Starting phenix.real_space_refine on Fri May 17 02:40:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/05_2024/8r65_18947_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/05_2024/8r65_18947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/05_2024/8r65_18947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/05_2024/8r65_18947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/05_2024/8r65_18947_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r65_18947/05_2024/8r65_18947_updated.pdb" } resolution = 4.23 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= 0.003 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 26 5.49 5 S 124 5.16 5 C 11292 2.51 5 N 3161 2.21 5 O 3476 1.98 5 H 17462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 493": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 558": "OE1" <-> "OE2" Residue "C GLU 578": "OE1" <-> "OE2" Residue "C ARG 650": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 720": "OE1" <-> "OE2" Residue "C ARG 737": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 35541 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11519 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "C" Number of atoms: 11651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 11651 Classifications: {'peptide': 737} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 29, 'TRANS': 707} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "X" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 197 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 7, 'TRANS': 17} Chain: "B" Number of atoms: 11428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 11428 Classifications: {'peptide': 718} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 687} Chain breaks: 2 Time building chain proxies: 15.55, per 1000 atoms: 0.44 Number of scatterers: 35541 At special positions: 0 Unit cell: (133.35, 114.45, 143.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 26 15.00 O 3476 8.00 N 3161 7.00 C 11292 6.00 H 17462 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.03 Conformation dependent library (CDL) restraints added in 3.4 seconds 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4134 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 18 sheets defined 40.3% alpha, 6.8% beta 2 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 20.59 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 165 through 185 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 210 through 217 removed outlier: 3.967A pdb=" N GLN A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 234 Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.880A pdb=" N SER A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 406 through 415 removed outlier: 3.673A pdb=" N CYS A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 454 through 473 Processing helix chain 'A' and resid 572 through 579 removed outlier: 3.658A pdb=" N LYS A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 602 removed outlier: 3.503A pdb=" N CYS A 584 " --> pdb=" O MET A 581 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER A 601 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 633 through 649 Processing helix chain 'A' and resid 653 through 673 removed outlier: 3.771A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 691 Processing helix chain 'A' and resid 698 through 713 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 14 through 22 Processing helix chain 'C' and resid 26 through 33 removed outlier: 3.785A pdb=" N ALA C 29 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.503A pdb=" N THR C 97 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 116 through 126 Processing helix chain 'C' and resid 156 through 167 Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 200 through 211 Processing helix chain 'C' and resid 226 through 231 removed outlier: 4.121A pdb=" N VAL C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 272 removed outlier: 3.877A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 Processing helix chain 'C' and resid 294 through 300 Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 391 through 405 Processing helix chain 'C' and resid 408 through 413 removed outlier: 4.130A pdb=" N ALA C 413 " --> pdb=" O CYS C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 439 removed outlier: 3.629A pdb=" N GLN C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 557 through 563 removed outlier: 4.355A pdb=" N ILE C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 572 No H-bonds generated for 'chain 'C' and resid 569 through 572' Processing helix chain 'C' and resid 578 through 581 No H-bonds