Starting phenix.real_space_refine on Fri Jun 28 18:52:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/06_2024/8z8x_39850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/06_2024/8z8x_39850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/06_2024/8z8x_39850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/06_2024/8z8x_39850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/06_2024/8z8x_39850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8x_39850/06_2024/8z8x_39850_updated.pdb" } resolution = 3.06 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 82 5.16 5 C 9238 2.51 5 N 2559 2.21 5 O 2853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A ASP 21": "OD1" <-> "OD2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 58": "OD1" <-> "OD2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 351": "OE1" <-> "OE2" Residue "B PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 587": "OD1" <-> "OD2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B PHE 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C ASP 127": "OD1" <-> "OD2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 14768 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5014 Classifications: {'peptide': 620} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 588} Chain: "B" Number of atoms: 5710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5710 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 39, 'TRANS': 670} Chain: "C" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3253 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 400, 3253 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 3317 Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 9} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AILE C 330 " occ=0.68 ... (14 atoms not shown) pdb=" CD1BILE C 330 " occ=0.32 residue: pdb=" N ASER C 336 " occ=0.72 ... (10 atoms not shown) pdb=" OG BSER C 336 " occ=0.28 residue: pdb=" N ASER C 384 " occ=0.56 ... (10 atoms not shown) pdb=" OG BSER C 384 " occ=0.44 Time building chain proxies: 9.78, per 1000 atoms: 0.66 Number of scatterers: 14768 At special positions: 0 Unit cell: (108.714, 105.12, 138.363, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 36 15.00 O 2853 8.00 N 2559 7.00 C 9238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.26 Conformation dependent library (CDL) restraints added in 3.1 seconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 17 sheets defined 40.2% alpha, 10.2% beta 8 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 6.19 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Processing helix chain 'A' and resid 28 through 44 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 127 through 131 Processing helix chain 'A' and resid 135 through 154 removed outlier: 3.529A pdb=" N TRP A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 removed outlier: 3.830A pdb=" N VAL A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.515A pdb=" N LEU A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASP A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.722A pdb=" N TRP A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.562A pdb=" N ILE A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 275 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.748A pdb=" N ILE A 298 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 301 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 363 through 380 Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.686A pdb=" N THR A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 494 through 516 removed outlier: 3.715A pdb=" N GLN A 500 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Proline residue: A 501 - end of helix Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 560 through 581 removed outlier: 4.465A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 600 removed outlier: 3.502A pdb=" N GLU A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N CYS A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 