Starting phenix.real_space_refine on Thu Mar 14 19:24:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4f_30572/03_2024/7d4f_30572_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4f_30572/03_2024/7d4f_30572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4f_30572/03_2024/7d4f_30572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4f_30572/03_2024/7d4f_30572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4f_30572/03_2024/7d4f_30572_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d4f_30572/03_2024/7d4f_30572_updated.pdb" } resolution = 2.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 76 5.16 5 C 6080 2.51 5 N 1589 2.21 5 O 1787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A GLU 919": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9534 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 882 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "C" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 485 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "G" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Chain: "A" Number of atoms: 7347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 902, 7347 Unusual residues: {' ZN': 2, 'H3U': 2} Classifications: {'peptide': 898, 'undetermined': 4} Link IDs: {'PTRANS': 30, 'TRANS': 867, None: 4} Not linked: pdbres="THR A 929 " pdbres=" ZN A1001 " Not linked: pdbres=" ZN A1001 " pdbres=" ZN A1002 " Not linked: pdbres=" ZN A1002 " pdbres="H3U A1003 " Not linked: pdbres="H3U A1003 " pdbres="H3U A1004 " Chain breaks: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4549 SG CYS A 301 40.622 64.140 49.126 1.00 43.57 S ATOM 4590 SG CYS A 306 40.066 63.364 45.411 1.00 41.16 S ATOM 4622 SG CYS A 310 43.866 63.104 46.921 1.00 37.28 S ATOM 6030 SG CYS A 487 23.435 59.649 59.210 1.00 46.10 S ATOM 7283 SG CYS A 645 22.049 59.178 55.510 1.00 50.36 S ATOM 7289 SG CYS A 646 25.497 61.610 56.659 1.00 49.35 S Time building chain proxies: 5.30, per 1000 atoms: 0.56 Number of scatterers: 9534 At special positions: 0 Unit cell: (99.417, 93.003, 133.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 76 16.00 O 1787 8.00 N 1589 7.00 C 6080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " Number of angles added : 3 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 8 sheets defined 44.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.651A pdb=" N ASN B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.777A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 41 Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.899A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 98 Processing helix chain 'G' and resid 101 through 112 Processing helix chain 'G' and resid 135 through 141 Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 77 through 90 removed outlier: 4.207A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.668A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 199 removed outlier: 3.567A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.027A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.611A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.048A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.539A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 505 through 508 removed outlier: 3.753A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 530 Processing helix chain 'A' and resid 562 through 579 removed outlier: 5.961A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.646A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 Processing helix chain 'A' and resid 685 through 708 removed outlier: 4.125A pdb=" N ALA A 688 " --> pdb=" O ALA A 685 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 690 " --> pdb=" O THR A 687 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 701 " --> pdb=" O GLN A 698 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 708 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 718 through 732 removed outlier: 3.582A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 