Starting phenix.real_space_refine on Thu Mar 14 16:59:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5u_0681/03_2024/6j5u_0681_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5u_0681/03_2024/6j5u_0681.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5u_0681/03_2024/6j5u_0681_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5u_0681/03_2024/6j5u_0681_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5u_0681/03_2024/6j5u_0681_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5u_0681/03_2024/6j5u_0681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5u_0681/03_2024/6j5u_0681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5u_0681/03_2024/6j5u_0681_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j5u_0681/03_2024/6j5u_0681_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 59 5.16 5 C 5895 2.51 5 N 1585 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 513": "NH1" <-> "NH2" Residue "A ARG 670": "NH1" <-> "NH2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 326": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9288 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5266 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 26, 'TRANS': 636} Chain breaks: 2 Chain: "C" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1340 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain breaks: 4 Chain: "B" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2629 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N BQL C 501 " occ=0.00 ... (24 atoms not shown) pdb=" P BQL C 501 " occ=0.00 Time building chain proxies: 5.15, per 1000 atoms: 0.55 Number of scatterers: 9288 At special positions: 0 Unit cell: (88.371, 92.735, 133.102, 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 59 16.00 P 2 15.00 O 1747 8.00 N 1585 7.00 C 5895 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 additional links: simple=2, symmetry=0 Simple link: pdb=" C VAL C 252 " - pdb=" N BQL C 501 " Simple link: pdb=" N LYS C 255 " - pdb=" C BQO C 502 " Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 8 sheets defined 34.9% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.659A pdb=" N VAL A 6 " --> pdb=" O VAL A 2 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 43 removed outlier: 5.364A pdb=" N GLU A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.617A pdb=" N ARG A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 80 removed outlier: 3.531A pdb=" N TYR A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.882A pdb=" N GLN A 90 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG A 91 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 93 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 97 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.713A pdb=" N TRP A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 376 through 390 removed outlier: 4.519A pdb=" N GLU A 389 " --> pdb=" O HIS A 385 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 406 through 409 No H-bonds generated for 'chain 'A' and resid 406 through 409' Processing helix chain 'A' and resid 413 through 423 removed outlier: 3.858A pdb=" N CYS A 418 " --> pdb=" O HIS A 414 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 443 removed outlier: 4.936A pdb=" N HIS A 438 " --> pdb=" O GLN A 434 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 467 removed outlier: 4.061A pdb=" N ASP A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 removed outlier: 4.042A pdb=" N LEU A 494 " --> pdb=" O MET A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 555 removed outlier: 3.710A pdb=" N LYS A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 584 No H-bonds generated for 'chain 'A' and resid 582 through 584' Processing helix chain 'A' and resid 628 through 631 removed outlier: 3.756A pdb=" N VAL A 631 " --> pdb=" O PRO A 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 628 through 631' Processing helix chain 'A' and resid 654 through 656 No H-bonds generated for 'chain 'A' and resid 654 through 656' Processing helix chain 'A' and resid 677 through 682 removed outlier: 4.944A pdb=" N ASN A 682 " --> pdb=" O SER A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 705 removed outlier: 4.148A pdb=" N ASP A 705 " --> pdb=" O GLU A 702 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 702 through 705' Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.777A pdb=" N THR A 730 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 808 through 814 Processing helix chain 'C' and resid 194 through 209 removed outlier: 3.914A pdb=" N PHE C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 291 Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 338 through 348 Processing helix chain 'C' and resid 362 through 366 removed outlier: 3.525A pdb=" N LEU C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 362 through 366' Processing helix chain 'B' and resid 19 through 38 removed outlier: 3.591A pdb=" N SER B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 removed outlier: 4.011A pdb=" N LYS B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 