600' Processing helix chain 'A' and resid 605 through 615 Processing helix chain 'B' and resid 12 through 19 removed outlier: 4.310A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 54 through 59 removed outlier: 4.180A pdb=" N ASP B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 96 through 108 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 135 through 150 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.737A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 251 through 267 removed outlier: 4.873A pdb=" N ASN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 311 through 325 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 375 through 379 removed outlier: 4.249A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 408 Processing helix chain 'B' and resid 433 through 450 removed outlier: 3.568A pdb=" N VAL B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 489 Proline residue: B 488 - end of helix Processing helix chain 'B' and resid 497 through 513 Processing helix chain 'B' and resid 519 through 536 Processing helix chain 'B' and resid 544 through 550 Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 576 through 583 Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.599A pdb=" N ARG B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 661 removed outlier: 4.245A pdb=" N ALA B 647 " --> pdb=" O PRO B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 694 Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'C' and resid 11 through 26 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.569A pdb=" N PHE C 41 " --> pdb=" O TYR C 38 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS C 42 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG C 43 " --> pdb=" O THR C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 103 through 109 removed outlier: 3.871A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 124 through 135 Processing helix chain 'C' and resid 167 through 175 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 193 through 203 Proline residue: C 202 - end of helix Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.932A pdb=" N HIS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 238 No H-bonds generated for 'chain 'C' and resid 236 through 238' Processing helix chain 'C' and resid 241 through 244 No H-bonds generated for 'chain 'C' and resid 241 through 244' Processing helix chain 'C' and resid 404 through 412 Processing helix chain 'C' and resid 432 through 445 Processing helix chain 'C' and resid 448 through 454 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 59 removed outlier: 7.579A pdb=" N HIS A 115 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N LEU A 99 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU A 117 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.842A pdb=" N ILE A 414 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N MET A 428 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N CYS A 412 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU A 430 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N THR A 410 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 259 through 262 removed outlier: 4.254A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 527 through 530 Processing sheet with id= E, first strand: chain 'B' and resid 173 through 175 Processing sheet with id= F, first strand: chain 'B' and resid 188 through 191 removed outlier: 4.894A pdb=" N GLN B 188 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 226 through 230 Processing sheet with id= H, first strand: chain 'B' and resid 460 through 462 Processing sheet with id= I, first strand: chain 'B' and resid 346 through 348 Processing sheet with id= J, first strand: chain 'B' and resid 353 through 357 removed outlier: 3.954A pdb=" N LEU B 360 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 467 through 470 Processing sheet with id= L, first strand: chain 'B' and resid 608 through 611 removed outlier: 3.701A pdb=" N MET