772 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 846 through 850 removed outlier: 3.674A pdb=" N THR A 850 " --> pdb=" O ASP A 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 846 through 850' Processing helix chain 'A' and resid 852 through 871 Proline residue: A 868 - end of helix removed outlier: 4.693A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 893 removed outlier: 4.081A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 removed outlier: 3.887A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.213A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.622A pdb=" N THR G 187 " --> pdb=" O GLN G 158 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN G 158 " --> pdb=" O THR G 187 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU G 189 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE G 156 " --> pdb=" O LEU G 189 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= D, first strand: chain 'A' and resid 32 through 38 Processing sheet with id= E, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.425A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 555 through 559 removed outlier: 4.717A pdb=" N ARG A 555 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= H, first strand: chain 'A' and resid 816 through 822 removed outlier: 4.056A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1564 1.31 - 1.45: 2749 1.45 - 1.58: 5307 1.58 - 1.71: 19 1.71 - 1.85: 111 Bond restraints: 9750 Sorted by residual: bond pdb=" O24 H3U A1003 " pdb=" S17 H3U A1003 " ideal model delta sigma weight residual 1.468 1.674 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" O34 H3U A1003 " pdb=" S31 H3U A1003 " ideal model delta sigma weight residual 1.472 1.665 -0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" O29 H3U A1003 " pdb=" S21 H3U A1003 " ideal model delta sigma weight residual 1.474 1.665 -0.191 2.00e-02 2.50e+03 9.12e+01 bond pdb=" O30 H3U A1004 " pdb=" S21 H3U A1004 " ideal model delta sigma weight residual 1.471 1.660 -0.189 2.00e-02 2.50e+03 8.92e+01 bond pdb=" O28 H3U A1004 " pdb=" S21 H3U A1004 " ideal model delta sigma weight residual 1.472 1.659 -0.187 2.00e-02 2.50e+03 8.75e+01 ... (remaining 9745 not shown) Histogram of bond angle deviations from ideal: 98.47 - 105.63: 166 105.63 - 112.78: 5037 112.78 - 119.94: 3644 119.94 - 127.10: 4316 127.10 - 134.26: 89 Bond angle restraints: 13252 Sorted by residual: angle pdb=" C VAL A 335 " pdb=" N ASP A 336 " pdb=" CA ASP A 336 " ideal model delta sigma weight residual 121.54 130.54 -9.00 1.91e+00 2.74e-01 2.22e+01 angle pdb=" CA ASP A 760 " pdb=" CB ASP A 760 " pdb=" CG ASP A 760 " ideal model delta sigma weight residual 112.60 116.98 -4.38 1.00e+00 1.00e+00 1.92e+01 angle pdb=" N MET A 242 " pdb=" CA MET A 242 " pdb=" C MET A 242 " ideal model delta sigma weight residual 113.45 118.87 -5.42 1.39e+00 5.18e-01 1.52e+01 angle pdb=" C2 H3U A1003 " pdb=" C5 H3U A1003 " pdb=" C8 H3U A1003 " ideal model delta sigma weight residual 123.83 112.53 11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CB ASP A 760 " pdb=" CG ASP A 760 " pdb=" OD1 ASP A 760 " ideal model delta sigma weight residual 118.40 126.86 -8.46 2.30e+00 1.89e-01 1.35e+01 ... (remaining 13247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5216 17.77 - 35.53: 471 35.53 - 53.30: 63 53.30 - 71.07: 13 71.07 - 88.84: 5 Dihedral angle restraints: 5768 sinusoidal: 2262 harmonic: 3506 Sorted by residual: dihedral pdb=" CA ASN A 611 " pdb=" C ASN A 611 " pdb=" N PRO A 612 " pdb=" CA PRO A 612 " ideal model delta harmonic sigma weight residual 180.00 -156.51 -23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA THR A 806 " pdb=" C THR A 806 " pdb=" N LYS A 807 " pdb=" CA LYS A 807 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ALA A 762 " pdb=" C ALA A 762 " pdb=" N VAL A 763 " pdb=" CA VAL A 763 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1080 0.065 - 0.130: 340 0.130 - 0.196: 48 0.196 - 0.261: 6 0.261 - 0.326: 3 Chirality restraints: 