98 through 116 removed outlier: 3.855A pdb=" N TYR B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 181 removed outlier: 4.368A pdb=" N ALA B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 249 through 263 removed outlier: 3.982A pdb=" N SER B 253 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 290 removed outlier: 3.856A pdb=" N ARG B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 327 through 329 No H-bonds generated for 'chain 'B' and resid 327 through 329' Processing helix chain 'B' and resid 333 through 346 removed outlier: 4.591A pdb=" N GLU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N SER B 346 " --> pdb=" O GLN B 342 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 515 through 517 Processing sheet with id= B, first strand: chain 'A' and resid 590 through 592 removed outlier: 6.762A pdb=" N ILE A 614 " --> pdb=" O LEU A 591 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 638 through 640 removed outlier: 6.812A pdb=" N VAL A 662 " --> pdb=" O LEU A 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 688 through 692 removed outlier: 6.575A pdb=" N SER A 715 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N LEU A 691 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N SER A 717 " --> pdb=" O LEU A 691 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 743 through 746 removed outlier: 6.050A pdb=" N TYR A 768 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU A 746 " --> pdb=" O TYR A 768 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N SER A 770 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY A 795 " --> pdb=" O MET A 769 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ILE A 771 " --> pdb=" O GLY A 795 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET A 797 " --> pdb=" O ILE A 771 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR A 820 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LEU A 798 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR A 822 " --> pdb=" O LEU A 798 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 82 through 87 removed outlier: 5.322A pdb=" N ARG B 76 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE B 65 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 125 through 127 removed outlier: 4.403A pdb=" N GLY B 125 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 186 through 189 removed outlier: 3.618A pdb=" N ILE B 186 " --> pdb=" O LEU B 216 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 603 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1562 1.31 - 1.44: 2405 1.44 - 1.57: 5410 1.57 - 1.69: 6 1.69 - 1.82: 86 Bond restraints: 9469 Sorted by residual: bond pdb=" C1' BQO C 502 " pdb=" C2' BQO C 502 " ideal model delta sigma weight residual 1.314 1.487 -0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C2' BQO C 502 " pdb=" C3' BQO C 502 " ideal model delta sigma weight residual 1.635 1.469 0.166 2.00e-02 2.50e+03 6.93e+01 bond pdb=" C3 BQO C 502 " pdb=" C3' BQO C 502 " ideal model delta sigma weight residual 1.322 1.481 -0.159 2.00e-02 2.50e+03 6.36e+01 bond pdb=" C2 BQO C 502 " pdb=" N1 BQO C 502 " ideal model delta sigma weight residual 1.512 1.354 0.158 2.00e-02 2.50e+03 6.28e+01 bond pdb=" C4 BQO C 502 " pdb=" C5 BQO C 502 " ideal model delta sigma weight residual 1.508 1.354 0.154 2.00e-02 2.50e+03 5.93e+01 ... (remaining 9464 not shown) Histogram of bond angle deviations from ideal: 94.45 - 102.92: 58 102.92 - 111.40: 3750 111.40 - 119.87: 4891 119.87 - 128.35: 4010 128.35 - 136.83: 92 Bond angle restraints: 12801 Sorted by residual: angle pdb=" C ALA B 182 " pdb=" N PHE B 183 " pdb=" CA PHE B 183 " ideal model delta sigma weight residual 123.96 116.27 7.69 1.44e+00 4.82e-01 2.85e+01 angle pdb=" N VAL A 631 " pdb=" CA VAL A 631 " pdb=" C VAL A 631 " ideal model delta sigma weight residual 112.29 107.40 4.89 9.40e-01 1.13e+00 2.71e+01 angle pdb=" N VAL A 400 " pdb=" CA VAL A 400 " pdb=" C VAL A 400 " ideal model delta sigma weight residual 113.47 108.69 4.78 1.01e+00 9.80e-01 2.24e+01 angle pdb=" CA THR A 541 " pdb=" CB THR A 541 " pdb=" CG2 THR A 541 " ideal model delta sigma weight residual 110.50 118.53 -8.03 1.70e+00 3.46e-01 2.23e+01 angle pdb=" C GLY B 274 " pdb=" N ASP B 275 " pdb=" CA ASP B 275 " ideal model delta sigma weight residual 121.54 130.52 -8.98 1.91e+00 2.74e-01 2.21e+01 ... (remaining 12796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 5323 22.19 - 44.38: 414 44.38 - 66.57: 24 66.57 - 88.76: 5 88.76 - 110.95: 2 Dihedral angle restraints: 5768 sinusoidal: 2386 harmonic: 3382 Sorted by residual: dihedral pdb=" CA LYS A 531 " pdb=" C LYS A 531 " pdb=" N LEU A 532 " pdb=" CA LEU A 532 " ideal model delta harmonic sigma weight residual 180.00 141.69 38.31 0 5.00e+00 4.00e-02 5.87e+01 dihedral pdb=" CA CYS A 649 " pdb=" C CYS A 649 " pdb=" N PHE A 650 " pdb=" CA PHE A 650 " ideal model delta harmonic sigma weight residual 180.00 143.18 36.82 0 5.00e+00 4.00e-02 5.42e+01 dihedral pdb=" CA GLU C 266 " pdb=" C GLU C 266 " pdb=" N TYR C 267 " pdb=" CA TYR C 267 " ideal model delta harmonic sigma