B 609 " --> pdb=" O MET B 621 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 67 through 69 Processing sheet with id= N, first strand: chain 'C' and resid 141 through 143 Processing sheet with id= O, first strand: chain 'C' and resid 149 through 154 Processing sheet with id= P, first strand: chain 'C' and resid 345 through 352 Processing sheet with id= Q, first strand: chain 'C' and resid 369 through 376 removed outlier: 3.523A pdb=" N LYS C 394 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 395 " --> pdb=" O THR C 482 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1303 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 6.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4723 1.34 - 1.47: 3681 1.47 - 1.60: 6603 1.60 - 1.72: 36 1.72 - 1.85: 135 Bond restraints: 15178 Sorted by residual: bond pdb=" N GLY C 455 " pdb=" CA GLY C 455 " ideal model delta sigma weight residual 1.449 1.471 -0.021 1.45e-02 4.76e+03 2.20e+00 bond pdb=" C3' A E 2 " pdb=" O3' A E 2 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.34e+00 bond pdb=" CG1 ILE A 393 " pdb=" CD1 ILE A 393 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.27e+00 bond pdb=" CB PRO B 644 " pdb=" CG PRO B 644 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.12e+00 bond pdb=" CB GLU B 263 " pdb=" CG GLU B 263 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.10e+00 ... (remaining 15173 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.73: 591 105.73 - 112.84: 8049 112.84 - 119.95: 5329 119.95 - 127.06: 6484 127.06 - 134.17: 269 Bond angle restraints: 20722 Sorted by residual: angle pdb=" C ARG C 62 " pdb=" N LYS C 63 " pdb=" CA LYS C 63 " ideal model delta sigma weight residual 120.49 129.87 -9.38 1.42e+00 4.96e-01 4.37e+01 angle pdb=" N VAL C 230 " pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 113.53 107.59 5.94 9.80e-01 1.04e+00 3.68e+01 angle pdb=" C VAL C 102 " pdb=" N VAL C 103 " pdb=" CA VAL C 103 " ideal model delta sigma weight residual 120.24 122.76 -2.52 6.30e-01 2.52e+00 1.60e+01 angle pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sigma weight residual 120.20 125.12 -4.92 1.50e+00 4.44e-01 1.07e+01 angle pdb=" N VAL A 597 " pdb=" CA VAL A 597 " pdb=" C VAL A 597 " ideal model delta sigma weight residual 111.81 109.14 2.67 8.60e-01 1.35e+00 9.67e+00 ... (remaining 20717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 9066 33.81 - 67.61: 229 67.61 - 101.42: 26 101.42 - 135.22: 1 135.22 - 169.03: 2 Dihedral angle restraints: 9324 sinusoidal: 4228 harmonic: 5096 Sorted by residual: dihedral pdb=" CA GLU A 456 " pdb=" C GLU A 456 " pdb=" N GLU A 457 " pdb=" CA GLU A 457 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sinusoidal sigma weight residual -110.00 59.03 -169.03 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' C E 7 " pdb=" C3' C E 7 " pdb=" O3' C E 7 " pdb=" P U E 8 " ideal model delta sinusoidal sigma weight residual 220.00 69.54 150.46 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 9321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1611 0.037 - 0.074: 496 0.074 - 0.111: 167 0.111 - 0.148: 37 0.148 - 0.185: 2 Chirality restraints: 2313 Sorted by residual: chirality pdb=" C3' A E 2 " pdb=" C4' A E 2 " pdb=" O3' A E 2 " pdb=" C2' A E 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA GLU B 263 " pdb=" N GLU B 263 " pdb=" C GLU B 263 " pdb=" CB GLU B 263 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE C 395 " pdb=" N ILE C 395 " pdb=" C ILE C 395 " pdb=" CB ILE C 395 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 2310 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 643 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 644 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 463 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO B 464 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 464 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 464 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 354 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.94e+00 