Starting phenix.real_space_refine on Thu Mar 21 22:21:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/03_2024/8spo_40680_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/03_2024/8spo_40680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/03_2024/8spo_40680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/03_2024/8spo_40680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/03_2024/8spo_40680_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spo_40680/03_2024/8spo_40680_neut_updated.pdb" } resolution = 2.98 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= 0.019 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 158 5.49 5 Mg 4 5.21 5 S 85 5.16 5 C 19663 2.51 5 N 5212 2.21 5 O 6185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 186": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31307 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3393 Classifications: {'peptide': 407} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 394} Chain breaks: 1 Chain: "B" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 372 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "E" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3140 Classifications: {'peptide': 380} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 369} Chain breaks: 3 Chain: "F" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20} Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "I" Number of atoms: 3063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3063 Classifications: {'peptide': 371} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 360} Chain breaks: 3 Chain: "J" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "K" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "L" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "M" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3265 Classifications: {'peptide': 394} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 383} Chain breaks: 2 Chain: "N" Number of atoms: 3787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3787 Classifications: {'peptide': 469} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "O" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 399 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 16} Chain: "P" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.95, per 1000 atoms: 0.54 Number of scatterers: 31307 At special positions: 0 Unit cell: (118.668, 176.204, 231.043, 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 85 16.00 P 158 15.00 Mg 4 11.99 O 6185 8.00 N 5212 7.00 C 19663 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: 12.70 Conformation dependent library (CDL) restraints added in 5.4 seconds 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6522 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 37 sheets defined 31.2% alpha, 14.8% beta 33 base pairs and 117 stacking pairs defined. Time for finding SS restraints: 14.20 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 Processing helix chain 'A' and resid 49 through 55 Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 148 through 158 removed outlier: 3.519A pdb=" N ILE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 258 through 279 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 370 through 384 removed outlier: 3.600A pdb=" N LEU A 384 " --> pdb=" O PHE A 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 23 through 29 Processing helix chain 'B' and resid 47 through 59 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 110 through 130 removed outlier: 3.646A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 150 removed outlier: 3.655A pdb=" N TYR B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 226 through 229 No H-bonds generated for 'chain 'B' and resid 226 through 229' Processing helix chain 'B' and resid 249 through 263 Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'B' and resid 367 through 374 Processing helix chain 'B' and resid 452 through 464 removed outlier: 3.728A pdb=" N THR B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.786A pdb=" N ALA B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'E' and resid 15 through 28 Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.626A pdb=" N ILE E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 88 Processing helix chain 'E' and resid 110 through 113 No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'E' and resid 125 through 138 Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 258 through 279 Processing helix chain 'E' and resid 354 through 366 removed outlier: 3.563A pdb=" N LYS E 366 " --> pdb=" O ARG E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 384 removed outlier: 3.768A pdb=" N LEU E 384 " --> pdb=" O PHE E 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 47 through 61 removed outlier: 3.899A pdb=" N GLN F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'F' and resid 98 through 104 Processing helix chain 'F' and resid 110 through 130 removed outlier: 3.679A pdb=" N LYS F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 206 through 213 Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 249 through 263 Processing helix chain 'F' and resid 332 through 350 Processing helix chain 'F' and resid 367 through 376 removed outlier: 3.965A pdb=" N VAL F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 463 removed outlier: 3.880A pdb=" N THR F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 480 No H-bonds generated for 'chain 'F' and resid 478 through 480' Processing helix chain 'F' and resid 482 through 491 removed outlier: 3.660A pdb=" N THR F 491 " --> pdb=" O GLY F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 505 No H-bonds generated for 'chain 'F' and resid 503 through 505' Processing helix chain 'I' and resid 15 through 28 Processing helix chain 'I' and resid 45 through 55 Processing helix chain 'I' and resid 72 through 88 Processing helix chain 'I' and resid 124 through 138 Processing helix chain 'I' and resid 150 through 155 Processing helix chain 'I' and resid 243 through 248 removed outlier: 4.215A pdb=" N SER I 248 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 279 Processing helix chain 'I' and resid 354 through 366 removed outlier: 3.669A pdb=" N LYS I 366 " --> pdb=" O ARG I 362 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 384 Processing helix chain 'L' and resid 15 through 17 No H-bonds generated for 'chain 'L' and resid 15 through 17' Processing helix chain 'L' and resid 23 through 29 Processing helix chain 'L' and resid 47 through 61 removed outlier: 3.790A pdb=" N GLN L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 98 through 104 Processing helix chain 'L' and resid 110 through 130 removed outlier: 4.109A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE L 125 " --> pdb=" O PHE L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 148 No H-bonds generated for 'chain 'L' and resid 145 through 148' Processing helix chain 'L' and resid 206 through 213 Processing helix chain 'L' and resid 226 through 229 No H-bonds