 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 144 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 99 ASN D 93 GLN D 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 15705 Z= 0.524 Angle : 0.635 8.311 22290 Z= 0.345 Chirality : 0.044 0.199 2581 Planarity : 0.005 0.043 1996 Dihedral : 22.717 172.612 4635 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.79 % Allowed : 9.72 % Favored : 89.49 % 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: 2.13 (0.24), residues: 1252 helix: 2.47 (0.18), residues: 819 sheet: -0.28 (0.35), residues: 143 loop : -0.83 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 46 HIS 0.009 0.001 HIS D 166 PHE 0.015 0.003 PHE C 231 TYR 0.023 0.002 TYR C 307 ARG 0.011 0.001 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 1.277 Fit side-chains REVERT: B 27 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7634 (mtm180) REVERT: B 51 LYS cc_start: 0.8656 (tppp) cc_final: 0.8452 (tppp) REVERT: B 238 ARG cc_start: 0.7491 (mtp180) cc_final: 0.7188 (tpt90) outliers start: 7 outliers final: 1 residues processed: 71 average time/residue: 1.5767 time to fit residues: 121.9797 Evaluate side-chains 72 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 144 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 84 optimal weight: 0.0980 chunk 54 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 99 ASN C 40 HIS D 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15705 Z= 0.166 Angle : 0.512 8.919 22290 Z= 0.281 Chirality : 0.034 0.178 2581 Planarity : 0.004 0.040 1996 Dihedral : 22.617 174.906 4635 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.49 % Allowed : 9.92 % Favored : 89.59 % 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: 2.42 (0.24), residues: 1252 helix: 2.68 (0.18), residues: 819 sheet: -0.07 (0.35), residues: 139 loop : -0.74 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 46 HIS 0.005 0.001 HIS C 54 PHE 0.010 0.001 PHE C 280 TYR 0.012 0.001 TYR D 307 ARG 0.013 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.265 Fit side-chains REVERT: B 51 LYS cc_start: 0.8619 (tppp) cc_final: 0.8417 (tppp) REVERT: B 144 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7852 (ttp) REVERT: B 238 ARG cc_start: 0.7401 (mtp180) cc_final: 0.7054 (tpt90) outliers start: 4 outliers final: 0 residues processed: 71 average time/residue: 1.4694 time to fit residues: 114.2256 Evaluate side-chains 71 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN D 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15705 Z= 0.253 Angle : 0.528 8.837 22290 Z= 0.289 Chirality : 0.036 0.181 2581 Planarity : 0.004 0.047 1996 Dihedral : 22.590 175.200 4635 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.39 % Allowed : 10.02 % Favored : 89.59 % 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: 2.45 (0.24), residues: 1252 helix: 2.71 (0.18), residues: 819 sheet: -0.04 (0.35), residues: 139 loop : -0.74 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 46 HIS 0.006 0.001 HIS D 166 PHE 0.010 0.002 PHE B 112 TYR 0.021 0.002 TYR C 307 ARG 0.014 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 1.297 Fit side-chains REVERT: B 27 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7536 (mtm180) REVERT: B 51 LYS cc_start: 0.8635 (tppp) cc_final: 0.8432 (tppp) REVERT: B 238 ARG cc_start: 0.7422 (mtp180) cc_final: 0.7096 (tpt90) REVERT: D 265 MET cc_start: 0.8126 (mmm) cc_final: 0.7534 (mmm) outliers start: 3 outliers final: 1 residues processed: 74 average time/residue: 1.6009 time to fit residues: 130.4276 Evaluate side-chains 74 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain B residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN D 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15705 Z= 0.176 Angle : 0.510 9.356 22290 Z= 0.280 Chirality : 0.034 0.182 2581 Planarity : 0.004 0.053 1996 Dihedral : 22.596 175.681 4635 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.69 % Allowed : 10.22 % Favored : 89.10 % 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: 2.48 (0.24), residues: 1252 helix: 2.72 (0.18), residues: 819 sheet: 0.03 (0.35), residues: 137 loop : -0.71 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 276 HIS 0.004 0.001 HIS C 54 PHE 0.009 0.001 PHE B 112 TYR 0.021 0.001 TYR C 307 ARG 0.014 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.295 Fit side-chains REVERT: B 27 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7497 (mtm180) REVERT: B 51 LYS cc_start: 0.8626 (tppp) cc_final: 0.8421 (tppp) REVERT: B 238 ARG cc_start: 0.7403 (mtp180) cc_final: 0.7079 (tpt90) REVERT: C 66 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7247 (ppp) REVERT: D 265 MET cc_start: 0.8051 (mmm) cc_final: 0.7442 (mmm) outliers start: 6 outliers final: 0 residues processed: 75 average time/residue: 1.6235 time to fit residues: 132.3549 Evaluate side-chains 74 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain C residue 66 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 111 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 287 ASN D 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15705 Z= 0.291 Angle : 0.537 9.010 22290 Z= 0.293 Chirality : 0.037 0.185 2581 Planarity : 0.004 0.052 1996 Dihedral : 22.591 174.820 4635 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.69 % Allowed : 10.22 % Favored : 89.10 % 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: 2.45 (0.24), residues: 1252 helix: 2.69 (0.18), residues: 819 sheet: 0.05 (0.35), residues: 137 loop : -0.75 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 46 HIS 0.005 0.001 HIS C 54 PHE 0.010 0.002 PHE B 112 TYR 0.023 0.002 TYR C 307 ARG 0.015 0.000 ARG C 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.381 Fit side-chains REVERT: B 27 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7497 (mtm180) REVERT: B 238 ARG cc_start: 0.7436 (mtp180) cc_final: 0.7127 (tpt90) REVERT: C 66 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7298 (ppp) REVERT: D 265 MET cc_start: 0.8106 (mmm) cc_final: 0.7465 (mmm) outliers start: 6 outliers final: 0 residues processed: 75 average time/residue: 1.7382 time to fit residues: 141.6468 Evaluate side-chains 76 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ARG Chi-restraints excluded: chain C residue 66 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 31 optimal weight: 7.9990 chunk 112 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 50 HIS C 287 ASN D 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.094259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.060441 restraints weight = 109768.623| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 3.61 r_work: 0.2663 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15705 Z= 0.167 Angle : 0.515 9.604 22290 Z= 0.281 Chirality : 0.034 0.184 2581 Planarity : 0.004 0.053 1996 Dihedral : 22.597 175.458 4635 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.13 % Favored : 98.78 % Rotamer: Outliers : 0.88 % Allowed : 10.31 % Favored : 88.80 % 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: 2.50 (0.24), residues: 1252 helix: 2.71 (0.18), residues: 819 sheet: 0.12 (0.36), residues: 139 loop : -0.68 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 46 HIS 0.004 0.001 HIS C 54 PHE 0.009 0.001 PHE B 112 TYR 0.021 0.001 TYR C 307 ARG 0.015 0.000 ARG C 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3600.26 seconds wall clock time: 65 minutes 21.70 seconds (3921.70 seconds total)