generated for 'chain 'C' and resid 578 through 581' Processing helix chain 'C' and resid 589 through 605 Processing helix chain 'C' and resid 612 through 618 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 18 through 21 Processing helix chain 'B' and resid 36 through 48 removed outlier: 3.785A pdb=" N MET B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 123 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.507A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 249 through 265 removed outlier: 3.801A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 removed outlier: 3.519A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 315 through 325 Processing helix chain 'B' and resid 331 through 346 removed outlier: 4.761A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.979A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 373 Processing helix chain 'B' and resid 385 through 395 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 413 through 427 removed outlier: 4.323A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 473 Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'B' and resid 519 through 535 Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 573 through 582 Processing helix chain 'B' and resid 586 through 588 No H-bonds generated for 'chain 'B' and resid 586 through 588' Processing helix chain 'B' and resid 591 through 593 No H-bonds generated for 'chain 'B' and resid 591 through 593' Processing helix chain 'B' and resid 608 through 611 No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 673 through 676 removed outlier: 3.839A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 676' Processing helix chain 'B' and resid 682 through 699 Processing helix chain 'B' and resid 701 through 703 No H-bonds generated for 'chain 'B' and resid 701 through 703' Processing helix chain 'B' and resid 714 through 731 Processing helix chain 'B' and resid 737 through 755 Processing sheet with id= A, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.964A pdb=" N HIS A 144 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLY A 121 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N HIS A 146 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 487 through 490 Processing sheet with id= C, first strand: chain 'A' and resid 502 through 506 removed outlier: 3.536A pdb=" N VAL A 521 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 543 through 547 removed outlier: 7.006A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.064A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 133 through 135 Processing sheet with id= G, first strand: chain 'C' and resid 143 through 146 Processing sheet with id= H, first strand: chain 'C' and resid 342 through 345 Processing sheet with id= I, first strand: chain 'C' and resid 329 through 334 removed outlier: 6.143A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA C 377 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 635 through 639 Processing sheet with id= K, first strand: chain 'C' and resid 656 through 658 Processing sheet with id= L, first strand: chain 'C' and resid 722 through 726 removed outlier: 3.650A pdb=" N LEU C 733 " --> pdb=" O GLY C 698 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY C 698 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N MET C 735 " --> pdb=" O ILE C 696 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE C 696 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 54 through 57 Processing sheet with id= N, first strand: chain 'B' and resid 128 through 130 removed outlier: 4.031A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 179 through 181 Processing sheet with id= P, first strand: chain 'B' and resid 224 through 228 Processing sheet with id= Q, first strand: chain 'B' and resid 298 through 302 removed outlier: 3.615A pdb=" N ALA B 453 " --> pdb=" O LEU B 298 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 348 through 350 629 hydrogen bonds defined for protein. 1665 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 14.10 Time building geometry restraints manager: 31.