1477 Sorted by residual: chirality pdb=" CA TYR A 606 " pdb=" N TYR A 606 " pdb=" C TYR A 606 " pdb=" CB TYR A 606 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA ASP A 760 " pdb=" N ASP A 760 " pdb=" C ASP A 760 " pdb=" CB ASP A 760 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA PHE G 92 " pdb=" N PHE G 92 " pdb=" C PHE G 92 " pdb=" CB PHE G 92 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1474 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 177 " -0.045 5.00e-02 4.00e+02 6.74e-02 7.27e+00 pdb=" N PRO G 178 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO G 178 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 178 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO B 178 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 H3U A1003 " 0.016 2.00e-02 2.50e+03 2.36e-02 6.98e+00 pdb=" C3 H3U A1003 " -0.028 2.00e-02 2.50e+03 pdb=" C5 H3U A1003 " -0.023 2.00e-02 2.50e+03 pdb=" N1 H3U A1003 " 0.034 2.00e-02 2.50e+03 pdb=" O4 H3U A1003 " 0.001 2.00e-02 2.50e+03 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 1486 2.76 - 3.47: 12578 3.47 - 4.19: 23948 4.19 - 4.90: 41869 Nonbonded interactions: 79882 Sorted by model distance: nonbonded pdb=" CG1 VAL A 14 " pdb=" OD2 ASP A 100 " model vdw 1.326 3.460 nonbonded pdb=" N1 H3U A1003 " pdb=" O25 H3U A1003 " model vdw 2.076 2.520 nonbonded pdb=" OG1 THR A 540 " pdb=" OE1 GLU A 665 " model vdw 2.237 2.440 nonbonded pdb=" OD2 ASP B 112 " pdb=" OH TYR A 273 " model vdw 2.283 2.440 nonbonded pdb=" OG SER G 173 " pdb=" OD1 ASP G 175 " model vdw 2.292 2.440 ... (remaining 79877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 84 through 179 or resid 182 through 191)) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.160 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.550 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.012 0.206 9750 Z= 0.788 Angle : 0.948 11.298 13252 Z= 0.563 Chirality : 0.064 0.326 1477 Planarity : 0.006 0.067 1682 Dihedral : 13.567 88.836 3498 Min Nonbonded Distance : 1.326 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.76 % Allowed : 5.15 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.21), residues: 1165 helix: -1.81 (0.18), residues: 522 sheet: -1.47 (0.37), residues: 153 loop : -1.31 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 182 HIS 0.010 0.002 HIS A 613 PHE 0.026 0.003 PHE A 741 TYR 0.020 0.003 TYR A 867 ARG 0.005 0.001 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 1.147 Fit side-chains REVERT: B 80 ARG cc_start: 0.8156 (ttt90) cc_final: 0.7873 (ttt180) REVERT: B 88 GLN cc_start: 0.8467 (tt0) cc_final: 0.8216 (tt0) REVERT: B 127 LYS cc_start: 0.8817 (mttt) cc_final: 0.8336 (mtmt) REVERT: C 34 GLN cc_start: 0.8292 (tp40) cc_final: 0.7650 (tm-30) REVERT: C 44 ASP cc_start: 0.8175 (p0) cc_final: 0.7970 (p0) REVERT: G 106 ILE cc_start: 0.8094 (mt) cc_final: 0.7778 (mp) REVERT: G 111 ARG cc_start: 0.6329 (ttt180) cc_final: 0.6021 (tpp-160) REVERT: A 66 ILE cc_start: 0.7487 (tp) cc_final: 0.7237 (OUTLIER) REVERT: A 91 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8164 (ptmt) REVERT: A 104 PHE cc_start: 0.8104 (t80) cc_final: 0.7807 (t80) REVERT: A 110 MET cc_start: 0.6345 (mmm) cc_final: 0.5890 (mmp) REVERT: A 452 ASP cc_start: 0.8529 (t70) cc_final: 0.8016 (t0) REVERT: A 497 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8073 (p0) REVERT: A 520 SER cc_start: 0.8341 (m) cc_final: 0.8114 (p) REVERT: A 555 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.7960 (mmm160) REVERT: A 601 MET cc_start: 0.8967 (mtp) cc_final: 0.8733 (mtm) outliers start: 8 outliers final: 5 residues processed: 179 average time/residue: 1.1414 time to fit residues: 219.4256 Evaluate side-chains 148 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 142 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 497 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN C 18 GLN C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 109 ASN A 81 GLN A 113 HIS A 117 GLN A 138 ASN A 158 