weight residual 180.00 145.84 34.16 0 5.00e+00 4.00e-02 4.67e+01 ... (remaining 5765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1061 0.073 - 0.147: 316 0.147 - 0.220: 60 0.220 - 0.294: 10 0.294 - 0.367: 2 Chirality restraints: 1449 Sorted by residual: chirality pdb=" CB THR C 190 " pdb=" CA THR C 190 " pdb=" OG1 THR C 190 " pdb=" CG2 THR C 190 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB ILE A 614 " pdb=" CA ILE A 614 " pdb=" CG1 ILE A 614 " pdb=" CG2 ILE A 614 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ASP B 209 " pdb=" N ASP B 209 " pdb=" C ASP B 209 " pdb=" CB ASP B 209 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1446 not shown) Planarity restraints: 1623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 43 " 0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO B 44 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 525 " 0.015 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C GLN A 525 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN A 525 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE A 526 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 101 " 0.049 5.00e-02 4.00e+02 7.41e-02 8.80e+00 pdb=" N PRO A 102 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 102 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 102 " 0.041 5.00e-02 4.00e+02 ... (remaining 1620 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 9 2.26 - 2.92: 3913 2.92 - 3.58: 14467 3.58 - 4.24: 22798 4.24 - 4.90: 35616 Nonbonded interactions: 76803 Sorted by model distance: nonbonded pdb=" CA GLU A 396 " pdb=" ND2 ASN A 399 " model vdw 1.599 3.550 nonbonded pdb=" C GLU A 396 " pdb=" ND2 ASN A 399 " model vdw 1.680 3.350 nonbonded pdb=" O GLU A 396 " pdb=" ND2 ASN A 399 " model vdw 1.843 2.520 nonbonded pdb=" O PHE C 182 " pdb=" N ARG C 184 " model vdw 1.936 2.520 nonbonded pdb=" O SER A 395 " pdb=" CG ASN A 399 " model vdw 1.946 3.270 ... (remaining 76798 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.320 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 26.510 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 0.010 0.173 9469 Z= 0.613 Angle : 1.375 13.827 12801 Z= 0.701 Chirality : 0.072 0.367 1449 Planarity : 0.008 0.089 1621 Dihedral : 14.579 110.947 3568 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.36 % Favored : 85.29 % Rotamer: Outliers : 2.32 % Allowed : 12.17 % Favored : 85.51 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: -5.13 (0.20), residues: 1142 helix: -3.59 (0.16), residues: 414 sheet: -3.38 (0.51), residues: 88 loop : -3.37 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 162 HIS 0.012 0.003 HIS B 180 PHE 0.031 0.004 PHE B 232 TYR 0.047 0.003 TYR A 560 ARG 0.024 0.002 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 323 time to evaluate : 1.008 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: A 96 TRP cc_start: 0.7644 (p90) cc_final: 0.6901 (p90) REVERT: A 351 ILE cc_start: 0.9141 (mp) cc_final: 0.8689 (mm) REVERT: A 359 PRO cc_start: 0.8918 (Cg_exo) cc_final: 0.7782 (Cg_endo) REVERT: A 381 ARG cc_start: 0.8873 (tmt90) cc_final: 0.8608 (ttp-110) REVERT: A 425 TYR cc_start: 0.7944 (m-80) cc_final: 0.7654 (m-10) REVERT: A 435 GLN cc_start: 0.8037 (mt0) cc_final: 0.7637 (tp-100) REVERT: A 513 ARG cc_start: 0.6683 (tpm170) cc_final: 0.6410 (tpp-160) REVERT: A 614 ILE cc_start: 0.8837 (pp) cc_final: 0.8578 (pt) REVERT: A 746 LEU cc_start: 0.8534 (pt) cc_final: 0.8289 (pt) REVERT: C 184 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7150 (tpt-90) REVERT: C 196 LYS cc_start: 0.7193 (mttt) cc_final: 0.6724 (mmtm) REVERT: C 267 TYR cc_start: 0.8046 (t80) cc_final: 0.7705 (t80) REVERT: B 114 MET cc_start: 0.7710 (tpp) cc_final: 0.6805 (tpp) REVERT: B 164 VAL cc_start: 0.9130 (m) cc_final: 0.8641 (t) REVERT: B 168 ILE cc_start: 0.9523 (pt) cc_final: 0.8934 (mt) REVERT: B 190 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6976 (ptt90) REVERT: B 192 VAL cc_start: 0.9082 (OUTLIER) cc_final: 0.8592 (m) REVERT: B 201 LYS cc_start: 0.8682 (pptt) cc_final: 0.7963 (tttp) REVERT: B 202 ASN cc_start: 0.8634 (t0) cc_final: 0.8422 (t0) REVERT: B 342 GLN cc_start: 0.7931 (pp30) cc_final: 0.7715 (pp30) outliers start: 24 outliers final: 10 residues processed: 337 average time/residue: 0.2346 time to fit residues: 104.8512 Evaluate side-chains 226 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 213 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 0.0870 chunk 104 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 35 GLN ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN A 377 HIS ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 HIS A 488 HIS A 525 GLN A 627 GLN A 643 ASN A 673 ASN A 786 ASN C 343 ASN B 39 ASN B 52 GLN B 59 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9469 Z= 0.209 Angle : 0.840 14.049 12801 Z= 0.414 Chirality : 0.049 0.220 1449 Planarity : 0.006 0.078 1621 Dihedral : 11.046 106.939 1318 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 5.60 % Allowed : 17.87 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.32 (0.21), residues: 1142 helix: -2.62 (0.20), residues: 429 sheet: -3.21 (0.53), residues: 79 loop : -3.09 (0.22), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 227 HIS 0.007 0.001 HIS A 385 PHE 0.023 0.002 PHE A 633 TYR 0.026 0.002 TYR B 105 ARG 0.005 0.001 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 245 time to evaluate : 0.944 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 149 ARG cc_start: 0.8767 (ttp-110) cc_final: 0.8564 (mtm110) REVERT: A 351 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9048 (mm) REVERT: A 359 PRO cc_start: 0.8942 (Cg_exo) cc_final: 0.8242 (Cg_endo) REVERT: A 381 ARG cc_start: 0.8947 (tmt90) cc_final: 0.8602 (tmm-80) REVERT: A 417 SER cc_start: 0.9036 (OUTLIER) cc_final: 0.8821 (t) REVERT: A 424 LEU cc_start: 0.9025 (tp) cc_final: 0.8795 (tp) REVERT: A 435 GLN cc_start: 0.8042 (mt0) cc_final: 0.7591 (tp-100) REVERT: A 546 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7563 (mmtp) REVERT: A 614 ILE cc_start: 0.8937 (pp) cc_final: 0.8692 (pt) REVERT: A 688 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8398 (mtpp) REVERT: A 721 TYR cc_start: 0.6057 (t80) cc_final: 0.4374 (t80) REVERT: C 187 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7138 (tp40) REVERT: C 196 LYS cc_start: 0.7192 (mttt) cc_final: 0.6837 (mmtm) REVERT: C 288 GLU cc_start: 0.8258 (tp30) cc_final: 0.7658 (tp30) REVERT: C 310 TRP cc_start: 0.8824 (t60) cc_final: 0.8520 (t60) REVERT: C 359 MET cc_start: 0.7039 (tpp) cc_final: 0.6231 (pmm) REVERT: B 113 ARG cc_start: 0.8774 (tmm-80) cc_final: 0.8376 (ttt-90) REVERT: B 114 MET cc_start: 0.7665 (tpp) cc_final: 0.6873 (mpp) REVERT: B 119 ASN cc_start: 0.7379 (t0) cc_final: 0.7131 (t0) REVERT: B 160 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8156 (pp) REVERT: B 164 VAL cc_start: 0.9041 (m) cc_final: 0.8655 (t) REVERT: B 168 ILE cc_start: 0.9451 (pt) cc_final: 0.8836 (mt) REVERT: B 170 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8533 (pmtt) REVERT: B 342 GLN cc_start: 0.7789 (pp30) cc_final: 0.7482 (pp30) outliers start: 58 outliers final: 22 residues processed: 282 average time/residue: 0.2213 time to fit residues: 84.0077 Evaluate side-chains 232 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 205 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 83 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: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 434 GLN A 622 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9469 Z= 0.298 Angle : 0.833 15.771 12801 Z= 0.411 Chirality : 0.049 0.208 1449 Planarity : 0.005 0.073 1621 Dihedral : 9.966 94.592 1303 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 6.96 % Allowed : 19.03 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.23), residues: 1142 helix: -2.07 (0.22), residues: 416 sheet: -3.22 (0.54), residues: 74 loop : -2.92 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 227 HIS 0.008 0.002 HIS B 240 PHE 0.018 0.002 PHE B 232 TYR 0.019 0.002 TYR B 239 ARG 0.005 0.001 ARG C 272 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 213 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8484 (ptm-80) REVERT: A 149 ARG cc_start: 0.8741 (ttp-110) cc_final: 0.8540 (mtm110) REVERT: A 351 ILE cc_start: 0.9487 (OUTLIER) cc_final: 0.9151 (mm) REVERT: A 359 PRO cc_start: 0.8884 (Cg_exo) cc_final: 0.8264 (Cg_endo) REVERT: A 381 ARG cc_start: 0.8966 (tmt90) cc_final: 0.8753 (tmm-80) REVERT: A 424 LEU cc_start: 0.9124 (tp) cc_final: 0.8855 (tp) REVERT: A 435 GLN cc_start: 0.8225 (mt0) cc_final: 0.7816 (tp-100) REVERT: A 546 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7826 (mmtp) REVERT: A 614 ILE cc_start: 0.8971 (pp) cc_final: 0.8715 (pt) REVERT: A 832 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: C 187 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6340 (tm130) REVERT: C 196 LYS cc_start: 0.7226 (mttt) cc_final: 0.6801 (mmtm) REVERT: C 288 GLU cc_start: 0.8272 (tp30) cc_final: 0.7584 (tp30) REVERT: C 310 TRP cc_start: 0.8722 (t60) cc_final: 0.8487 (t60) REVERT: C 361 GLU cc_start: 0.8497 (tt0) cc_final: 0.7698 (tm-30) REVERT: B 113 ARG cc_start: 0.8767 (tmm-80) cc_final: 0.8258 (ttt-90) REVERT: B 114 MET cc_start: 0.7796 (tpp) cc_final: 0.7122 (mpp) REVERT: B 122 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: B 160 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8202 (pp) REVERT: B 164 VAL cc_start: 0.9071 (m) cc_final: 0.8717 (t) REVERT: B 168 ILE cc_start: 0.9470 (pt) cc_final: 0.8795 (mt) REVERT: B 170 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8608 (pmtt) REVERT: B 333 MET cc_start: 0.7611 (mmm) cc_final: 0.7070 (mmm) REVERT: B 342 GLN cc_start: 0.7979 (pp30) cc_final: 0.7668 (pp30) outliers start: 72 outliers final: 37 residues processed: 261 average time/residue: 0.2219 time to fit residues: 78.7138 Evaluate side-chains 232 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 188 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ARG Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9469 Z= 0.297 Angle : 0.836 15.967 12801 Z= 0.412 Chirality : 0.050 0.212 1449 Planarity : 0.005 0.075 1621 Dihedral : 9.463 80.903 1303 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 25.