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 17432 1.00 - 1.21: 31 1.21 - 1.41: 7434 1.41 - 1.61: 10824 1.61 - 1.81: 221 Bond restraints: 35942 Sorted by residual: bond pdb=" C ILE C 319 " pdb=" O ILE C 319 " ideal model delta sigma weight residual 1.235 1.164 0.072 1.05e-02 9.07e+03 4.67e+01 bond pdb=" N ILE C 319 " pdb=" CA ILE C 319 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.15e-02 7.56e+03 1.63e+01 bond pdb=" N SER C 320 " pdb=" CA SER C 320 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL C 494 " pdb=" CA VAL C 494 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.94e+00 bond pdb=" NE2 GLN C 426 " pdb="HE22 GLN C 426 " ideal model delta sigma weight residual 0.860 0.803 0.057 2.00e-02 2.50e+03 8.02e+00 ... (remaining 35937 not shown) Histogram of bond angle deviations from ideal: 83.71 - 95.16: 3 95.16 - 106.60: 744 106.60 - 118.04: 47533 118.04 - 129.48: 16385 129.48 - 140.93: 118 Bond angle restraints: 64783 Sorted by residual: angle pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" C MET C 536 " ideal model delta sigma weight residual 108.07 121.75 -13.68 1.38e+00 5.25e-01 9.83e+01 angle pdb=" C MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 110.00 83.71 26.29 3.00e+00 1.11e-01 7.68e+01 angle pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 110.00 83.87 26.13 3.00e+00 1.11e-01 7.59e+01 angle pdb=" N PRO C 542 " pdb=" CA PRO C 542 " pdb=" C PRO C 542 " ideal model delta sigma weight residual 113.53 102.89 10.64 1.39e+00 5.18e-01 5.86e+01 angle pdb=" CB MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 109.00 86.32 22.68 3.00e+00 1.11e-01 5.72e+01 ... (remaining 64778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15281 17.93 - 35.86: 1158 35.86 - 53.79: 336 53.79 - 71.71: 118 71.71 - 89.64: 28 Dihedral angle restraints: 16921 sinusoidal: 9540 harmonic: 7381 Sorted by residual: dihedral pdb=" C MET C 536 " pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" CB MET C 536 " ideal model delta harmonic sigma weight residual -122.60 -161.29 38.69 0 2.50e+00 1.60e-01 2.39e+02 dihedral pdb=" N MET C 536 " pdb=" C MET C 536 " pdb=" CA MET C 536 " pdb=" CB MET C 536 " ideal model delta harmonic sigma weight residual 122.80 161.21 -38.41 0 2.50e+00 1.60e-01 2.36e+02 dihedral pdb=" CD ARG C 493 " pdb=" NE ARG C 493 " pdb=" CZ ARG C 493 " pdb=" NH1 ARG C 493 " ideal model delta sinusoidal sigma weight residual 0.00 -39.85 39.85 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 16918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.332: 2769 0.332 - 0.663: 0 0.663 - 0.995: 0 0.995 - 1.327: 0 1.327 - 1.658: 1 Chirality restraints: 2770 Sorted by residual: chirality pdb=" CA MET C 536 " pdb=" N MET C 536 " pdb=" C MET C 536 " pdb=" CB MET C 536 " both_signs ideal model delta sigma weight residual False 2.51 0.85 1.66 2.00e-01 2.50e+01 6.87e+01 chirality pdb=" CA ILE C 319 " pdb=" N ILE C 319 " pdb=" C ILE C 319 " pdb=" CB ILE C 319 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA VAL C 495 " pdb=" N VAL C 495 " pdb=" C VAL C 495 " pdb=" CB VAL C 495 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2767 not shown) Planarity restraints: 5236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 641 " 0.413 9.50e-02 1.11e+02 4.66e-01 4.48e+03 pdb=" NE ARG C 641 " 0.117 2.00e-02 2.50e+03 pdb=" CZ ARG C 641 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG C 641 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG C 641 " -0.061 2.00e-02 2.50e+03 pdb="HH11 ARG C 641 " -0.543 2.00e-02 2.50e+03 pdb="HH12 ARG C 641 " 0.592 2.00e-02 2.50e+03 pdb="HH21 ARG C 641 " -0.834 2.00e-02 2.50e+03 pdb="HH22 ARG C 641 " 0.652 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 548 " 0.048 2.00e-02 2.50e+03 4.40e-01 2.91e+03 pdb=" CG ASN C 548 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN C 548 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN C 548 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 548 " 0.764 2.00e-02 2.50e+03 pdb="HD22 ASN C 548 " -0.759 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 493 " -0.676 9.50e-02 1.11e+02 2.60e-01 4.31e+02 pdb=" NE ARG C 493 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG C 493 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C 493 " -0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG C 493 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG C 493 " -0.200 2.00e-02 2.50e+03 pdb="HH12 ARG C 493 " 0.113 2.00e-02 2.50e+03 pdb="HH21 ARG C 493 " 0.237 2.00e-02 2.50e+03 pdb="HH22 ARG C 493 " -0.194 2.00e-02 2.50e+03 ... (remaining 5233 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 63 1.73 - 2.45: 21576 2.45 - 3.17: 108995 3.17 - 3.88: 141207 3.88 - 4.60: 227717 Nonbonded interactions: 499558 Sorted by model distance: nonbonded pdb=" H GLY C 223 " pdb=" OE2 GLU C 525 " model vdw 1.014 1.850 nonbonded pdb=" HE1 HIS A 437 " pdb="HH12 ARG C 646 " model vdw 1.085 2.100 nonbonded pdb="HH12 ARG C 143 " pdb=" OG1 THR C 524 " model vdw 1.216 1.850 nonbonded pdb=" HB3 PRO C 276 " pdb="HD11 LEU C 502 " model vdw 1.338 2.440 nonbonded pdb="HH22 ARG C 143 " pdb="HG21 THR C 524 " model vdw 1.354 2.270 ... (remaining 499553 