ASN A 191 GLN A 357 GLN A 408 GLN A 497 ASN A 543 ASN A 642 HIS A 705 ASN A 790 ASN A 791 ASN A 822 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9750 Z= 0.172 Angle : 0.534 9.131 13252 Z= 0.275 Chirality : 0.042 0.170 1477 Planarity : 0.007 0.217 1682 Dihedral : 6.006 60.803 1310 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.39 % Allowed : 11.26 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.11 (0.22), residues: 1165 helix: -0.52 (0.21), residues: 534 sheet: -0.74 (0.38), residues: 150 loop : -0.78 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 154 HIS 0.009 0.001 HIS C 36 PHE 0.020 0.001 PHE A 652 TYR 0.014 0.001 TYR A 788 ARG 0.039 0.001 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 157 time to evaluate : 1.104 Fit side-chains REVERT: B 80 ARG cc_start: 0.8114 (ttt90) cc_final: 0.7786 (ttt180) REVERT: B 88 GLN cc_start: 0.8396 (tt0) cc_final: 0.8044 (tt0) REVERT: B 105 ASN cc_start: 0.7923 (t0) cc_final: 0.7632 (t0) REVERT: C 26 SER cc_start: 0.7968 (OUTLIER) cc_final: 0.7571 (p) REVERT: C 34 GLN cc_start: 0.8193 (tp40) cc_final: 0.7550 (tm-30) REVERT: G 111 ARG cc_start: 0.6277 (ttt180) cc_final: 0.6024 (tpp-160) REVERT: G 129 MET cc_start: 0.8245 (mtm) cc_final: 0.7994 (mtm) REVERT: A 98 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8147 (mptt) REVERT: A 104 PHE cc_start: 0.7775 (t80) cc_final: 0.7300 (t80) REVERT: A 110 MET cc_start: 0.6167 (mmm) cc_final: 0.5724 (mmp) REVERT: A 136 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6738 (pt0) REVERT: A 452 ASP cc_start: 0.8530 (t70) cc_final: 0.8318 (t70) REVERT: A 714 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8437 (ptpt) outliers start: 25 outliers final: 10 residues processed: 169 average time/residue: 1.1343 time to fit residues: 206.3089 Evaluate side-chains 156 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 153 LEU Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 717 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 ASN B 109 ASN C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 108 ASN A 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9750 Z= 0.192 Angle : 0.509 7.708 13252 Z= 0.265 Chirality : 0.042 0.167 1477 Planarity : 0.006 0.172 1682 Dihedral : 5.477 63.441 1300 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.44 % Allowed : 11.93 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.63 (0.23), residues: 1165 helix: -0.05 (0.22), residues: 534 sheet: -0.49 (0.38), residues: 150 loop : -0.64 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 154 HIS 0.009 0.001 HIS C 36 PHE 0.018 0.001 PHE A 652 TYR 0.016 0.001 TYR A 788 ARG 0.038 0.001 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 0.851 Fit side-chains REVERT: B 80 ARG cc_start: 0.8044 (ttt90) cc_final: 0.7735 (ttt180) REVERT: B 88 GLN cc_start: 0.8378 (tt0) cc_final: 0.7924 (mt0) REVERT: B 127 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8582 (ttpt) REVERT: C 26 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7529 (m) REVERT: C 34 GLN cc_start: 0.8190 (tp40) cc_final: 0.7542 (tm-30) REVERT: G 111 ARG cc_start: 0.6181 (ttt180) cc_final: 0.5954 (tpp-160) REVERT: G 129 MET cc_start: 0.8180 (mtm) cc_final: 0.7979 (mtm) REVERT: A 98 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8120 (mptt) REVERT: A 104 PHE cc_start: 0.7867 (t80) cc_final: 0.7385 (t80) REVERT: A 110 MET cc_start: 0.6005 (mmm) cc_final: 0.5530 (mmp) REVERT: A 136 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6686 (pt0) REVERT: A 153 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6279 (p0) REVERT: A 452 ASP cc_start: 0.8489 (t70) cc_final: 0.7965 (t0) REVERT: A 556 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.9018 (p) REVERT: A 568 ASN cc_start: 0.8109 (m-40) cc_final: 0.7677 (m-40) REVERT: A 714 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8427 (ptpt) outliers start: 36 outliers final: 15 residues processed: 158 average time/residue: 1.1115 time to fit residues: 189.2211 Evaluate side-chains 