generated for 'chain 'L' and resid 226 through 229' Processing helix chain 'L' and resid 249 through 263 Processing helix chain 'L' and resid 332 through 350 removed outlier: 3.591A pdb=" N ALA L 337 " --> pdb=" O LYS L 333 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU L 338 " --> pdb=" O GLU L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 372 removed outlier: 3.595A pdb=" N ALA L 372 " --> pdb=" O GLN L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 463 removed outlier: 3.741A pdb=" N THR L 463 " --> pdb=" O ILE L 459 " (cutoff:3.500A) Processing helix chain 'L' and resid 478 through 490 removed outlier: 3.830A pdb=" N ALA L 483 " --> pdb=" O THR L 479 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP L 484 " --> pdb=" O LEU L 480 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY L 487 " --> pdb=" O ALA L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 503 through 505 No H-bonds generated for 'chain 'L' and resid 503 through 505' Processing helix chain 'M' and resid 15 through 28 Processing helix chain 'M' and resid 47 through 55 Processing helix chain 'M' and resid 72 through 88 Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 124 through 138 Processing helix chain 'M' and resid 147 through 159 removed outlier: 3.766A pdb=" N ILE M 157 " --> pdb=" O LEU M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 248 Processing helix chain 'M' and resid 258 through 279 Processing helix chain 'M' and resid 301 through 303 No H-bonds generated for 'chain 'M' and resid 301 through 303' Processing helix chain 'M' and resid 354 through 367 removed outlier: 3.832A pdb=" N LYS M 366 " --> pdb=" O ARG M 362 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASN M 367 " --> pdb=" O ARG M 363 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 384 removed outlier: 3.812A pdb=" N LEU M 384 " --> pdb=" O PHE M 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 17 No H-bonds generated for 'chain 'N' and resid 15 through 17' Processing helix chain 'N' and resid 23 through 29 Processing helix chain 'N' and resid 47 through 60 Processing helix chain 'N' and resid 78 through 82 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 110 through 130 removed outlier: 3.926A pdb=" N LYS N 124 " --> pdb=" O LEU N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 150 removed outlier: 3.573A pdb=" N TYR N 150 " --> pdb=" O GLU N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 213 Processing helix chain 'N' and resid 215 through 217 No H-bonds generated for 'chain 'N' and resid 215 through 217' Processing helix chain 'N' and resid 226 through 229 No H-bonds generated for 'chain 'N' and resid 226 through 229' Processing helix chain 'N' and resid 249 through 263 Processing helix chain 'N' and resid 332 through 350 Processing helix chain 'N' and resid 367 through 375 Processing helix chain 'N' and resid 452 through 464 removed outlier: 3.827A pdb=" N THR N 463 " --> pdb=" O ILE N 459 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS N 464 " --> pdb=" O LEU N 460 " (cutoff:3.500A) Processing helix chain 'N' and resid 482 through 489 Processing helix chain 'N' and resid 503 through 505 No H-bonds generated for 'chain 'N' and resid 503 through 505' Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 removed outlier: 7.412A pdb=" N PHE A 6 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE A 60 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N SER A 8 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU A 62 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 169 through 172 Processing sheet with id= C, first strand: chain 'A' and resid 175 through 177 removed outlier: 3.517A pdb=" N SER A 324 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 184 through 187 removed outlier: 3.566A pdb=" N ILE A 239 " --> pdb=" O PHE A 187 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 207 through 210 removed outlier: 3.568A pdb=" N TYR A 210 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 283 through 286 Processing sheet with id= G, first strand: chain 'A' and resid 390 through 396 removed outlier: 5.931A pdb=" N GLU A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= I, first strand: chain 'B' and resid 91 through 95 removed outlier: 7.139A pdb=" N SER B 41 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LYS B 94 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 43 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B 138 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE B 44 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE B 140 " --> pdb=" O ILE B 44 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 320 through 322 removed outlier: 6.575A pdb=" N GLU B 356 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU B 281 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE B 358 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU B 283 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N HIS B 360 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N TYR B 285 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N SER B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILE B 443 " --> pdb=" O SER B 389 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 300 through 304 Processing sheet with id= L, first strand: chain 'E' and resid 5 through 8 removed outlier: 6.685A pdb=" N LYS E 59 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N SER E 8 " --> pdb=" O LYS E 59 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU E 61 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 169 through 171 Processing sheet with id= N, first strand: chain 'E' and resid 175 through 177 removed outlier: 3.561A pdb=" N LEU E 176 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 208 through 210 removed outlier: 3.575A pdb=" N TYR E 210 " --> pdb=" O TYR E 213 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 283 through 286 Processing sheet with id= Q, first strand: chain 'E' and resid 390 through 394 Processing sheet with id= R, first strand: chain 'F' and resid 12 through 14 removed outlier: 3.695A pdb=" N GLN F 18 " --> pdb=" O PHE F 14 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 93 through 95 removed outlier: 8.461A pdb=" N LYS F 94 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL F 43 " --> pdb=" O LYS F 94 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL F 138 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE F 44 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE F 140 " --> pdb=" O ILE F 44 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 311 through 315 removed outlier: 4.565A pdb=" N LEU F 305 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL F 278 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU F 356 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU F 281 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE F 358 " --> pdb=" O LEU F 281 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ASN F 382 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE F 359 " --> pdb=" O ASN F 382 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL F 384 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA F 361 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL F 386 " --> pdb=" O ALA F 361 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS F 447 " --> pdb=" O GLY F 385 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR F 387 " --> pdb=" O ILE F 445 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ILE F 445 " --> pdb=" O THR F 387 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N SER F 389 " --> pdb=" O ILE F 443 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE F 443 " --> pdb=" O SER F 389 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER F 417 " --> pdb=" O ASN F 414 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N PHE F 419 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL F 412 " --> pdb=" O PHE F 419 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 284 through 286 removed outlier: 3.706A pdb=" N VAL F 284 " --> pdb=" O CYS F 299 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 5 through 8 removed outlier: 6.352A pdb=" N LYS I 59 " --> pdb=" O PHE I 6 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER I 8 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU I 61 " --> pdb=" O SER I 8 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 175 through 177 removed outlier: 3.563A pdb=" N TRP I 319 " --> pdb=" O GLY I 312 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 208 through 210 removed outlier: 3.581A pdb=" N TYR I 210 " --> pdb=" O TYR I 213 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 283 through 286 Processing sheet with id= Z, first strand: chain 'I' and resid 390 through 394 Processing sheet with id= AA, first strand: chain 'L' and resid 91 through 95 removed outlier: 7.003A pdb=" N SER L 41 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LYS L 94 " --> pdb=" O SER L 41 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL L 43 " --> pdb=" O LYS L 94 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL L 138 " --> pdb=" O GLY L 42 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE L 44 " --> pdb=" O VAL L 138 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE L 140 " --> pdb=" O ILE L 44 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 310 through 316 removed outlier: 3.533A pdb=" N GLY L 310 " --> pdb=" O ASP L 306 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE L 304 " --> pdb=" O VAL L 312 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ARG L 295 " --> pdb=" O VAL L 288 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 286 " --> pdb=" O ALA L 297 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU L 305 " --> pdb=" O VAL L 278 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL L 278 " --> pdb=" O LEU L 305 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLU L 356 " --> pdb=" O CYS L 279 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU L 281 " --> pdb=" O GLU L 356 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE L 358 " --> pdb=" O LEU L 281 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU L 283 " --> pdb=" O PHE L 358 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N HIS L 360 " --> pdb=" O LEU L 283 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N TYR L 285 " --> pdb=" O HIS L 360 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASN L 382 " --> pdb=" O VAL L 357 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE L 359 " --> pdb=" O ASN L 382 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL L 384 " --> pdb=" O ILE L 359 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA L 361 " --> pdb=" O VAL L 384 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL L 386 " --> pdb=" O ALA L 361 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR L 387 " --> pdb=" O ILE L 445 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ILE L 445 " --> pdb=" O THR L 387 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER L 389 " --> pdb=" O ILE L 443 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE L 443 " --> pdb=" O SER L 389 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 31 through 33 removed outlier: 6.443A pdb=" N LYS M 59 " --> pdb=" O PHE M 6 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER M 8 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU M 61 " --> pdb=" O SER M 8 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU M 62 " --> pdb=" O ILE M 95 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'M' and resid 169 through 172 Processing sheet with id= AE, first strand: chain 'M' and resid 175 through 177 removed outlier: 3.537A pdb=" N LYS M 328 " --> pdb=" O VAL M 334 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER M 324 " --> pdb=" O SER M 338 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 208 through 210 Processing sheet with id= AG, first strand: chain 'M' and resid 283 through 286 Processing sheet with id= AH, first strand: chain 'M' and resid 390 through 394 Processing sheet with id= AI, first strand: chain 'N' and resid 92 through 95 removed outlier: 6.520A pdb=" N VAL N 138 " --> pdb=" O GLY N 42 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE N 44 " --> pdb=" O VAL N 138 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N PHE N 140 " --> pdb=" O ILE N 44 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'N' and resid 320 through 322 removed outlier: 6.685A pdb=" N GLU N 356 " --> pdb=" O CYS N 279 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LEU N 281 " --> pdb=" O GLU N 356 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE N 358 " --> pdb=" O LEU N 281 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU N 283 " --> pdb=" O PHE N 358 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS N 360 " --> pdb=" O LEU N 283 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N TYR N 285 " --> pdb=" O HIS N 360 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN N 382 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE N 359 " --> pdb=" O ASN N 382 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL N 384 " --> pdb=" O ILE N 359 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA N 361 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL N 386 " --> pdb=" O ALA N 361 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR N 387 " --> pdb=" O ILE N 445 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE N 445 " --> pdb=" O THR N 387 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N SER N 389 " --> pdb=" O ILE N 443 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE N 443 " --> pdb=" O SER N 389 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'N' and resid 302 through 304 892 hydrogen bonds defined for protein. 