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=1.00 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.530 Extract box with map and model: 5.570 Check model and map are aligned: 0.330 Set scattering table: 0.350 Process input model: 126.740 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 : 0.005 0.086 18480 Z= 0.308 Angle : 0.621 13.679 25043 Z= 0.359 Chirality : 0.053 1.658 2770 Planarity : 0.007 0.307 3147 Dihedral : 14.382 89.080 7214 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.71 % Favored : 92.78 % Rotamer: Outliers : 1.85 % Allowed : 6.85 % Favored : 91.29 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 2175 helix: 1.04 (0.17), residues: 944 sheet: -2.50 (0.32), residues: 221 loop : -1.99 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 537 HIS 0.005 0.001 HIS C 437 PHE 0.020 0.001 PHE C 323 TYR 0.011 0.001 TYR B 555 ARG 0.010 0.000 ARG C 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 485 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 449 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1 MET cc_start: 0.8901 (ptm) cc_final: 0.8505 (tpt) REVERT: A 540 TYR cc_start: 0.8608 (m-80) cc_final: 0.8062 (m-80) REVERT: A 570 THR cc_start: 0.7711 (t) cc_final: 0.7382 (t) REVERT: A 584 CYS cc_start: 0.9378 (m) cc_final: 0.9129 (m) REVERT: A 587 GLN cc_start: 0.9419 (tt0) cc_final: 0.9057 (tp-100) REVERT: A 594 SER cc_start: 0.9898 (t) cc_final: 0.9680 (p) REVERT: A 649 LEU cc_start: 0.9086 (mt) cc_final: 0.8877 (mt) REVERT: C 26 ASP cc_start: 0.8215 (m-30) cc_final: 0.7844 (m-30) REVERT: C 69 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8594 (tp30) REVERT: C 90 MET cc_start: 0.9378 (mmm) cc_final: 0.9157 (mmm) REVERT: C 153 ASP cc_start: 0.8865 (t70) cc_final: 0.7975 (m-30) REVERT: C 164 MET cc_start: 0.9138 (mtp) cc_final: 0.8821 (tpp) REVERT: C 483 MET cc_start: 0.6425 (mmp) cc_final: 0.6138 (ptp) REVERT: B 131 TRP cc_start: 0.8706 (p-90) cc_final: 0.7716 (p-90) REVERT: B 137 GLN cc_start: 0.9525 (mm-40) cc_final: 0.9291 (mp10) REVERT: B 303 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7491 (p) REVERT: B 508 GLU cc_start: 0.9253 (mp0) cc_final: 0.8910 (mp0) REVERT: B 519 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8624 (mt-10) REVERT: B 538 ASP cc_start: 0.9650 (m-30) cc_final: 0.9295 (p0) REVERT: B 599 TYR cc_start: 0.9272 (m-80) cc_final: 0.8622 (m-80) REVERT: B 606 ILE cc_start: 0.8709 (mt) cc_final: 0.8198 (mp) REVERT: B 657 TYR cc_start: 0.8920 (p90) cc_final: 0.8046 (p90) REVERT: B 687 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8934 (mm-40) outliers start: 36 outliers final: 16 residues processed: 478 average time/residue: 0.8760 time to fit residues: 593.5276 Evaluate side-chains 347 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 328 time to evaluate : 2.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 111 optimal weight: 30.0000 chunk 88 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN A 614 ASN C 27 HIS C 100 ASN ** C 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 18480 Z= 0.255 Angle : 0.568 6.570 25043 Z= 0.312 Chirality : 0.040 0.509 2770 Planarity : 0.005 0.068 3147 Dihedral : 10.023 86.253 2762 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.06 % Favored : 94.71 % Rotamer: Outliers : 0.05 % Allowed : 1.44 % Favored : 98.51 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2175 helix: 0.80 (0.17), residues: 956 sheet: -2.20 (0.32), residues: 222 loop : -1.84 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 537 HIS 0.005 0.001 HIS A 41 PHE 0.058 0.002 PHE B 333 TYR 0.021 0.001 TYR C 228 ARG 0.008 0.000 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 339 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8998 (ptm) cc_final: 0.8504 (tpt) REVERT: A 285 MET cc_start: 0.9295 (ttp) cc_final: 0.8914 (ttp) REVERT: A 311 MET cc_start: 0.9544 (mmp) cc_final: 0.9274 (mmp) REVERT: A 485 MET cc_start: 0.6607 (mtm) cc_final: 0.6239 (mtt) REVERT: A 575 MET cc_start: 0.9250 (mtp) cc_final: 0.8881 (mtm) REVERT: A 581 MET cc_start: 0.9043 (ttm) cc_final: 0.8534 (ttm) REVERT: A 587 GLN cc_start: 0.9419 (tt0) cc_final: 0.9105 (tp-100) REVERT: C 283 MET cc_start: 0.9288 (mmm) cc_final: 0.9031 (tpp) REVERT: C 289 ILE cc_start: 0.8189 (mp) cc_final: 0.7931 (mp) REVERT: C 429 ASN cc_start: 0.6005 (m-40) cc_final: 0.5677 (m-40) REVERT: C 483 MET cc_start: 0.6588 (mmp) cc_final: 0.6263 (mtp) REVERT: B 111 MET cc_start: 0.7315 (mtp) cc_final: 0.6962 (mtt) REVERT: B 137 GLN cc_start: 0.9468 (mm-40) cc_final: 0.8997 (mp10) REVERT: B 321 MET cc_start: 0.9529 (mtt) cc_final: 0.8959 (mtt) REVERT: B 339 ILE cc_start: 0.9706 (tp) cc_final: 0.9476 (tp) REVERT: B 408 MET