pdb=" N PRO C 355 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 355 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 355 " -0.034 5.00e-02 4.00e+02 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 437 2.70 - 3.25: 15074 3.25 - 3.80: 23979 3.80 - 4.35: 32879 4.35 - 4.90: 52966 Nonbonded interactions: 125335 Sorted by model distance: nonbonded pdb=" OE1 GLU A 126 " pdb=" OG SER A 128 " model vdw 2.148 2.440 nonbonded pdb=" OG1 THR C 229 " pdb=" O VAL C 231 " model vdw 2.158 2.440 nonbonded pdb=" OD2 ASP B 500 " pdb=" OH TYR B 537 " model vdw 2.184 2.440 nonbonded pdb=" OE1 GLU C 10 " pdb=" OG1 THR C 12 " model vdw 2.220 2.440 nonbonded pdb=" OD1 ASN B 132 " pdb=" ND2 ASN B 227 " model vdw 2.264 2.520 ... (remaining 125330 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.28 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 2.120 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 46.410 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 : 0.003 0.053 15178 Z= 0.172 Angle : 0.610 9.385 20722 Z= 0.328 Chirality : 0.041 0.185 2313 Planarity : 0.006 0.083 2532 Dihedral : 14.960 169.029 6016 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1729 helix: 0.66 (0.20), residues: 715 sheet: -0.83 (0.37), residues: 207 loop : -1.33 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 185 HIS 0.003 0.001 HIS C 242 PHE 0.024 0.002 PHE C 335 TYR 0.010 0.001 TYR B 533 ARG 0.008 0.001 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8841 (m-30) cc_final: 0.8636 (m-30) REVERT: A 150 GLU cc_start: 0.8924 (mp0) cc_final: 0.8692 (pm20) REVERT: B 259 ASP cc_start: 0.8364 (m-30) cc_final: 0.8147 (m-30) REVERT: C 380 GLN cc_start: 0.8244 (pm20) cc_final: 0.7997 (pm20) REVERT: C 383 PHE cc_start: 0.8549 (p90) cc_final: 0.8223 (p90) REVERT: C 410 ILE cc_start: 0.8952 (mt) cc_final: 0.8511 (mt) REVERT: C 421 PHE cc_start: 0.7675 (m-80) cc_final: 0.7413 (m-80) REVERT: C 433 ARG cc_start: 0.8001 (tpp-160) cc_final: 0.7538 (tpp80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2953 time to fit residues: 100.7688 Evaluate side-chains 199 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 158 optimal weight: 50.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 257 GLN B 123 GLN B 476 HIS B 663 ASN C 39 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15178 Z= 0.340 Angle : 0.614 7.348 20722 Z= 0.318 Chirality : 0.044 0.171 2313 Planarity : 0.006 0.066 2532 Dihedral : 13.445 169.446 2463 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.41 % Allowed : 6.99 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1729 helix: 0.59 (0.20), residues: 723 sheet: -1.05 (0.34), residues: 226 loop : -1.38 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.010 0.001 HIS C 233 PHE 0.027 0.002 PHE C 41 TYR 0.031 0.002 TYR C 382 ARG 0.005 0.000 ARG A 592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 1.774 Fit side-chains revert: symmetry clash REVERT: B 167 ASP cc_start: 0.8026 (m-30) cc_final: 0.7781 (m-30) REVERT: B 259 ASP cc_start: 0.8489 (m-30) cc_final: 0.8140 (m-30) REVERT: B 650 ASN cc_start: 0.8530 (m110) cc_final: 0.8268 (m110) REVERT: C 110 TYR cc_start: 0.8311 (m-80) cc_final: 0.8066 (m-80) REVERT: C 346 GLU cc_start: 0.9017 (tt0) cc_final: 0.8322 (tm-30) REVERT: C 349 LYS cc_start: 0.7547 (tptp) cc_final: 0.7308 (tmtt) REVERT: C 380 GLN cc_start: 0.8495 (pm20) cc_final: 0.8239 (pm20) REVERT: C 383 PHE cc_start: 0.8421 (p90) cc_final: 0.8121 (p90) REVERT: C 410 ILE cc_start: 0.8924 (mt) cc_final: 0.8655 (mt) REVERT: C 416 PHE cc_start: 0.8517 (m-80) cc_final: 0.8253 (m-10) REVERT: C 433 ARG cc_start: 0.8032 (tpp-160) cc_final: 0.7577 (tpp80) outliers start: 22 outliers final: 14 residues processed: 215 average time/residue: 0.3203 time to fit residues: 95.9896 Evaluate side-chains 203 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 189 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Chi-restraints excluded: chain C residue 377 