2562 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 166 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 117 stacking parallelities Total time for adding SS restraints: 10.95 Time building geometry restraints manager: 13.79 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: 6587 1.33 - 1.45: 8124 1.45 - 1.57: 17225 1.57 - 1.69: 308 1.69 - 1.81: 126 Bond restraints: 32370 Sorted by residual: bond pdb=" C SER N 109 " pdb=" N THR N 110 " ideal model delta sigma weight residual 1.335 1.247 0.088 1.31e-02 5.83e+03 4.48e+01 bond pdb=" C ASP N 137 " pdb=" N VAL N 138 " ideal model delta sigma weight residual 1.332 1.268 0.064 1.37e-02 5.33e+03 2.20e+01 bond pdb=" C ILE N 91 " pdb=" N THR N 92 " ideal model delta sigma weight residual 1.331 1.276 0.055 1.38e-02 5.25e+03 1.58e+01 bond pdb=" C TYR A 154 " pdb=" O TYR A 154 " ideal model delta sigma weight residual 1.236 1.281 -0.045 1.15e-02 7.56e+03 1.51e+01 bond pdb=" C GLY L 90 " pdb=" N ILE L 91 " ideal model delta sigma weight residual 1.329 1.391 -0.062 1.69e-02 3.50e+03 1.33e+01 ... (remaining 32365 not shown) Histogram of bond angle deviations from ideal: 99.36 - 106.46: 1589 106.46 - 113.56: 17693 113.56 - 120.66: 13724 120.66 - 127.76: 10919 127.76 - 134.87: 524 Bond angle restraints: 44449 Sorted by residual: angle pdb=" N ASN E 48 " pdb=" CA ASN E 48 " pdb=" C ASN E 48 " ideal model delta sigma weight residual 113.72 104.86 8.86 1.30e+00 5.92e-01 4.64e+01 angle pdb=" C ASN E 48 " pdb=" CA ASN E 48 " pdb=" CB ASN E 48 " ideal model delta sigma weight residual 109.55 118.58 -9.03 1.68e+00 3.54e-01 2.89e+01 angle pdb=" N SER A 148 " pdb=" CA SER A 148 " pdb=" C SER A 148 " ideal model delta sigma weight residual 111.28 105.58 5.70 1.09e+00 8.42e-01 2.74e+01 angle pdb=" CA ILE E 157 " pdb=" C ILE E 157 " pdb=" O ILE E 157 " ideal model delta sigma weight residual 121.98 115.83 6.15 1.21e+00 6.83e-01 2.59e+01 angle pdb=" C VAL M 164 " pdb=" N ILE M 165 " pdb=" CA ILE M 165 " ideal model delta sigma weight residual 123.19 117.09 6.10 1.24e+00 6.50e-01 2.42e+01 ... (remaining 44444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 18641 35.93 - 71.85: 616 71.85 - 107.78: 44 107.78 - 143.70: 9 143.70 - 179.63: 32 Dihedral angle restraints: 19342 sinusoidal: 9256 harmonic: 10086 Sorted by residual: dihedral pdb=" O4' U J 17 " pdb=" C1' U J 17 " pdb=" N1 U J 17 " pdb=" C2 U J 17 " ideal model delta sinusoidal sigma weight residual -160.00 19.63 -179.63 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U O 17 " pdb=" C1' U O 17 " pdb=" N1 U O 17 " pdb=" C2 U O 17 " ideal model delta sinusoidal sigma weight residual -160.00 19.61 -179.61 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U G 13 " pdb=" C1' U G 13 " pdb=" N1 U G 13 " pdb=" C2 U G 13 " ideal model delta sinusoidal sigma weight residual -160.00 16.40 -176.40 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 19339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.105: 4889 1.105 - 2.210: 0 2.210 - 3.315: 0 3.315 - 4.421: 0 4.421 - 5.526: 12 Chirality restraints: 4901 Sorted by residual: chirality pdb=" C3D NAD E 501 " pdb=" C2D NAD E 501 " pdb=" C4D NAD E 501 " pdb=" O3D NAD E 501 " both_signs ideal model delta sigma weight residual False -2.73 2.80 -5.53 2.00e-01 2.50e+01 7.63e+02 chirality pdb=" C3D NAD I 501 " pdb=" C2D NAD I 501 " pdb=" C4D NAD I 501 " pdb=" O3D NAD I 501 " both_signs ideal model delta sigma weight residual False -2.73 2.79 -5.51 2.00e-01 2.50e+01 7.60e+02 chirality pdb=" C3B NAD E 501 " pdb=" C2B NAD E 501 " pdb=" C4B NAD E 501 " pdb=" O3B NAD E 501 " both_signs ideal model delta sigma weight residual False -2.71 2.71 -5.42 2.00e-01 2.50e+01 7.35e+02 ... (remaining 4898 not shown) Planarity restraints: 5060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 146 " 0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ASP A 146 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP A 146 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA A 147 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR M 154 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C TYR M 154 " 0.057 2.00e-02 2.50e+03 pdb=" O TYR M 154 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN M 155 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 105 " -0.033 2.00e-02 2.50e+03 1.97e-02 7.78e+00 pdb=" CG TYR A 105 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 105 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 105 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 105 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 105 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 105 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 105 " -0.009 2.00e-02 2.50e+03 ... (remaining 5057 not shown) Histogram of nonbonded interaction distances: 0.33 - 1.25: 37 1.25 - 2.16: 200 2.16 - 3.07: 20772 3.07 - 3.99: 79752 3.99 - 4.90: 152058 Warning: very small nonbonded interaction distances. Nonbonded interactions: 252819 Sorted by model distance: nonbonded pdb=" CD LYS B 504 " pdb=" CA ASP F 133 " model vdw 0.334 3.870 nonbonded pdb=" NZ LYS B 504 " pdb=" N GLU F 134 " model vdw 0.498 3.200 nonbonded pdb=" N ASP B 133 " pdb=" NZ LYS F 504 " model vdw 0.527 3.200 nonbonded pdb=" C ASP L 133 " pdb=" CE LYS N 504 " model vdw 0.589 3.670 nonbonded pdb=" CB LYS B 504 " pdb=" OD1 ASP F 133 " model vdw 0.663 3.440 ... (remaining 252814 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 2 through 156 or resid 169 through 186 or resid 200 throug \ h 216 or resid 241 through 420)) selection = (chain 'E' and (resid 2 through 156 or resid 169 through 238 or resid 241 throug \ h 296 or resid 309 through 420)) selection = (chain 'I' and (resid 2 through 216 or resid 241 through 296 or resid 309 throug \ h 420)) selection = (chain 'M' and (resid 2 through 156 or resid 169 through 186 or resid 200 throug \ h 216 or resid 241 through 296 or resid 309 through 420)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 1 through 19) selection = (chain 'J' and resid 1 through 19) selection = chain 'O' } ncs_group { reference = (chain 'D' and resid 8 through 23) selection = (chain 'H' and resid 8 through 23) selection = (chain 'K' and resid 8 through 23) selection = chain 'P' } 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: 4.740 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: 0.030 Extract box with map and model: 18.070 Check model and map are aligned: 0.440 Set scattering table: 0.290 Process input model: 90.920 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.170 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2871 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 : 0.004 0.088 32370 Z= 0.233 Angle : 0.597 9.028 44449 Z= 0.351 Chirality : 0.258 5.526 4901 Planarity : 0.004 0.087 5060 Dihedral : 18.839 179.631 12820 Min Nonbonded Distance : 0.334 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.15 (0.14), residues: 3386 helix: 1.00 (0.16), residues: 1111 sheet: -0.99 (0.19), residues: 704 loop : -1.99 (0.14), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 33 HIS 0.006 0.001 HIS M 188 PHE 0.015 0.001 PHE F 14 TYR 0.044 0.001 TYR A 105 ARG 0.003 0.000 ARG F 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 ILE cc_start: 0.6983 (mt) cc_final: 0.6556 (mt) REVERT: A 277 MET cc_start: -0.0343 (mmm) cc_final: -0.1430 (mmm) REVERT: B 307 ASN cc_start: 0.6718 (p0) cc_final: 0.6435 (p0) REVERT: B 345 SER cc_start: 0.4870 (t) cc_final: 0.4639 (m) REVERT: F 490 LEU cc_start: 0.6896 (pp) cc_final: 0.6693 (pp) REVERT: L 280 TYR cc_start: 0.1927 (m-80) cc_final: 0.1375 (m-80) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 1.2199 time to fit residues: 455.5529 Evaluate side-chains 249 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 20.0000 chunk 265 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 274 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 166 optimal weight: 0.3980 chunk 204 optimal weight: 8.9990 chunk 317 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN B 129 ASN B 217 HIS F 16 HIS F 18 GLN F 129 ASN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN M 358 HIS N 129 ASN ** N 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 207 HIS N 329 HIS ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 GLN ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3688 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 32370 Z= 0.377 Angle : 0.839 21.111 44449 Z= 0.435 Chirality : 0.050 0.480 4901 Planarity : 0.006 0.058 5060 Dihedral : 18.888 179.715 5854 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.93 % Allowed : 7.51 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.42 (0.14), residues: 3386 helix: 0.56 (0.16), residues: 1081 sheet: -0.79 (0.20), residues: 653 loop : -2.09 (0.13), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 20 HIS 0.014 0.002 HIS L 207 PHE 0.031 0.003 PHE F 503 TYR 0.038 0.003 TYR F 505 ARG 0.014 0.001 ARG L 481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 265 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.6126 (OUTLIER) cc_final: 0.5910 (mt0) REVERT: A 277 MET cc_start: -0.0279 (mmm) cc_final: -0.0894 (mmm) REVERT: B 92 THR cc_start: 0.7021 (OUTLIER) cc_final: 0.5431 (m) REVERT: B 140 PHE cc_start: 0.7380 (m-80) cc_final: 0.7105 (m-80) REVERT: E 274 GLU cc_start: 0.3955 (OUTLIER) cc_final: 0.3652 (mp0) REVERT: F 1 MET cc_start: 0.2125 (mmm) cc_final: 0.1822 (mmm) REVERT: F 14 PHE cc_start: 0.5784 (m-80) cc_final: 0.5402 (m-80) REVERT: F 223 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6824 (mm) REVERT: F 445 ILE cc_start: 0.6842 (tt) cc_final: 0.6565 (tt) REVERT: F 490 LEU cc_start: 0.7717 (pp) cc_final: 0.7433 (pp) REVERT: I 277 MET cc_start: 0.4001 (tpp) cc_final: 0.3670 (mmm) REVERT: L 219 ILE cc_start: 0.6394 (OUTLIER) cc_final: 0.6088 (mp) REVERT: M 122 MET cc_start: 0.5730 (mmp) cc_final: 0.5501 (mmm) outliers start: 59 outliers final: 18 residues processed: 307 average time/residue: 1.0896 time to fit residues: 413.6000 Evaluate side-chains 266 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 243 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 219 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 264 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 318 optimal weight: 5.9990 chunk 343 optimal weight: 0.5980 chunk 283 optimal weight: 1.9990 chunk 315 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 314 GLN A 358 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN F 129 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 ASN L 251 HIS ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN M 358 HIS N 135 ASN N 205 GLN ** N 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3775 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32370 Z= 0.249 Angle : 0.645 19.217 44449 Z= 0.337 Chirality : 0.044 0.264 4901 Planarity : 0.004 0.059 5060 Dihedral : 18.555 179.240 5854 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.68 % Allowed : 10.88 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.19 (0.14), residues: 3386 helix: 0.82 (0.16), residues: 1103 sheet: -0.55 (0.21), residues: 591 loop : -2.04 (0.13), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP M 369 HIS 0.008 0.001 HIS L 207 PHE 0.028 0.002 PHE F 261 TYR 0.022 0.001 TYR M 210 ARG 0.007 0.001 ARG L 481 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 259 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: -0.0649 (mmm) cc_final: -0.1258 (mmm) REVERT: A 395 MET cc_start: 0.0948 (tpp) cc_final: 0.0029 (pmt) REVERT: E 271 LYS cc_start: 0.4697 (mmmt) cc_final: 0.4388 (mmmt) REVERT: F 1 MET cc_start: 0.2397 (mmm) cc_final: 0.2021 (mmm) REVERT: F 14 PHE cc_start: 0.6136 (m-80) cc_final: 0.4923 (m-80) REVERT: F 219 ILE cc_start: 0.6139 (OUTLIER) cc_final: 0.5906 (mp) REVERT: F 223 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6804 (mm) REVERT: F 490 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7464 (pp) REVERT: I 277 MET cc_start: 0.3855 (tpp) cc_final: 0.3563 (mmm) REVERT: I 336 MET cc_start: 0.4205 (mpt) cc_final: 0.3918 (mpt) REVERT: L 370 TRP cc_start: 0.1354 (t-100) cc_final: 0.0552 (t-100) REVERT: M 122 MET cc_start: 0.5820 (mmp) cc_final: 0.5504 (mmm) REVERT: M 126 ARG cc_start: 0.4191 (tpm170) cc_final: 0.3899 (tpm170) REVERT: M 370 ASN cc_start: 0.2035 (OUTLIER) cc_final: 0.1721 (t0) REVERT: N 19 LYS cc_start: 0.6361 (mptp) cc_final: 0.6142 (ttmm) outliers start: 82 outliers final: 37 residues processed: 310 average time/residue: 1.0011 time to fit residues: 391.1779 Evaluate side-chains 278 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 237 time to evaluate : 2.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 454 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 334 VAL Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 489 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 381 THR Chi-restraints excluded: chain N residue 463 THR Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 151 optimal weight: 0.0770 chunk 213 optimal weight: 5.9990 chunk 319 optimal weight: 0.8980 chunk 338 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 302 optimal weight: 0.1980 chunk 91 optimal weight: 0.0050 overall best weight: 0.4352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN F 98 ASN F 205 GLN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 ASN M 258 ASN M 358 HIS N 205 GLN ** N 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 430 GLN N 446 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3745 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32370 Z= 0.171 Angle : 0.567 17.445 44449 Z= 0.293 Chirality : 0.041 0.234 4901 Planarity : 0.004 0.056 5060 Dihedral : 18.399 179.915 5854 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.25 % Allowed : 12.48 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.90 (0.14), residues: 3386 helix: 1.15 (0.16), residues: 1102 sheet: -0.38 (0.21), residues: 589 loop : -1.95 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 20 HIS 0.004 0.001 HIS L 207 PHE 0.025 0.002 PHE I 120 TYR 0.021 0.001 TYR M 210 ARG 0.012 0.000 ARG M 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 242 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.5927 (OUTLIER) cc_final: 0.5374 (mt0) REVERT: A 277 MET cc_start: -0.0127 (mmm) cc_final: -0.1314 (mmm) REVERT: A 395 MET cc_start: 0.0891 (tpp) cc_final: 