cc_start: 0.8035 (tpt) cc_final: 0.7400 (tpt) REVERT: B 415 LEU cc_start: 0.9413 (tp) cc_final: 0.9148 (tp) REVERT: B 508 GLU cc_start: 0.8639 (mp0) cc_final: 0.8265 (mp0) REVERT: B 519 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8833 (mt-10) REVERT: B 527 VAL cc_start: 0.9527 (t) cc_final: 0.9225 (p) REVERT: B 599 TYR cc_start: 0.9302 (m-80) cc_final: 0.8623 (m-10) REVERT: B 606 ILE cc_start: 0.8800 (mt) cc_final: 0.8304 (mp) REVERT: B 657 TYR cc_start: 0.8880 (p90) cc_final: 0.8009 (p90) REVERT: B 690 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8962 (tp-100) outliers start: 1 outliers final: 1 residues processed: 340 average time/residue: 0.8282 time to fit residues: 407.9129 Evaluate side-chains 288 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 110 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 164 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 chunk 198 optimal weight: 7.9990 chunk 214 optimal weight: 10.0000 chunk 176 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 18480 Z= 0.285 Angle : 0.586 8.749 25043 Z= 0.322 Chirality : 0.039 0.440 2770 Planarity : 0.004 0.056 3147 Dihedral : 10.032 83.125 2762 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.61 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.18), residues: 2175 helix: 0.54 (0.17), residues: 959 sheet: -2.06 (0.31), residues: 242 loop : -1.77 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 537 HIS 0.005 0.001 HIS B 99 PHE 0.026 0.002 PHE A 446 TYR 0.010 0.001 TYR X 22 ARG 0.005 0.000 ARG A 443 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.9602 (mmp) cc_final: 0.9319 (mmp) REVERT: A 360 MET cc_start: 0.6853 (mmm) cc_final: 0.6374 (mmm) REVERT: A 431 ASP cc_start: 0.8958 (p0) cc_final: 0.8579 (m-30) REVERT: A 485 MET cc_start: 0.6559 (mtm) cc_final: 0.6208 (mtt) REVERT: A 581 MET cc_start: 0.9195 (ttm) cc_final: 0.8707 (ttm) REVERT: A 587 GLN cc_start: 0.9369 (tt0) cc_final: 0.8984 (tp40) REVERT: A 607 MET cc_start: 0.9009 (mmt) cc_final: 0.8526 (mmm) REVERT: A 612 PHE cc_start: 0.8809 (m-80) cc_final: 0.8453 (m-10) REVERT: C 90 MET cc_start: 0.8509 (mmp) cc_final: 0.8217 (mmm) REVERT: C 146 ASP cc_start: 0.8335 (m-30) cc_final: 0.8065 (t70) REVERT: C 317 LEU cc_start: 0.8539 (mm) cc_final: 0.8028 (pp) REVERT: C 483 MET cc_start: 0.6685 (mmp) cc_final: 0.6262 (mtp) REVERT: B 137 GLN cc_start: 0.9452 (mm-40) cc_final: 0.9056 (mp10) REVERT: B 348 MET cc_start: 0.9028 (mmt) cc_final: 0.8726 (mmt) REVERT: B 527 VAL cc_start: 0.9564 (t) cc_final: 0.9326 (p) REVERT: B 546 MET cc_start: 0.9494 (mmp) cc_final: 0.9084 (mmm) REVERT: B 606 ILE cc_start: 0.9006 (mt) cc_final: 0.8744 (mp) REVERT: B 690 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8920 (tp-100) outliers start: 0 outliers final: 0 residues processed: 309 average time/residue: 0.7582 time to fit residues: 345.0774 Evaluate side-chains 267 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 20.0000 chunk 149 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 188 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18480 Z= 0.198 Angle : 0.531 7.009 25043 Z= 0.288 Chirality : 0.038 0.400 2770 Planarity : 0.004 0.054 3147 Dihedral : 9.998 81.843 2762 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.20 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.18), residues: 2175 helix: 0.60 (0.16), residues: 953 sheet: -1.88 (0.31), residues: 238 loop : -1.56 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.005 0.001 HIS B 99 PHE 0.015 0.001 PHE C 330 TYR 0.018 0.001 TYR B 217 ARG 0.007 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 298 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.1163 (ttm) cc_final: 0.0959 (ttm) REVERT: A 311 MET cc_start: 0.9618 (mmp) cc_final: 0.9270 (mmp) REVERT: A 360 MET cc_start: 0.6577 (mmm) cc_final: 0.6362 (mmm) REVERT: A 431 ASP cc_start: 0.8935 (p0) cc_final: 0.8370 (m-30) REVERT: A 436 GLU cc_start: 0.8727 (mt-10) cc_final: 0.7920 (mt-10) REVERT: A 460 MET cc_start: 0.9183 (tmm) cc_final: 0.8866 (tmm) REVERT: A 581 MET cc_start: 0.9080 (ttm) cc_final: 0.8697 (ttm) REVERT: A 587 GLN cc_start: 0.9339 (tt0) cc_final: 0.8950 (tp40) REVERT: A 607 MET cc_start: 0.8969 (mmt) cc_final: 0.8431 (mmm) REVERT: A 612 PHE cc_start: 0.8738 (m-80) cc_final: 0.8474 (m-10) REVERT: C 50 MET cc_start: 0.9401 (tpp) cc_final: 0.9191 (tpp) REVERT: C 90 MET cc_start: 0.8550 (mmp) cc_final: 0.8304 (mmm) REVERT: C 146 ASP cc_start: 0.8292 (m-30) cc_final: 0.7932 (t70) REVERT: C 317 LEU cc_start: 0.8626 (mm) cc_final: 0.8091 (pp) REVERT: C 483 MET cc_start: 0.6827 (mmp) cc_final: 0.6437 (mtp) REVERT: B 137 GLN cc_start: 0.9440 (mm-40) cc_final: 0.9011 (mp10) REVERT: B 251 PHE cc_start: 0.9644 (m-10) cc_final: 0.9388 (m-80) REVERT: B 348 MET cc_start: 0.8947 (mmt) cc_final: 0.8607 (mmt) REVERT: B 519 GLU cc_start: 0.9042 (pt0) cc_final: 0.8591 (pt0) REVERT: B 527 VAL cc_start: 0.9463 (t) cc_final: 0.9233 (p) REVERT: B 546 MET cc_start: 0.9471 (mmp) cc_final: 0.9046 (mmm) REVERT: B 593 ASP cc_start: 0.7122 (m-30) cc_final: 0.6762 (m-30) REVERT: B 606 ILE cc_start: 0.8996 (mt) cc_final: 0.8724 (mp) REVERT: B 690 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8858 (tp-100) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.7745 time to fit residues: 341.7725 Evaluate side-chains 260 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 18480 Z= 0.302 Angle : 0.612 5.669 25043 Z= 0.337 Chirality : 0.039 0.375 2770 Planarity : 0.005 0.056 3147 Dihedral : 10.126 77.937 2762 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.39 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2175 helix: 0.13 (0.16), residues: 939 sheet: -2.02 (0.31), residues: 238 loop : -1.70 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 55 HIS 0.008 0.001 HIS B 99 PHE 0.017 0.002 PHE B 512 TYR 0.014 0.002 TYR A 393 ARG 0.006 0.001 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.7320 (mmm) cc_final: 0.6825 (mmm) REVERT: A 587 GLN cc_start: 0.9368 (tt0) cc_final: 0.9017 (tp40) REVERT: A 607 MET cc_start: 0.8968 (mmt) cc_final: 0.8580 (mmm) REVERT: A 612 PHE cc_start: 0.8772 (m-80) cc_final: 0.8510 (m-10) REVERT: C 90 MET cc_start: 0.8645 (mmp) cc_final: 0.8169 (mmp) REVERT: C 146 ASP cc_start: 0.8704 (m-30) cc_final: 0.8393 (t70) REVERT: C 164 MET cc_start: 0.9354 (mtp) cc_final: 0.9046 (ptt) REVERT: C 483 MET cc_start: 0.6956 (mmp) cc_final: 0.6657 (mtp) REVERT: C 735 MET cc_start: 0.9533 (tpt) cc_final: 0.9275 (tpp) REVERT: B 137 GLN cc_start: 0.9447 (mm-40) cc_final: 0.9226 (mp10) REVERT: B 348 MET cc_start: 0.8775 (mmt) cc_final: 0.8557 (mmt) REVERT: B 414 MET cc_start: 0.7834 (mmm) cc_final: 0.7311 (tpp) REVERT: B 534 MET cc_start: 0.9397 (tpt) cc_final: 0.9180 (tpt) REVERT: B 606 ILE cc_start: 0.9078 (mt) cc_final: 0.8833 (mp) REVERT: B 690 GLN cc_start: 0.9129 (tp-100) cc_final: 0.8900 (tp-100) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.7665 time to fit residues: 325.0778 Evaluate side-chains 254 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 70 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 210 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18480 Z= 0.208 Angle : 0.530 4.470 25043 Z= 0.290 Chirality : 0.038 0.394 2770 Planarity : 0.004 0.062 3147 Dihedral : 10.060 77.256 2762 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2175 helix: 0.37 (0.16), residues: 940 sheet: -1.97 (0.31), residues: 236 loop : -1.59 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 55 HIS 0.014 0.001 HIS A 437 PHE 0.014 0.002 PHE B 696 TYR 0.016 0.001 TYR C 205 ARG 0.004 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 47 MET cc_start: 0.0899 (ttm) cc_final: 0.0630 (ttm) REVERT: A 311 MET cc_start: 0.9686 (mmp) cc_final: 0.9318 (mmp) REVERT: A 360 MET cc_start: 0.7231 (mmm) cc_final: 0.6706 (mmm) REVERT: A 431 ASP cc_start: 0.8822 (p0) cc_final: 0.8317 (m-30) REVERT: A 436 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8228 (mt-10) REVERT: A 460 MET cc_start: 0.8947 (tmm) cc_final: 0.8676 (tmm) REVERT: A 587 GLN cc_start: 0.9425 (tt0) cc_final: 0.9051 (tp40) REVERT: A 607 MET cc_start: 0.8979 (mmt) cc_final: 0.8487 (mmm) REVERT: A 612 PHE cc_start: 0.8801 (m-80) cc_final: 0.8573 (m-80) REVERT: C 90 MET cc_start: 0.8642 (mmp) cc_final: 0.8284 (mmp) REVERT: C 146 ASP cc_start: 0.8669 (m-30) cc_final: 0.8369 (t70) REVERT: C 164 MET cc_start: 0.9382 (mtp) cc_final: 0.9058 (ptt) REVERT: C 483 MET cc_start: 0.6837 (mmp) cc_final: 0.6596 (mtp) REVERT: B 227 MET cc_start: 0.8007 (pmm) cc_final: 0.7692 (pmm) REVERT: B 348 MET cc_start: 0.8827 (mmt) cc_final: 0.8599 (mmt) REVERT: B 353 LYS cc_start: 0.8998 (mptt) cc_final: 0.8769 (tptp) REVERT: B 414 MET cc_start: 0.7768 (mmm) cc_final: 0.7201 (tpp) REVERT: B 508 GLU cc_start: 0.8525 (mp0) cc_final: 0.8320 (mp0) REVERT: B 593 ASP cc_start: 0.7851 (m-30) cc_final: 0.7641 (m-30) REVERT: B 606 ILE cc_start: 0.9047 (mt) cc_final: 0.8838 (mp) REVERT: B 664 HIS cc_start: 0.9313 (m-70) cc_final: 0.9071 (m-70) REVERT: B 690 GLN cc_start: 0.9163 (tp-100) cc_final: 0.8913 (tp-100) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.7673 time to fit residues: 327.0102 Evaluate side-chains 257 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 117 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18480 Z= 0.220 Angle : 0.528 