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 6.76 % Allowed : 22.61 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.23), residues: 1142 helix: -1.87 (0.23), residues: 421 sheet: -3.09 (0.56), residues: 71 loop : -2.76 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 227 HIS 0.010 0.002 HIS B 240 PHE 0.016 0.002 PHE A 521 TYR 0.017 0.002 TYR C 267 ARG 0.006 0.001 ARG A 695 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 215 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7509 (p90) cc_final: 0.6709 (p90) REVERT: A 149 ARG cc_start: 0.8718 (ttp-110) cc_final: 0.8456 (mtm110) REVERT: A 351 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9205 (mm) REVERT: A 359 PRO cc_start: 0.9011 (Cg_exo) cc_final: 0.8466 (Cg_endo) REVERT: A 381 ARG cc_start: 0.8916 (tmt90) cc_final: 0.8614 (tmm-80) REVERT: A 416 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7917 (tttp) REVERT: A 435 GLN cc_start: 0.8257 (mt0) cc_final: 0.7817 (tp-100) REVERT: A 614 ILE cc_start: 0.8952 (pp) cc_final: 0.8709 (pt) REVERT: A 801 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7942 (pt) REVERT: C 187 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6151 (tm130) REVERT: C 196 LYS cc_start: 0.7231 (mttt) cc_final: 0.6804 (mmtm) REVERT: C 255 LYS cc_start: 0.7604 (pttp) cc_final: 0.7335 (pttp) REVERT: C 310 TRP cc_start: 0.8791 (t60) cc_final: 0.8572 (t60) REVERT: C 325 MET cc_start: 0.6671 (OUTLIER) cc_final: 0.6005 (pp-130) REVERT: C 361 GLU cc_start: 0.8513 (tt0) cc_final: 0.7848 (tm-30) REVERT: B 29 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9061 (tt) REVERT: B 114 MET cc_start: 0.7885 (tpp) cc_final: 0.6947 (mpp) REVERT: B 122 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8483 (tt0) REVERT: B 160 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8361 (pp) REVERT: B 164 VAL cc_start: 0.9081 (m) cc_final: 0.8725 (t) REVERT: B 168 ILE cc_start: 0.9459 (pt) cc_final: 0.8866 (mt) REVERT: B 190 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7227 (ptt90) REVERT: B 333 MET cc_start: 0.7665 (mmm) cc_final: 0.7350 (mmm) REVERT: B 342 GLN cc_start: 0.8084 (pp30) cc_final: 0.7791 (pp30) outliers start: 70 outliers final: 40 residues processed: 258 average time/residue: 0.2238 time to fit residues: 78.1261 Evaluate side-chains 236 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 402 SER Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 545 ASN Chi-restraints excluded: chain A residue 565 ASP Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 771 ILE Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain A residue 837 VAL Chi-restraints excluded: chain C residue 187 GLN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 241 LYS Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 340 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 GLN A 673 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9469 Z= 0.208 Angle : 0.800 14.259 12801 Z= 0.388 Chirality : 0.049 0.234 1449 Planarity : 0.005 0.073 1621 Dihedral : 8.771 75.462 1303 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 5.99 % Allowed : 23.86 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.22 % 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: -3.36 (0.23), residues: 1142 helix: -1.68 (0.23), residues: 432 sheet: -3.18 (0.55), residues: 66 loop : -2.59 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 150 HIS 0.010 0.001 HIS B 240 PHE 0.021 0.002 PHE A 832 TYR 0.014 0.001 TYR B 239 ARG 0.008 0.001 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 213 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 ARG cc_start: 0.8697 (ttp-110) cc_final: 0.8467 (mtm110) REVERT: A 317 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8335 (mm) REVERT: A 351 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9169 (mm) REVERT: A 359 PRO cc_start: 0.8996 (Cg_exo) cc_final: 0.8513 (Cg_endo) REVERT: A 401 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8212 (tpt) REVERT: A 417 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8740 (t) REVERT: A 614 ILE cc_start: 0.8815 (pp) cc_final: 0.8507 (pt) REVERT: A 666 PHE cc_start: 0.6940 (t80) cc_final: 0.6705 (t80) REVERT: A 721 TYR cc_start: 0.6414 (t80) cc_final: 0.4825 (t80) REVERT: A 746 LEU cc_start: 0.8760 (pt) cc_final: 0.8487 (pt) REVERT: C 196 LYS cc_start: 0.7142 (mttt) cc_final: 0.6755 (mmtm) REVERT: C 310 TRP cc_start: 0.8830 (t60) cc_final: 0.8409 (t60) REVERT: C 325 MET cc_start: 0.6581 (OUTLIER) cc_final: 0.5915 (pp-130) REVERT: C 361 GLU cc_start: 0.8425 (tt0) cc_final: 0.7853 (tm-30) REVERT: B 18 LYS cc_start: 0.8372 (mmtt) cc_final: 0.8137 (tppt) REVERT: B 122 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8532 (tm-30) REVERT: B 123 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8832 (tt) REVERT: B 160 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8350 (pp) REVERT: B 164 VAL cc_start: 0.8996 (m) cc_final: 0.8692 (t) REVERT: B 168 ILE cc_start: 0.9453 (pt) cc_final: 0.8864 (mt) REVERT: B 190 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.6927 (ptt90) REVERT: B 342 GLN cc_start: 0.7969 (pp30) cc_final: 0.7662 (pp30) outliers start: 62 outliers final: 32 residues processed: 255 average time/residue: 0.2098 time to fit residues: 73.7745 Evaluate side-chains 231 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 0.0170 chunk 27 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.0270 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 107 optimal weight: 0.2980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9469 Z= 0.184 Angle : 0.802 13.066 12801 Z= 0.383 Chirality : 0.048 0.199 1449 Planarity : 0.005 0.072 1621 Dihedral : 7.976 68.954 1298 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 5.02 % Allowed : 24.64 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.23 (0.23), residues: 1142 helix: -1.49 (0.24), residues: 425 sheet: -3.08 (0.56), residues: 66 loop : -2.58 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 808 HIS 0.008 0.001 HIS A 377 PHE 0.024 0.002 PHE B 232 TYR 0.015 0.001 TYR B 239 ARG 0.006 0.001 ARG A 381 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 222 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7276 (pp20) cc_final: 0.7053 (pp20) REVERT: A 149 ARG cc_start: 0.8651 (ttp-110) cc_final: 0.8410 (mtm110) REVERT: A 351 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9165 (mm) REVERT: A 356 LYS cc_start: 0.8663 (mmpt) cc_final: 0.8456 (mmpt) REVERT: A 363 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8544 (ptmt) REVERT: A 417 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8755 (t) REVERT: A 614 ILE cc_start: 0.8718 (pp) cc_final: 0.8445 (pt) REVERT: A 721 TYR cc_start: 0.6326 (t80) cc_final: 0.4644 (t80) REVERT: C 196 LYS cc_start: 0.7280 (mttt) cc_final: 0.6910 (mmtm) REVERT: C 267 TYR cc_start: 0.7743 (t80) cc_final: 0.7362 (t80) REVERT: C 310 TRP cc_start: 0.8791 (t60) cc_final: 0.8397 (t60) REVERT: C 325 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.5883 (pp-130) REVERT: C 361 GLU cc_start: 0.8343 (tt0) cc_final: 0.7860 (tm-30) REVERT: B 114 MET cc_start: 0.7579 (tpp) cc_final: 0.6804 (mpp) REVERT: B 122 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8486 (tm-30) REVERT: B 123 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8805 (tt) REVERT: B 160 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8320 (pp) REVERT: B 164 VAL cc_start: 0.9000 (m) cc_final: 0.8675 (t) REVERT: B 168 ILE cc_start: 0.9404 (pt) cc_final: 0.8859 (mt) REVERT: B 190 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.6797 (ptt90) REVERT: B 342 GLN cc_start: 0.8038 (pp30) cc_final: 0.7697 (pp30) outliers start: 52 outliers final: 36 residues processed: 251 average time/residue: 0.2117 time to fit residues: 73.4814 Evaluate side-chains 242 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 199 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9469 Z= 0.238 Angle : 0.813 14.006 12801 Z= 0.395 Chirality : 0.049 0.226 1449 Planarity : 0.005 0.072 1621 Dihedral : 7.850 68.379 1295 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 5.12 % Allowed : 25.60 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.21 (0.24), residues: 1142 helix: -1.41 (0.24), residues: 421 sheet: -3.09 (0.57), residues: 68 loop : -2.61 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 22 HIS 0.009 0.002 HIS C 209 PHE 0.022 0.002 PHE B 232 TYR 0.020 0.002 TYR A 749 ARG 0.004 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6614 (ptm) cc_final: 0.6396 (ptt) REVERT: A 56 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7874 (tm-30) REVERT: A 73 GLU cc_start: 0.7503 (pp20) cc_final: 0.7268 (pp20) REVERT: A 149 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.8399 (mtm110) REVERT: A 317 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8213 (mm) REVERT: A 344 LEU cc_start: 0.8205 (mp) cc_final: 0.7843 (pp) REVERT: A 351 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9210 (mm) REVERT: A 363 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8558 (mmtt) REVERT: A 417 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8676 (t) REVERT: A 614 ILE cc_start: 0.8841 (pp) cc_final: 0.8577 (pt) REVERT: A 721 TYR cc_start: 0.6502 (t80) cc_final: 0.4761 (t80) REVERT: C 196 LYS cc_start: 0.7276 (mttt) cc_final: 0.6915 (mmtm) REVERT: C 267 TYR cc_start: 0.7995 (t80) cc_final: 0.7625 (t80) REVERT: C 310 TRP cc_start: 0.8812 (t60) cc_final: 0.8512 (t60) REVERT: C 325 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6159 (pp-130) REVERT: C 361 GLU cc_start: 0.8328 (tt0) cc_final: 0.7841 (tm-30) REVERT: B 113 ARG cc_start: 0.8749 (tmm-80) cc_final: 0.8507 (ttp80) REVERT: B 114 MET cc_start: 0.7745 (tpp) cc_final: 0.6897 (mpp) REVERT: B 122 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8569 (tm-30) REVERT: B 123 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8866 (tt) REVERT: B 160 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8292 (pp) REVERT: B 164 VAL cc_start: 0.9040 (m) cc_final: 0.8721 (t) REVERT: B 168 ILE cc_start: 0.9495 (pt) cc_final: 0.8980 (mt) REVERT: B 190 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7139 (ptt90) REVERT: B 342 GLN cc_start: 0.8085 (pp30) cc_final: 0.7804 (pp30) outliers start: 53 outliers final: 36 residues processed: 226 average time/residue: 0.2072 time to fit residues: 65.4919 Evaluate side-chains 231 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9469 Z= 0.255 Angle : 0.830 13.739 12801 Z= 0.401 Chirality : 0.049 0.259 1449 Planarity : 0.005 0.073 1621 Dihedral : 7.835 67.433 1295 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 5.41 % Allowed : 25.70 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.16 (0.24), residues: 1142 helix: -1.30 (0.24), residues: 422 sheet: -3.18 (0.56), residues: 68 loop : -2.61 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP B 22 HIS 0.010 0.002 HIS C 209 PHE 0.021 0.002 PHE B 232 TYR 0.019 0.002 TYR A 749 ARG 0.005 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 195 time to evaluate : 1.096 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 56 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7912 (tm-30) REVERT: A 73 GLU cc_start: 0.7525 (pp20) cc_final: 0.7296 (pp20) REVERT: A 149 ARG cc_start: 0.8703 (ttp-110) cc_final: 0.8495 (mtm110) REVERT: A 317 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8158 (mm) REVERT: A 344 LEU cc_start: 0.8235 (mp) cc_final: 0.7936 (pp) REVERT: A 351 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9210 (mm) REVERT: A 363 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8604 (mmtt) REVERT: A 417 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8706 (t) REVERT: A 487 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8635 (pp) REVERT: A 525 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7476 (pp30) REVERT: A 614 ILE cc_start: 0.8712 (pp) cc_final: 0.8455 (pt) REVERT: A 721 TYR cc_start: 0.6606 (t80) cc_final: 0.4791 (t80) REVERT: A 832 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: A 845 MET cc_start: 0.6078 (tmm) cc_final: 0.5848 (tmm) REVERT: C 196 LYS cc_start: 0.7252 (mttt) cc_final: 0.6859 (mmtm) REVERT: C 267 TYR cc_start: 0.8103 (t80) cc_final: 0.7749 (t80) REVERT: C 272 ARG cc_start: 0.6917 (mtm-85) cc_final: 0.6675 (ptp-170) REVERT: C 310 TRP cc_start: 0.8822 (t60) cc_final: 0.8568 (t60) REVERT: C 325 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6273 (pp-130) REVERT: C 361 GLU cc_start: 0.8294 (tt0) cc_final: 0.7846 (tm-30) REVERT: B 113 ARG cc_start: 0.8799 (tmm-80) cc_final: 0.8573 (ttp80) REVERT: B 114 MET cc_start: 0.7671 (tpp) cc_final: 0.6953 (mpp) REVERT: B 122 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8587 (tm-30) REVERT: B 123 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8909 (tt) REVERT: B 160 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8419 (pp) REVERT: B 164 VAL cc_start: 0.9030 (m) cc_final: 0.8700 (t) REVERT: B 168 ILE cc_start: 0.9503 (pt) cc_final: 0.8969 (mt) REVERT: B 342 GLN cc_start: 0.8158 (pp30) cc_final: 0.7890 (pp30) outliers start: 56 outliers final: 38 residues processed: 232 average time/residue: 0.2135 time to fit residues: 68.6696 Evaluate side-chains 232 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 185 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9469 Z= 0.220 Angle : 0.827 13.401 12801 Z= 0.395 Chirality : 0.048 0.249 1449 Planarity : 0.005 0.073 1621 Dihedral : 7.736 67.546 1295 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 4.83 % Allowed : 26.47 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.06 (0.24), residues: 1142 helix: -1.20 (0.25), residues: 421 sheet: -3.18 (0.57), residues: 68 loop : -2.55 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 22 HIS 0.013 0.002 HIS C 209 PHE 0.031 0.002 PHE B 232 TYR 0.015 0.001 TYR A 749 ARG 0.005 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 192 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLN cc_start: 0.8720 (pt0) cc_final: 0.8492 (mt0) REVERT: A 56 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 149 ARG cc_start: 0.8685 (ttp-110) cc_final: 0.8460 (mtm110) REVERT: A 317 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8044 (mm) REVERT: A 344 LEU cc_start: 0.8076 (mp) cc_final: 0.7823 (pp) REVERT: A 351 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9187 (mm) REVERT: A 358 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8711 (pp) REVERT: A 363 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8592 (mmtt) REVERT: A 417 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8718 (t) REVERT: A 513 ARG cc_start: 0.6621 (tpm170) cc_final: 0.6254 (tpp-160) REVERT: A 721 TYR cc_start: 0.6556 (t80) cc_final: 0.4735 (t80) REVERT: A 815 MET cc_start: 0.8223 (mtm) cc_final: 0.7991 (mtm) REVERT: A 845 MET cc_start: 0.5998 (tmm) cc_final: 0.5761 (tmm) REVERT: C 196 LYS cc_start: 0.7248 (mttt) cc_final: 0.6887 (mmtm) REVERT: C 267 TYR cc_start: 0.8121 (t80) cc_final: 0.7766 (t80) REVERT: C 310 TRP cc_start: 0.8844 (t60) cc_final: 0.8609 (t60) REVERT: C 325 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.6212 (pp-130) REVERT: C 361 GLU cc_start: 0.8298 (tt0) cc_final: 0.7851 (tm-30) REVERT: B 113 ARG cc_start: 0.8762 (tmm-80) cc_final: 0.8422 (ttp80) REVERT: B 114 MET cc_start: 0.7664 (tpp) cc_final: 0.6976 (mpp) REVERT: B 122 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8556 (tm-30) REVERT: B 123 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8860 (tt) REVERT: B 164 VAL cc_start: 0.9015 (m) cc_final: 0.8707 (t) REVERT: B 168 ILE cc_start: 0.9482 (pt) cc_final: 0.8958 (mt) REVERT: B 342 GLN cc_start: 0.8141 (pp30) cc_final: 0.7890 (pp30) outliers start: 50 outliers final: 36 residues processed: 220 average time/residue: 0.2152 time to fit residues: 65.8964 Evaluate side-chains 232 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 189 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 650 PHE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 744 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 806 MET Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 611 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9469 Z= 0.192 Angle : 0.829 14.303 12801 Z= 0.392 Chirality : 0.048 0.256 1449 Planarity : 0.005 0.073 1621 Dihedral : 7.555 67.197 1295 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 4.35 % Allowed : 27.25 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.93 (0.24), residues: 1142 helix: -1.14 (0.25), residues: 421 sheet: -2.80 (0.59), residues: 63 loop : -2.50 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 22 HIS 0.014 0.001 HIS C 209 PHE 0.018 0.002 PHE A 521 TYR 0.013 0.001 TYR B 239 ARG 0.006 0.001 ARG C 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 205 time to evaluate : 1.119 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 56 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7892 (tm-30) REVERT: A 71 GLU cc_start: 0.8192 (tp30) cc_final: 0.7991 (tp30) REVERT: A 149 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8368 (mtm110) REVERT: A 317 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7995 (mm) REVERT: A 344 LEU cc_start: 0.8091 (mp) cc_final: 0.7812 (pp) REVERT: A 351 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9149 (mm) REVERT: A 358 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8660 (pp) REVERT: A 363 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8525 (mmtt) REVERT: A 417 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8662 (t) REVERT: A 513 ARG cc_start: 0.6573 (tpm170) cc_final: 0.6259 (tpp-160) REVERT: A 525 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7378 (pp30) REVERT: A 721 TYR cc_start: 0.6385 (t80) cc_final: 0.4678 (t80) REVERT: A 815 MET cc_start: 0.8266 (mtm) cc_final: 0.8039 (mtp) REVERT: A 845 MET cc_start: 0.5893 (tmm) cc_final: 0.5677 (tmm) REVERT: C 183 ARG cc_start: 0.8069 (tpp80) cc_final: 0.7863 (tpp80) REVERT: C 195 MET cc_start: 0.7688 (mpp) cc_final: 0.7358 (pmm) REVERT: C 196 LYS cc_start: 0.7145 (mttt) cc_final: 0.6876 (mmtm) REVERT: C 267 TYR cc_start: 0.7916 (t80) cc_final: 0.7588 (t80) REVERT: C 310 TRP cc_start: 0.8796 (t60) cc_final: 0.8584 (t60) REVERT: C 325 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.6094 (pp-130) REVERT: C 361 GLU cc_start: 0.8278 (tt0) cc_final: 0.7837 (tm-30) REVERT: B 113 ARG cc_start: 0.8749 (tmm-80) cc_final: 0.8409 (ttp80) REVERT: B 114 MET cc_start: 0.7653 (tpp) cc_final: 0.6995 (mpp) REVERT: B 122 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8519 (tm-30) REVERT: B 123 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8942 (tt) REVERT: B 164 VAL cc_start: 0.9025 (m) cc_final: 0.8634 (t) REVERT: B 168 ILE cc_start: 0.9460 (pt) cc_final: 0.8914 (mt) REVERT: B 335 GLN cc_start: 0.7900 (pm20) cc_final: 0.7661 (pm20) REVERT: B 342 GLN cc_start: 0.8178 (pp30) cc_final: 0.7925 (pp30) outliers start: 45 outliers final: 31 residues processed: 229 average time/residue: 0.2146 time to fit residues: 67.8150 Evaluate side-chains 231 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 543 GLU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 683 LEU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 93 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.142787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.113995 restraints weight = 19039.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117305 restraints weight = 11352.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.119572 restraints weight = 7963.334| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9469 Z= 0.193 Angle : 0.827 13.982 12801 Z= 0.391 Chirality : 0.048 0.224 1449 Planarity : 0.005 0.072 1621 Dihedral : 7.530 66.682 1295 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 4.15 % Allowed : 28.12 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.88 (0.24), residues: 1142 helix: -1.11 (0.25), residues: 421 sheet: -2.65 (0.61), residues: 58 loop : -2.49 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 22 HIS 0.013 0.001 HIS C 209 PHE 0.018 0.002 PHE A 521 TYR 0.015 0.001 TYR A 749 ARG 0.006 0.000 ARG C 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2153.15 seconds wall clock time: 39 minutes 46.34 seconds (2386.34 seconds total)