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 GLN C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15178 Z= 0.307 Angle : 0.583 7.452 20722 Z= 0.300 Chirality : 0.043 0.175 2313 Planarity : 0.005 0.055 2532 Dihedral : 13.408 169.440 2463 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.41 % Allowed : 10.13 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1729 helix: 0.54 (0.20), residues: 720 sheet: -1.02 (0.34), residues: 225 loop : -1.40 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.009 0.001 HIS C 233 PHE 0.025 0.002 PHE C 41 TYR 0.013 0.001 TYR C 413 ARG 0.005 0.000 ARG B 708 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8674 (m-30) cc_final: 0.8411 (p0) REVERT: A 159 GLN cc_start: 0.9080 (tp40) cc_final: 0.8763 (tp-100) REVERT: A 569 MET cc_start: 0.8711 (tpp) cc_final: 0.8423 (tpt) REVERT: B 151 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.7978 (mtt180) REVERT: B 167 ASP cc_start: 0.8039 (m-30) cc_final: 0.7793 (m-30) REVERT: B 259 ASP cc_start: 0.8504 (m-30) cc_final: 0.8207 (m-30) REVERT: B 473 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7510 (mtmm) REVERT: C 110 TYR cc_start: 0.8309 (m-80) cc_final: 0.8091 (m-80) REVERT: C 346 GLU cc_start: 0.9029 (tt0) cc_final: 0.8362 (tm-30) REVERT: C 349 LYS cc_start: 0.7698 (tptp) cc_final: 0.7486 (tmtt) REVERT: C 380 GLN cc_start: 0.8474 (pm20) cc_final: 0.8233 (pm20) REVERT: C 383 PHE cc_start: 0.8617 (p90) cc_final: 0.8124 (p90) REVERT: C 410 ILE cc_start: 0.8873 (mt) cc_final: 0.8673 (mt) REVERT: C 433 ARG cc_start: 0.8025 (tpp-160) cc_final: 0.7565 (tpp80) outliers start: 22 outliers final: 18 residues processed: 207 average time/residue: 0.3180 time to fit residues: 91.4982 Evaluate side-chains 200 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Chi-restraints excluded: chain C residue 377 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 159 optimal weight: 30.0000 chunk 169 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 151 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 ASN B 663 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15178 Z= 0.288 Angle : 0.573 7.414 20722 Z= 0.293 Chirality : 0.042 0.176 2313 Planarity : 0.005 0.052 2532 Dihedral : 13.383 169.603 2463 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.37 % Allowed : 10.51 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1729 helix: 0.55 (0.20), residues: 725 sheet: -1.01 (0.34), residues: 226 loop : -1.38 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 470 HIS 0.004 0.001 HIS A 573 PHE 0.024 0.002 PHE C 41 TYR 0.012 0.001 TYR C 413 ARG 0.006 0.000 ARG B 708 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 1.525 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.9115 (tp40) cc_final: 0.8767 (tp-100) REVERT: A 569 MET cc_start: 0.8698 (tpp) cc_final: 0.8414 (tpt) REVERT: B 151 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.8017 (mtt180) REVERT: B 167 ASP cc_start: 0.8048 (m-30) cc_final: 0.7648 (m-30) REVERT: B 186 ASP cc_start: 0.8754 (t70) cc_final: 0.8391 (t0) REVERT: B 473 LYS cc_start: 0.7933 (mmmt) cc_final: 0.7550 (mtmm) REVERT: C 110 TYR cc_start: 0.8318 (m-80) cc_final: 0.8085 (m-80) REVERT: C 346 GLU cc_start: 0.9018 (tt0) cc_final: 0.8379 (tm-30) REVERT: C 349 LYS cc_start: 0.7774 (tptp) cc_final: 0.7570 (tmtt) REVERT: C 380 GLN cc_start: 0.8469 (pm20) cc_final: 0.8199 (pm20) REVERT: C 410 ILE cc_start: 0.8877 (mt) cc_final: 0.8676 (mt) REVERT: C 437 ASP cc_start: 0.8835 (m-30) cc_final: 0.8571 (m-30) outliers start: 37 outliers final: 27 residues processed: 216 average time/residue: 0.3019 time to fit residues: 91.7229 Evaluate side-chains 208 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Chi-restraints excluded: chain C residue 377 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 144 optimal weight: 0.0770 chunk 116 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN C 233 HIS ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15178 Z= 0.168 Angle : 0.532 6.822 20722 Z= 0.271 Chirality : 0.040 