5.236 25043 Z= 0.289 Chirality : 0.038 0.391 2770 Planarity : 0.004 0.046 3147 Dihedral : 10.056 75.845 2762 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.21 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.17), residues: 2175 helix: 0.37 (0.16), residues: 946 sheet: -1.90 (0.32), residues: 219 loop : -1.63 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 537 HIS 0.011 0.001 HIS A 437 PHE 0.032 0.002 PHE C 600 TYR 0.012 0.001 TYR B 82 ARG 0.005 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.0946 (ttm) cc_final: 0.0689 (ttm) REVERT: A 311 MET cc_start: 0.9690 (mmp) cc_final: 0.9314 (mmp) REVERT: A 360 MET cc_start: 0.7522 (mmm) cc_final: 0.7025 (mmm) REVERT: A 431 ASP cc_start: 0.8872 (p0) cc_final: 0.8549 (m-30) REVERT: A 485 MET cc_start: 0.8493 (mtm) cc_final: 0.8035 (mtm) REVERT: A 587 GLN cc_start: 0.9448 (tt0) cc_final: 0.9069 (tp40) REVERT: A 607 MET cc_start: 0.9002 (mmt) cc_final: 0.8506 (mmm) REVERT: A 612 PHE cc_start: 0.8769 (m-80) cc_final: 0.8564 (m-80) REVERT: A 646 PHE cc_start: 0.9322 (m-80) cc_final: 0.8866 (m-80) REVERT: C 90 MET cc_start: 0.8568 (mmp) cc_final: 0.8232 (mmp) REVERT: C 146 ASP cc_start: 0.8758 (m-30) cc_final: 0.8415 (t70) REVERT: C 164 MET cc_start: 0.9404 (mtp) cc_final: 0.9083 (ptt) REVERT: C 483 MET cc_start: 0.6874 (mmp) cc_final: 0.6633 (mtp) REVERT: B 7 LEU cc_start: 0.9592 (tp) cc_final: 0.9388 (tp) REVERT: B 227 MET cc_start: 0.7989 (pmm) cc_final: 0.7685 (pmm) REVERT: B 251 PHE cc_start: 0.9688 (m-10) cc_final: 0.9372 (m-80) REVERT: B 348 MET cc_start: 0.8820 (mmt) cc_final: 0.8597 (mmt) REVERT: B 414 MET cc_start: 0.7721 (mmm) cc_final: 0.7114 (tpp) REVERT: B 508 GLU cc_start: 0.8477 (mp0) cc_final: 0.8276 (mp0) REVERT: B 593 ASP cc_start: 0.7947 (m-30) cc_final: 0.7695 (m-30) REVERT: B 599 TYR cc_start: 0.9287 (m-80) cc_final: 0.8798 (m-80) REVERT: B 605 HIS cc_start: 0.8973 (p-80) cc_final: 0.8707 (p-80) REVERT: B 606 ILE cc_start: 0.9083 (mt) cc_final: 0.8576 (mp) REVERT: B 690 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8898 (tp-100) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.8138 time to fit residues: 337.4993 Evaluate side-chains 263 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 129 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18480 Z= 0.221 Angle : 0.532 5.550 25043 Z= 0.291 Chirality : 0.038 0.388 2770 Planarity : 0.004 0.045 3147 Dihedral : 10.075 73.581 2762 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.25 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.18), residues: 2175 helix: 0.39 (0.17), residues: 947 sheet: -1.91 (0.32), residues: 218 loop : -1.61 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 188 HIS 0.011 0.001 HIS A 437 PHE 0.013 0.002 PHE B 512 TYR 0.016 0.001 TYR B 559 ARG 0.005 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.1017 (ttm) cc_final: 0.0722 (ttm) REVERT: A 285 MET cc_start: 0.9553 (ttm) cc_final: 0.9309 (ptp) REVERT: A 311 MET cc_start: 0.9694 (mmp) cc_final: 0.9303 (mmp) REVERT: A 587 GLN cc_start: 0.9466 (tt0) cc_final: 0.9084 (tp40) REVERT: A 607 MET cc_start: 0.8976 (mmt) cc_final: 0.8477 (mmm) REVERT: A 612 PHE cc_start: 0.8805 (m-80) cc_final: 0.8605 (m-80) REVERT: A 646 PHE cc_start: 0.9380 (m-80) cc_final: 0.8937 (m-80) REVERT: A 694 LEU cc_start: 0.8966 (mt) cc_final: 0.8755 (mm) REVERT: C 90 MET cc_start: 0.8585 (mmp) cc_final: 0.8240 (mmp) REVERT: C 146 ASP cc_start: 0.8831 (m-30) cc_final: 0.8411 (t70) REVERT: C 164 MET cc_start: 0.9421 (mtp) cc_final: 0.9094 (ptt) REVERT: B 7 LEU cc_start: 0.9570 (tp) cc_final: 0.9361 (tp) REVERT: B 251 PHE cc_start: 0.9710 (m-10) cc_final: 0.9395 (m-80) REVERT: B 348 MET cc_start: 0.8758 (mmt) cc_final: 0.8553 (mmt) REVERT: B 414 MET cc_start: 0.7717 (mmm) cc_final: 0.7097 (tpp) REVERT: B 508 GLU cc_start: 0.8463 (mp0) cc_final: 0.8256 (mp0) REVERT: B 545 GLN cc_start: 0.9433 (mt0) cc_final: 0.9090 (mt0) REVERT: B 599 TYR cc_start: 0.9306 (m-80) cc_final: 0.8903 (m-80) REVERT: B 605 HIS cc_start: 0.9111 (p-80) cc_final: 0.8871 (p-80) REVERT: B 606 ILE cc_start: 0.9080 (mt) cc_final: 0.8570 (mp) REVERT: B 664 HIS cc_start: 0.9279 (m-70) cc_final: 0.8676 (m-70) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.8035 time to fit residues: 329.1373 Evaluate side-chains 257 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 191 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 176 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18480 Z= 0.147 Angle : 0.490 5.687 25043 Z= 0.260 Chirality : 0.038 0.381 2770 Planarity : 0.004 0.049 3147 Dihedral : 9.945 73.602 2762 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.97 