0.0281 (pmt) REVERT: F 1 MET cc_start: 0.2401 (mmm) cc_final: 0.2048 (mmm) REVERT: F 14 PHE cc_start: 0.5956 (m-80) cc_final: 0.4834 (m-80) REVERT: F 33 LEU cc_start: 0.7186 (tt) cc_final: 0.6980 (tt) REVERT: F 223 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6787 (mm) REVERT: F 283 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4750 (tp) REVERT: F 364 ARG cc_start: 0.4814 (OUTLIER) cc_final: 0.3987 (mmm-85) REVERT: F 490 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7487 (pp) REVERT: I 277 MET cc_start: 0.3825 (tpp) cc_final: 0.3491 (mmm) REVERT: I 336 MET cc_start: 0.4061 (mpt) cc_final: 0.3814 (mpt) REVERT: I 395 MET cc_start: 0.2897 (OUTLIER) cc_final: 0.2621 (ppp) REVERT: M 15 ASN cc_start: 0.1677 (OUTLIER) cc_final: 0.1235 (m-40) REVERT: M 277 MET cc_start: -0.2643 (tpp) cc_final: -0.3020 (tpp) REVERT: M 395 MET cc_start: 0.2334 (ppp) cc_final: -0.0442 (pmm) outliers start: 69 outliers final: 35 residues processed: 293 average time/residue: 1.0443 time to fit residues: 381.9919 Evaluate side-chains 276 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain E residue 14 ASP Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 389 SER Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 490 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 105 TYR Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 370 ASN Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 429 ILE Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 251 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 chunk 233 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN E 405 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN N 66 ASN ** N 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 446 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4016 moved from start: 0.6413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32370 Z= 0.328 Angle : 0.736 29.328 44449 Z= 0.381 Chirality : 0.047 0.312 4901 Planarity : 0.005 0.067 5060 Dihedral : 18.719 177.967 5854 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.40 % Allowed : 13.03 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.49 (0.14), residues: 3386 helix: 0.52 (0.16), residues: 1081 sheet: -0.76 (0.21), residues: 598 loop : -2.14 (0.13), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 20 HIS 0.008 0.002 HIS L 207 PHE 0.031 0.002 PHE I 120 TYR 0.025 0.002 TYR B 6 ARG 0.010 0.001 ARG L 481 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 252 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: -0.0224 (mmm) cc_final: -0.1737 (mmm) REVERT: B 1 MET cc_start: 0.1084 (OUTLIER) cc_final: -0.0832 (mmt) REVERT: F 1 MET cc_start: 0.2411 (mmm) cc_final: 0.2002 (mmm) REVERT: F 14 PHE cc_start: 0.6104 (m-80) cc_final: 0.4991 (m-80) REVERT: F 283 LEU cc_start: 0.4631 (OUTLIER) cc_final: 0.4355 (tp) REVERT: I 14 ASP cc_start: 0.5644 (m-30) cc_final: 0.5334 (m-30) REVERT: I 135 PHE cc_start: 0.5744 (m-10) cc_final: 0.5389 (m-10) REVERT: I 277 MET cc_start: 0.3799 (tpp) cc_final: 0.3539 (mmm) REVERT: I 336 MET cc_start: 0.4443 (mpt) cc_final: 0.4175 (mpt) REVERT: I 395 MET cc_start: 0.3677 (OUTLIER) cc_final: 0.3280 (pp-130) REVERT: M 15 ASN cc_start: 0.2231 (OUTLIER) cc_final: 0.1679 (t0) REVERT: M 210 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.4449 (t80) REVERT: M 277 MET cc_start: -0.2736 (tpp) cc_final: -0.3096 (tpp) REVERT: N 490 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.5413 (pt) outliers start: 104 outliers final: 51 residues processed: 325 average time/residue: 1.0150 time to fit residues: 414.1504 Evaluate side-chains 293 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 236 time to evaluate : 3.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 223 ILE Chi-restraints excluded: chain L residue 258 THR Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 494 THR Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain M residue 210 TYR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 256 ILE Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 5.9990 chunk 304 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 338 optimal weight: 0.5980 chunk 281 optimal weight: 0.0980 chunk 156 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 254 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 207 HIS N 217 HIS N 222 GLN ** N 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3982 moved from start: 0.6723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32370 Z= 0.248 Angle : 0.643 25.328 44449 Z= 0.331 Chirality : 0.043 0.197 4901 Planarity : 0.004 0.059 5060 Dihedral : 18.514 179.308 5854 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.94 % Allowed : 15.09 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.38 (0.14), residues: 3386 helix: 0.66 (0.16), residues: 1080 sheet: -0.75 (0.21), residues: 616 loop : -2.09 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 20 HIS 0.007 0.001 HIS L 207 PHE 0.026 0.002 PHE I 45 TYR 0.028 0.001 TYR B 6 ARG 0.005 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 239 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 MET cc_start: -0.0142 (mmm) cc_final: -0.1669 (mmm) REVERT: B 132 GLU cc_start: 0.5061 (OUTLIER) cc_final: 0.4763 (mt-10) REVERT: F 1 MET cc_start: 0.2424 (mmm) cc_final: 0.2040 (mmm) REVERT: F 14 PHE cc_start: 0.6082 (m-80) cc_final: 0.5044 (m-80) REVERT: F 223 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6639 (mm) REVERT: F 283 LEU cc_start: 0.4859 (OUTLIER) cc_final: 0.4558 (tp) REVERT: F 296 ASN cc_start: 0.5784 (OUTLIER) cc_final: 0.4826 (m110) REVERT: I 24 LYS cc_start: 0.4624 (OUTLIER) cc_final: 0.4212 (tppp) REVERT: I 277 MET cc_start: 0.3757 (tpp) cc_final: 0.3504 (mmm) REVERT: I 370 ASN cc_start: 0.5213 (OUTLIER) cc_final: 0.4968 (t0) REVERT: I 395 MET cc_start: 0.3742 (OUTLIER) cc_final: 0.3401 (pp-130) REVERT: M 15 ASN cc_start: 0.2017 (OUTLIER) cc_final: 0.1447 (t0) REVERT: M 210 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.4384 (t80) REVERT: M 277 MET cc_start: -0.2660 (tpp) cc_final: -0.2992 (tpp) REVERT: M 395 MET cc_start: 0.0833 (ppp) cc_final: 0.0113 (ppp) REVERT: N 60 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6979 (mt) REVERT: N 370 TRP cc_start: 0.2857 (t-100) cc_final: 0.2421 (t-100) REVERT: N 490 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.5378 (pt) outliers start: 90 outliers final: 51 residues processed: 306 average time/residue: 1.0422 time to fit residues: 399.5127 Evaluate side-chains 287 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 225 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 24 LYS Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 370 ASN Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 251 HIS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain M residue 210 TYR Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 60 ILE Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 381 THR Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 495 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 247 