0.177 2313 Planarity : 0.005 0.052 2532 Dihedral : 13.247 168.845 2463 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.54 % Allowed : 11.79 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1729 helix: 0.71 (0.20), residues: 724 sheet: -0.90 (0.34), residues: 226 loop : -1.29 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS C 443 PHE 0.022 0.001 PHE C 41 TYR 0.011 0.001 TYR B 533 ARG 0.005 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8667 (m-30) cc_final: 0.8429 (p0) REVERT: A 159 GLN cc_start: 0.9125 (tp40) cc_final: 0.8766 (tp-100) REVERT: A 607 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.9022 (t) REVERT: B 151 ARG cc_start: 0.8339 (mtm-85) cc_final: 0.8024 (mtt180) REVERT: B 167 ASP cc_start: 0.8015 (m-30) cc_final: 0.7608 (m-30) REVERT: B 186 ASP cc_start: 0.8748 (t70) cc_final: 0.8386 (t0) REVERT: B 435 GLU cc_start: 0.8612 (tp30) cc_final: 0.8400 (tp30) REVERT: B 473 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7534 (mtmm) REVERT: B 693 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 18 GLU cc_start: 0.7081 (tp30) cc_final: 0.6856 (tp30) REVERT: C 110 TYR cc_start: 0.8275 (m-80) cc_final: 0.8034 (m-80) REVERT: C 160 GLU cc_start: 0.8073 (tp30) cc_final: 0.7847 (tp30) REVERT: C 346 GLU cc_start: 0.8996 (tt0) cc_final: 0.8385 (tm-30) REVERT: C 380 GLN cc_start: 0.8439 (pm20) cc_final: 0.8155 (pm20) REVERT: C 437 ASP cc_start: 0.8829 (m-30) cc_final: 0.8618 (m-30) outliers start: 24 outliers final: 17 residues processed: 212 average time/residue: 0.3104 time to fit residues: 92.6389 Evaluate side-chains 201 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 4.9990 chunk 152 optimal weight: 0.0670 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 163 optimal weight: 20.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 663 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15178 Z= 0.314 Angle : 0.571 8.286 20722 Z= 0.292 Chirality : 0.043 0.178 2313 Planarity : 0.005 0.052 2532 Dihedral : 13.307 169.671 2463 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.79 % Allowed : 11.99 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1729 helix: 0.67 (0.20), residues: 726 sheet: -0.86 (0.34), residues: 228 loop : -1.29 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 470 HIS 0.010 0.001 HIS C 233 PHE 0.024 0.002 PHE C 41 TYR 0.012 0.001 TYR B 537 ARG 0.006 0.000 ARG B 708 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 1.645 Fit side-chains REVERT: A 140 ASP cc_start: 0.8671 (m-30) cc_final: 0.8440 (p0) REVERT: A 159 GLN cc_start: 0.9133 (tp40) cc_final: 0.8778 (tp-100) REVERT: A 569 MET cc_start: 0.8696 (tpp) cc_final: 0.8429 (tpt) REVERT: A 607 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9018 (t) REVERT: B 151 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.8039 (mtt180) REVERT: B 167 ASP cc_start: 0.8060 (m-30) cc_final: 0.7654 (m-30) REVERT: B 186 ASP cc_start: 0.8771 (t70) cc_final: 0.8344 (t0) REVERT: B 255 LYS cc_start: 0.8869 (ttmm) cc_final: 0.8509 (tttp) REVERT: B 435 GLU cc_start: 0.8664 (tp30) cc_final: 0.8455 (tp30) REVERT: B 473 LYS cc_start: 0.7920 (mmmt) cc_final: 0.7607 (mtmm) REVERT: C 110 TYR cc_start: 0.8331 (m-80) cc_final: 0.8092 (m-80) REVERT: C 346 GLU cc_start: 0.8987 (tt0) cc_final: 0.8433 (tm-30) REVERT: C 380 GLN cc_start: 0.8433 (pm20) cc_final: 0.8151 (pm20) REVERT: C 472 GLU cc_start: 0.7779 (pt0) cc_final: 0.7526 (pt0) outliers start: 28 outliers final: 22 residues processed: 209 average time/residue: 0.3176 time to fit residues: 93.0299 Evaluate side-chains 205 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.0470 chunk 96 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15178 Z= 0.148 Angle : 0.533 7.828 20722 Z= 0.271 Chirality : 0.040 0.179 2313 Planarity : 0.005 0.052 2532 Dihedral : 13.177 168.650 2463 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.60 % Allowed : 12.50 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.20), residues: 1729 helix: 0.83 (0.20), residues: 722 sheet: -0.74 (0.35), residues: 226 loop : -1.23 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.008 0.001 HIS C 233 PHE 0.021 0.001 PHE C 41 TYR 0.020 0.001 TYR C 382 ARG 0.006 0.000 ARG B 708 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 198 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8656 (m-30) cc_final: 0.8432 (p0) REVERT: A 159 GLN cc_start: 0.9123 (tp40) cc_final: 0.8753 (tp-100) REVERT: A 607 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.9010 (t) REVERT: B 151 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.8026 (mtt180) REVERT: B 186 ASP cc_start: 0.8745 (t70) cc_final: 0.8394 (t0) REVERT: B 248 MET cc_start: 0.9106 (tpp) cc_final: 0.8808 (tpt) REVERT: B 255 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8464 (tttp) REVERT: B 435 GLU cc_start: 0.8631 (tp30) cc_final: 0.8431 (tp30) REVERT: B 473 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7498 (mtmm) REVERT: C 110 TYR cc_start: 0.8261 (m-80) cc_final: 0.8037 (m-80) REVERT: C 346 GLU cc_start: 0.8969 (tt0) cc_final: 0.8444 (tm-30) REVERT: C 380 GLN cc_start: 0.8419 (pm20) cc_final: 0.8124 (pm20) outliers start: 25 outliers final: 20 residues processed: 217 average time/residue: 0.3082 time to fit residues: 94.6900 Evaluate side-chains 208 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 187 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 132 optimal weight: 9.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 528 GLN A 535 GLN B 663 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15178 Z= 0.253 Angle : 0.561 8.429 20722 Z= 0.284 Chirality : 0.042 0.278 2313 Planarity : 0.005 0.054 2532 Dihedral : 13.222 169.265 2463 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.86 % Allowed : 12.95 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.20), residues: 1729 helix: 0.85 (0.20), residues: 723 sheet: -0.66 (0.35), residues: 223 loop : -1.27 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 185 HIS 0.004 0.001 HIS A 573 PHE 0.022 0.001 PHE C 41 TYR 0.022 0.001 TYR B 632 ARG 0.006 0.000 ARG B 708 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 190 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8658 (m-30) cc_final: 0.8442 (p0) REVERT: A 159 GLN cc_start: 0.9150 (tp40) cc_final: 0.8775 (tp-100) REVERT: A 607 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9017 (t) REVERT: B 151 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.8042 (mtt180) REVERT: B 167 ASP cc_start: 0.8029 (m-30) cc_final: 0.7676 (m-30) REVERT: B 186 ASP cc_start: 0.8746 (t70) cc_final: 0.8395 (t0) REVERT: B 248 MET cc_start: 0.9127 (tpp) cc_final: 0.8845 (tpt) REVERT: B 255 LYS cc_start: 0.8855 (ttmm) cc_final: 0.8508 (tttp) REVERT: B 473 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7616 (mtmm) REVERT: C 18 GLU cc_start: 0.7025 (tp30) cc_final: 0.6824 (tp30) REVERT: C 110 TYR cc_start: 0.8331 (m-80) cc_final: 0.8100 (m-80) REVERT: C 346 GLU cc_start: 0.8960 (tt0) cc_final: 0.8485 (tm-30) REVERT: C 380 GLN cc_start: 0.8428 (pm20) cc_final: 0.8133 (pm20) outliers start: 29 outliers final: 24 residues processed: 213 average time/residue: 0.3201 time to fit residues: 95.8663 Evaluate side-chains 211 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 20.0000 chunk 147 optimal weight: 0.0000 chunk 157 optimal weight: 10.0000 chunk 94 optimal weight: 0.0570 chunk 68 optimal weight: 0.4980 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 148 optimal weight: 0.2980 chunk 156 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 overall best weight: 0.