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.18), residues: 2175 helix: 0.85 (0.17), residues: 946 sheet: -1.81 (0.31), residues: 237 loop : -1.35 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 438 HIS 0.003 0.001 HIS A 437 PHE 0.018 0.001 PHE C 694 TYR 0.015 0.001 TYR B 217 ARG 0.004 0.000 ARG C 641 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.1093 (ttm) cc_final: 0.0780 (ttm) REVERT: A 311 MET cc_start: 0.9669 (mmp) cc_final: 0.9197 (mmp) REVERT: A 431 ASP cc_start: 0.8804 (p0) cc_final: 0.8414 (m-30) REVERT: A 436 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 485 MET cc_start: 0.8417 (mtm) cc_final: 0.8167 (mtt) REVERT: A 525 PHE cc_start: 0.9186 (m-80) cc_final: 0.8802 (m-80) REVERT: A 587 GLN cc_start: 0.9457 (tt0) cc_final: 0.9045 (tp40) REVERT: A 607 MET cc_start: 0.8996 (mmt) cc_final: 0.8431 (mmm) REVERT: A 646 PHE cc_start: 0.9306 (m-80) cc_final: 0.8831 (m-80) REVERT: C 90 MET cc_start: 0.8609 (mmp) cc_final: 0.8273 (mmp) REVERT: C 146 ASP cc_start: 0.8524 (m-30) cc_final: 0.8290 (t0) REVERT: C 164 MET cc_start: 0.9380 (mtp) cc_final: 0.9004 (ptm) REVERT: B 251 PHE cc_start: 0.9671 (m-10) cc_final: 0.9361 (m-80) REVERT: B 534 MET cc_start: 0.9431 (tpt) cc_final: 0.9221 (tpt) REVERT: B 593 ASP cc_start: 0.7954 (m-30) cc_final: 0.7723 (m-30) REVERT: B 599 TYR cc_start: 0.9282 (m-80) cc_final: 0.8863 (m-80) REVERT: B 606 ILE cc_start: 0.9032 (mt) cc_final: 0.8535 (mp) REVERT: B 657 TYR cc_start: 0.8761 (p90) cc_final: 0.8182 (p90) REVERT: B 664 HIS cc_start: 0.8978 (m-70) cc_final: 0.8726 (m-70) REVERT: B 690 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8917 (tp-100) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.7663 time to fit residues: 322.3468 Evaluate side-chains 260 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 207 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18480 Z= 0.225 Angle : 0.532 6.698 25043 Z= 0.291 Chirality : 0.038 0.387 2770 Planarity : 0.004 0.056 3147 Dihedral : 10.004 73.541 2762 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2175 helix: 0.62 (0.17), residues: 951 sheet: -1.79 (0.33), residues: 213 loop : -1.48 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 55 HIS 0.007 0.001 HIS A 437 PHE 0.020 0.002 PHE B 492 TYR 0.025 0.002 TYR A 445 ARG 0.006 0.000 ARG C 505 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.1249 (ttm) cc_final: 0.0905 (ttm) REVERT: A 285 MET cc_start: 0.9535 (ttm) cc_final: 0.9309 (ptp) REVERT: A 311 MET cc_start: 0.9700 (mmp) cc_final: 0.9317 (mmp) REVERT: A 360 MET cc_start: 0.7867 (mmm) cc_final: 0.7383 (mmm) REVERT: A 431 ASP cc_start: 0.8809 (p0) cc_final: 0.8538 (m-30) REVERT: A 587 GLN cc_start: 0.9487 (tt0) cc_final: 0.9135 (tp40) REVERT: A 607 MET cc_start: 0.8995 (mmt) cc_final: 0.8479 (mmm) REVERT: A 646 PHE cc_start: 0.9349 (m-80) cc_final: 0.8881 (m-80) REVERT: C 90 MET cc_start: 0.8578 (mmp) cc_final: 0.8255 (mmp) REVERT: C 146 ASP cc_start: 0.8726 (m-30) cc_final: 0.8481 (t70) REVERT: C 153 ASP cc_start: 0.8742 (t0) cc_final: 0.7970 (m-30) REVERT: C 164 MET cc_start: 0.9403 (mtp) cc_final: 0.9051 (ptm) REVERT: B 7 LEU cc_start: 0.9543 (tp) cc_final: 0.9340 (tp) REVERT: B 414 MET cc_start: 0.7680 (mmm) cc_final: 0.7167 (tpp) REVERT: B 534 MET cc_start: 0.9471 (tpt) cc_final: 0.9243 (tpt) REVERT: B 599 TYR cc_start: 0.9304 (m-80) cc_final: 0.8919 (m-80) REVERT: B 606 ILE cc_start: 0.9054 (mt) cc_final: 0.8559 (mp) REVERT: B 690 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8936 (tp-100) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.7805 time to fit residues: 322.0803 Evaluate side-chains 258 residues out of total 1941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.071860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.052517 restraints weight = 347451.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.054983 restraints weight = 207551.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.056753 restraints weight = 141004.646| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18480 Z= 0.225 Angle : 0.542 6.204 25043 Z= 0.297 Chirality : 0.039 0.388 2770 Planarity : 0.004 0.057 3147 Dihedral : 10.065 73.381 2762 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.44 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2175 helix: 0.34 (0.17), residues: 959 sheet: -1.64 (0.34), residues: 197 loop : -1.57 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 55 HIS 0.009 0.001 HIS A 437 PHE 0.015 0.002 PHE B 492 TYR 0.015 0.002 TYR A 334 ARG 0.005 0.000 ARG C 269 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8211.93 seconds wall clock time: 147 minutes 48.06 seconds (8868.06 seconds total)