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 285 optimal weight: 0.0050 chunk 189 optimal weight: 1.9990 chunk 337 optimal weight: 0.2980 chunk 211 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3932 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32370 Z= 0.192 Angle : 0.597 22.650 44449 Z= 0.304 Chirality : 0.042 0.198 4901 Planarity : 0.004 0.054 5060 Dihedral : 18.313 179.993 5854 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.16 % Allowed : 16.40 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.19 (0.14), residues: 3386 helix: 0.89 (0.16), residues: 1078 sheet: -0.69 (0.22), residues: 606 loop : -2.00 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP A 20 HIS 0.004 0.001 HIS L 207 PHE 0.027 0.002 PHE I 120 TYR 0.014 0.001 TYR A 154 ARG 0.008 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 245 time to evaluate : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.5816 (m) cc_final: 0.5595 (m) REVERT: A 156 GLN cc_start: 0.6031 (OUTLIER) cc_final: 0.5766 (mt0) REVERT: A 277 MET cc_start: -0.0093 (mmm) cc_final: -0.1591 (mmm) REVERT: B 132 GLU cc_start: 0.4946 (OUTLIER) cc_final: 0.4705 (mt-10) REVERT: F 1 MET cc_start: 0.2423 (mmm) cc_final: 0.2003 (mmm) REVERT: F 14 PHE cc_start: 0.6014 (m-80) cc_final: 0.4999 (m-80) REVERT: F 223 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6630 (mm) REVERT: F 296 ASN cc_start: 0.5702 (OUTLIER) cc_final: 0.4750 (m110) REVERT: I 277 MET cc_start: 0.3593 (tpp) cc_final: 0.3317 (mmm) REVERT: I 327 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7522 (p) REVERT: I 395 MET cc_start: 0.3776 (OUTLIER) cc_final: 0.3509 (pp-130) REVERT: L 7 ILE cc_start: -0.0101 (OUTLIER) cc_final: -0.0396 (pt) REVERT: M 15 ASN cc_start: 0.1907 (OUTLIER) cc_final: 0.1467 (m-40) REVERT: M 277 MET cc_start: -0.2743 (tpp) cc_final: -0.3058 (tpp) REVERT: M 395 MET cc_start: 0.0825 (ppp) cc_final: 0.0169 (ppp) REVERT: N 370 TRP cc_start: 0.2723 (t-100) cc_final: 0.2324 (t-100) REVERT: N 490 LEU cc_start: 0.5560 (OUTLIER) cc_final: 0.5068 (pt) outliers start: 66 outliers final: 42 residues processed: 290 average time/residue: 1.1055 time to fit residues: 395.8900 Evaluate side-chains 291 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain N residue 74 MET Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 381 THR Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 490 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 214 optimal weight: 3.9990 chunk 229 optimal weight: 0.1980 chunk 166 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS E 405 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3965 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 32370 Z= 0.212 Angle : 0.618 22.389 44449 Z= 0.314 Chirality : 0.042 0.363 4901 Planarity : 0.004 0.056 5060 Dihedral : 18.275 179.758 5854 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.45 % Allowed : 16.89 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.16 (0.14), residues: 3386 helix: 0.82 (0.16), residues: 1082 sheet: -0.54 (0.22), residues: 574 loop : -1.97 (0.14), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.002 TRP I 20 HIS 0.005 0.001 HIS B 207 PHE 0.030 0.002 PHE A 17 TYR 0.028 0.001 TYR B 6 ARG 0.008 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 237 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.5871 (m) cc_final: 0.5657 (m) REVERT: A 156 GLN cc_start: 0.6079 (OUTLIER) cc_final: 0.5869 (mt0) REVERT: A 268 LEU cc_start: 0.3729 (OUTLIER) cc_final: 0.3348 (pp) REVERT: A 277 MET cc_start: -0.0084 (mmm) cc_final: -0.1601 (mmm) REVERT: B 132 GLU cc_start: 0.5054 (OUTLIER) cc_final: 0.4798 (mt-10) REVERT: E 274 GLU cc_start: 0.3580 (OUTLIER) cc_final: 0.3105 (mp0) REVERT: F 1 MET cc_start: 0.2461 (mmm) cc_final: 0.2062 (mmm) REVERT: F 14 PHE cc_start: 0.6071 (m-80) cc_final: 0.5115 (m-80) REVERT: F 33 LEU cc_start: 0.7160 (tt) cc_final: 0.6952 (tt) REVERT: F 283 LEU cc_start: 0.4939 (OUTLIER) cc_final: 0.4677 (tp) REVERT: F 296 ASN cc_start: 0.5718 (OUTLIER) cc_final: 0.4734 (m110) REVERT: F 497 LYS cc_start: 0.6651 (ttpp) cc_final: 0.6398 (ttmm) REVERT: I 277 MET cc_start: 0.3528 (tpp) cc_final: 0.3242 (mmm) REVERT: I 395 MET cc_start: 0.4002 (OUTLIER) cc_final: 0.3667 (pp-130) REVERT: L 7 ILE cc_start: -0.0172 (OUTLIER) cc_final: -0.0496 (pt) REVERT: M 15 ASN cc_start: 0.1971 (OUTLIER) cc_final: 0.1508 (m-40) REVERT: M 277 MET cc_start: -0.2710 (tpp) cc_final: -0.3016 (tpp) REVERT: M 395 MET cc_start: 0.0905 (ppp) cc_final: -0.0015 (ppp) REVERT: N 370 TRP cc_start: 0.2648 (t-100) cc_final: 0.2263 (t-100) REVERT: N 490 LEU cc_start: 0.5585 (OUTLIER) cc_final: 0.5164 (pt) outliers start: 75 outliers final: 47 residues processed: 288 average time/residue: 1.1006 time to fit residues: 399.3692 Evaluate side-chains 288 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 231 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 267 LYS Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 298 CYS Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 395 MET Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 251 HIS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 489 ILE Chi-restraints excluded: chain M residue 5 ILE Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 490 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 294 optimal weight: 0.9990 chunk 314 optimal weight: 0.6980 chunk 189 optimal weight: 0.3980 chunk 136 optimal weight: 30.0000 chunk 246 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 284 optimal weight: 7.9990 chunk 297 optimal weight: 0.9980 chunk 313 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS E 405 ASN ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3978 moved from start: 0.7502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32370 Z= 0.211 Angle : 0.619 22.048 44449 Z= 0.314 Chirality : 0.043 0.540 4901 Planarity : 0.004 0.055 5060 Dihedral : 18.258 179.299 5854 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.58 % Allowed : 17.25 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.14 (0.14), residues: 3386 helix: 0.80 (0.16), residues: 1088 sheet: -0.50 (0.22), residues: 548 loop : -1.92 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP I 20 HIS 0.012 0.001 HIS E 340 PHE 0.036 0.002 PHE A 17 TYR 0.015 0.001 TYR M 154 ARG 0.012 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 233 time to evaluate : 3.