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15178 Z= 0.142 Angle : 0.533 7.921 20722 Z= 0.268 Chirality : 0.040 0.215 2313 Planarity : 0.004 0.056 2532 Dihedral : 13.101 168.223 2463 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.60 % Allowed : 13.46 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1729 helix: 0.94 (0.20), residues: 721 sheet: -0.56 (0.35), residues: 223 loop : -1.19 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 185 HIS 0.004 0.001 HIS C 443 PHE 0.027 0.001 PHE C 383 TYR 0.013 0.001 TYR B 533 ARG 0.007 0.000 ARG B 701 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8660 (m-30) cc_final: 0.8444 (p0) REVERT: A 159 GLN cc_start: 0.9141 (tp40) cc_final: 0.8761 (tp-100) REVERT: A 607 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.9019 (t) REVERT: B 151 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.8025 (mtt180) REVERT: B 167 ASP cc_start: 0.8007 (m-30) cc_final: 0.7651 (m-30) REVERT: B 186 ASP cc_start: 0.8720 (t70) cc_final: 0.8402 (t0) REVERT: B 248 MET cc_start: 0.9080 (tpp) cc_final: 0.8737 (tpt) REVERT: B 255 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8521 (tttp) REVERT: B 473 LYS cc_start: 0.7854 (mmmt) cc_final: 0.7594 (mtmm) REVERT: C 18 GLU cc_start: 0.7052 (tp30) cc_final: 0.6837 (tp30) REVERT: C 110 TYR cc_start: 0.8277 (m-80) cc_final: 0.8024 (m-80) REVERT: C 346 GLU cc_start: 0.8958 (tt0) cc_final: 0.8459 (tm-30) REVERT: C 374 PHE cc_start: 0.8336 (p90) cc_final: 0.7986 (p90) REVERT: C 380 GLN cc_start: 0.8403 (pm20) cc_final: 0.8079 (pm20) outliers start: 25 outliers final: 22 residues processed: 216 average time/residue: 0.3194 time to fit residues: 97.3452 Evaluate side-chains 214 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.0060 chunk 115 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 160 optimal weight: 0.0970 chunk 138 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN B 123 GLN ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 15178 Z= 0.213 Angle : 0.766 59.199 20722 Z= 0.442 Chirality : 0.040 0.211 2313 Planarity : 0.005 0.097 2532 Dihedral : 13.099 168.230 2463 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.54 % Allowed : 13.65 % Favored : 84.81 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1729 helix: 0.93 (0.20), residues: 721 sheet: -0.54 (0.35), residues: 223 loop : -1.18 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 185 HIS 0.010 0.001 HIS C 233 PHE 0.026 0.001 PHE C 383 TYR 0.017 0.001 TYR C 382 ARG 0.006 0.000 ARG B 708 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8661 (m-30) cc_final: 0.8445 (p0) REVERT: A 159 GLN cc_start: 0.9141 (tp40) cc_final: 0.8761 (tp-100) REVERT: B 151 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.8025 (mtt180) REVERT: B 167 ASP cc_start: 0.8003 (m-30) cc_final: 0.7652 (m-30) REVERT: B 186 ASP cc_start: 0.8684 (t70) cc_final: 0.8400 (t0) REVERT: B 248 MET cc_start: 0.9079 (tpp) cc_final: 0.8741 (tpt) REVERT: B 255 LYS cc_start: 0.8819 (ttmm) cc_final: 0.8524 (tttp) REVERT: B 473 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7590 (mtmm) REVERT: C 110 TYR cc_start: 0.8255 (m-80) cc_final: 0.8003 (m-80) REVERT: C 346 GLU cc_start: 0.8958 (tt0) cc_final: 0.8460 (tm-30) REVERT: C 374 PHE cc_start: 0.8364 (p90) cc_final: 0.7995 (p90) REVERT: C 380 GLN cc_start: 0.8421 (pm20) cc_final: 0.8092 (pm20) outliers start: 24 outliers final: 20 residues processed: 207 average time/residue: 0.3280 time to fit residues: 95.9226 Evaluate side-chains 210 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.120737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.085618 restraints weight = 59805.464| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.60 r_work: 0.2847 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 15178 Z= 0.213 Angle : 0.766 59.199 20722 Z= 0.442 Chirality : 0.040 0.211 2313 Planarity : 0.005 0.097 2532 Dihedral : 13.099 168.230 2463 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.28 % Allowed : 13.97 % Favored : 84.74 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.20), residues: 1729 helix: 0.93 (0.20), residues: 721 sheet: -0.54 (0.35), residues: 223 loop : -1.18 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 185 HIS 0.010 0.001 HIS C 233 PHE 0.026 0.001 PHE C 383 TYR 0.017 0.001 TYR C 382 ARG 0.006 0.000 ARG B 708 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3149.73 seconds wall clock time: 57 minutes 6.50 seconds (3426.50 seconds total)