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.5868 (m) cc_final: 0.5666 (m) REVERT: A 277 MET cc_start: -0.0050 (mmm) cc_final: -0.1582 (mmm) REVERT: B 132 GLU cc_start: 0.5119 (OUTLIER) cc_final: 0.4862 (mt-10) REVERT: E 274 GLU cc_start: 0.3596 (OUTLIER) cc_final: 0.3100 (mp0) REVERT: F 1 MET cc_start: 0.2511 (mmm) cc_final: 0.2065 (mmm) REVERT: F 14 PHE cc_start: 0.6144 (m-80) cc_final: 0.5466 (m-80) REVERT: F 33 LEU cc_start: 0.7269 (tt) cc_final: 0.7041 (tt) REVERT: F 283 LEU cc_start: 0.4985 (OUTLIER) cc_final: 0.4702 (tp) REVERT: F 296 ASN cc_start: 0.5685 (OUTLIER) cc_final: 0.4780 (m110) REVERT: L 7 ILE cc_start: -0.0179 (OUTLIER) cc_final: -0.0505 (pt) REVERT: M 15 ASN cc_start: 0.1973 (OUTLIER) cc_final: 0.1538 (m-40) REVERT: M 395 MET cc_start: 0.0952 (ppp) cc_final: -0.0181 (ppp) REVERT: N 369 GLU cc_start: 0.3193 (mm-30) cc_final: 0.2824 (mt-10) REVERT: N 370 TRP cc_start: 0.2730 (t-100) cc_final: 0.2347 (t-100) REVERT: N 490 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5148 (pt) outliers start: 79 outliers final: 54 residues processed: 288 average time/residue: 1.0198 time to fit residues: 368.2489 Evaluate side-chains 290 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 229 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 340 HIS Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 251 HIS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 489 ILE Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 381 THR Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 507 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 10.0000 chunk 332 optimal weight: 0.7980 chunk 202 optimal weight: 0.8980 chunk 157 optimal weight: 0.5980 chunk 231 optimal weight: 0.3980 chunk 348 optimal weight: 4.9990 chunk 320 optimal weight: 0.3980 chunk 277 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 HIS ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 ASN L 68 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3974 moved from start: 0.7672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32370 Z= 0.206 Angle : 0.622 21.417 44449 Z= 0.314 Chirality : 0.042 0.498 4901 Planarity : 0.004 0.055 5060 Dihedral : 18.236 179.373 5854 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.16 % Allowed : 17.54 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.14 (0.14), residues: 3386 helix: 0.83 (0.16), residues: 1088 sheet: -0.66 (0.21), residues: 588 loop : -1.90 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP I 20 HIS 0.008 0.001 HIS E 340 PHE 0.032 0.002 PHE A 17 TYR 0.030 0.001 TYR B 6 ARG 0.003 0.000 ARG L 481 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6772 Ramachandran restraints generated. 3386 Oldfield, 0 Emsley, 3386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 234 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 THR cc_start: 0.5858 (m) cc_final: 0.5650 (m) REVERT: A 156 GLN cc_start: 0.5994 (OUTLIER) cc_final: 0.5335 (mt0) REVERT: A 268 LEU cc_start: 0.3975 (OUTLIER) cc_final: 0.3675 (pp) REVERT: A 277 MET cc_start: 0.0117 (mmm) cc_final: -0.1362 (mmm) REVERT: B 132 GLU cc_start: 0.5128 (OUTLIER) cc_final: 0.4896 (mt-10) REVERT: E 35 ASP cc_start: 0.4481 (OUTLIER) cc_final: 0.3787 (p0) REVERT: E 274 GLU cc_start: 0.3571 (OUTLIER) cc_final: 0.3185 (mp0) REVERT: F 14 PHE cc_start: 0.6270 (m-80) cc_final: 0.5554 (m-80) REVERT: F 33 LEU cc_start: 0.7291 (tt) cc_final: 0.7090 (tt) REVERT: F 296 ASN cc_start: 0.5621 (OUTLIER) cc_final: 0.4658 (m110) REVERT: I 327 SER cc_start: 0.8060 (OUTLIER) cc_final: 0.7577 (p) REVERT: I 336 MET cc_start: 0.4309 (mpt) cc_final: 0.3904 (mpt) REVERT: L 7 ILE cc_start: -0.0210 (OUTLIER) cc_final: -0.0544 (pt) REVERT: L 210 PHE cc_start: 0.4742 (t80) cc_final: 0.4037 (t80) REVERT: M 5 ILE cc_start: 0.7318 (mt) cc_final: 0.7117 (pt) REVERT: M 15 ASN cc_start: 0.1991 (OUTLIER) cc_final: 0.1546 (m-40) REVERT: M 395 MET cc_start: 0.1018 (ppp) cc_final: -0.0121 (ppp) REVERT: N 145 ASP cc_start: 0.2393 (m-30) cc_final: 0.2081 (m-30) REVERT: N 369 GLU cc_start: 0.3147 (mm-30) cc_final: 0.2823 (mt-10) REVERT: N 370 TRP cc_start: 0.2729 (t-100) cc_final: 0.2347 (t-100) REVERT: N 490 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.5026 (pt) outliers start: 66 outliers final: 50 residues processed: 280 average time/residue: 1.0546 time to fit residues: 367.5649 Evaluate side-chains 291 residues out of total 3061 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 231 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 158 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 507 ILE Chi-restraints excluded: chain E residue 16 ASP Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain E residue 309 MET Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 THR Chi-restraints excluded: chain F residue 44 ILE Chi-restraints excluded: chain F residue 227 SER Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 364 ARG Chi-restraints excluded: chain F residue 407 ARG Chi-restraints excluded: chain F residue 445 ILE Chi-restraints excluded: chain F residue 463 THR Chi-restraints excluded: chain F residue 465 LEU Chi-restraints excluded: chain F residue 491 THR Chi-restraints excluded: chain F residue 496 ILE Chi-restraints excluded: chain I residue 16 ASP Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 40 ASP Chi-restraints excluded: chain I residue 46 TRP Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 204 THR Chi-restraints excluded: chain I residue 327 SER Chi-restraints excluded: chain L residue 7 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 251 HIS Chi-restraints excluded: chain L residue 281 LEU Chi-restraints excluded: chain L residue 435 MET Chi-restraints excluded: chain L residue 479 THR Chi-restraints excluded: chain L residue 489 ILE Chi-restraints excluded: chain M residue 15 ASN Chi-restraints excluded: chain M residue 33 TRP Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 185 LEU Chi-restraints excluded: chain N residue 12 ILE Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 381 THR Chi-restraints excluded: chain N residue 386 VAL Chi-restraints excluded: chain N residue 490 LEU Chi-restraints excluded: chain N residue 507 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 0.0470 chunk 295 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 chunk 256 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 278 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 285 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 ASN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 ASN I 116 ASN ** M 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5368 r_free = 0.5368 target = 0.284495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5110 r_free = 0.5110 target = 0.252010 restraints weight = 46618.110| |-----------------------------------------------------------------------------| r_work (start): 0.5079 rms_B_bonded: 2.28 r_work: 0.4924 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4693 moved from start: 0.7875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32370 Z= 0.213 Angle : 0.629 21.502 44449 Z= 0.318 Chirality : 0.042 0.486 4901 Planarity : 0.004 0.054 5060 Dihedral : 18.234 179.766 5854 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.25 % Allowed : 17.61 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.13 (0.14), residues: 3386 helix: 0.82 (0.16), residues: 1087 sheet: -0.65 (0.22), residues: 574 loop : -1.87 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP I 20 HIS 0.005 0.001 HIS L 207 PHE 0.028 0.002 PHE N 53 TYR 0.015 0.001 TYR M 154 ARG 0.010 0.000 ARG E 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8896.30 seconds wall clock time: 160 minutes 24.71 seconds (9624.71 seconds total)