161 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 844 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 176 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN G 100 ASN G 104 ASN G 108 ASN A 113 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9750 Z= 0.265 Angle : 0.518 6.727 13252 Z= 0.277 Chirality : 0.044 0.172 1477 Planarity : 0.004 0.055 1682 Dihedral : 7.328 173.464 1299 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.63 % Allowed : 12.69 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -0.38 (0.24), residues: 1165 helix: 0.18 (0.22), residues: 540 sheet: -0.33 (0.39), residues: 150 loop : -0.57 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 154 HIS 0.008 0.001 HIS C 36 PHE 0.020 0.002 PHE A 652 TYR 0.015 0.002 TYR A 788 ARG 0.006 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: B 80 ARG cc_start: 0.8063 (ttt90) cc_final: 0.7784 (ttt180) REVERT: B 88 GLN cc_start: 0.8426 (tt0) cc_final: 0.8060 (mt0) REVERT: B 127 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8566 (ttpt) REVERT: C 26 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7528 (m) REVERT: C 34 GLN cc_start: 0.8274 (tp40) cc_final: 0.8047 (tp-100) REVERT: G 111 ARG cc_start: 0.6168 (ttt180) cc_final: 0.5944 (tpp-160) REVERT: G 129 MET cc_start: 0.8152 (mtm) cc_final: 0.7949 (mtm) REVERT: A 98 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8113 (mptt) REVERT: A 104 PHE cc_start: 0.7895 (t80) cc_final: 0.7387 (t80) REVERT: A 110 MET cc_start: 0.5998 (mmm) cc_final: 0.5529 (mmp) REVERT: A 136 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6708 (pt0) REVERT: A 153 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6467 (p0) REVERT: A 452 ASP cc_start: 0.8565 (t70) cc_final: 0.7954 (t0) REVERT: A 556 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9019 (p) REVERT: A 568 ASN cc_start: 0.8079 (m-40) cc_final: 0.7679 (m110) REVERT: A 714 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8454 (ptpt) outliers start: 38 outliers final: 18 residues processed: 158 average time/residue: 1.1740 time to fit residues: 198.8084 Evaluate side-chains 155 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 844 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.0030 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 176 ASN C 19 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN A 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9750 Z= 0.128 Angle : 0.434 5.550 13252 Z= 0.232 Chirality : 0.040 0.174 1477 Planarity : 0.004 0.087 1682 Dihedral : 7.086 169.630 1299 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.58 % Allowed : 14.03 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.02 (0.24), residues: 1165 helix: 0.49 (0.23), residues: 534 sheet: -0.07 (0.40), residues: 140 loop : -0.34 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 154 HIS 0.008 0.001 HIS C 36 PHE 0.014 0.001 PHE A 652 TYR 0.012 0.001 TYR A 788 ARG 0.005 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: B 78 ASP cc_start: 0.3692 (p0) cc_final: 0.3331 (p0) REVERT: B 80 ARG cc_start: 0.8030 (ttt90) cc_final: 0.7747 (ttt180) REVERT: B 88 GLN cc_start: 0.8434 (tt0) cc_final: 0.8043 (mt0) REVERT: B 127 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8483 (ttpt) REVERT: C 50 GLU cc_start: 0.5439 (OUTLIER) cc_final: 0.5065 (mp0) REVERT: G 111 ARG cc_start: 0.6218 (ttt180) cc_final: 0.5988 (tpp-160) REVERT: A 98 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8101 (mptt) REVERT: A 104 PHE cc_start: 0.7904 (t80) cc_final: 0.7427 (t80) REVERT: A 110 MET cc_start: 0.6021 (mmm) cc_final: 0.5541 (mmp) REVERT: A 452 ASP cc_start: 0.8435 (t70) cc_final: 0.8046 (t0) REVERT: A 568 ASN cc_start: 0.8097 (m-40) cc_final: 0.7691 (m-40) REVERT: A 714 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8374 (ptpt) REVERT: A 857 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7654 (mt-10) outliers start: 27 outliers final: 10 residues processed: 153 average time/residue: 1.1310 time to fit residues: 186.3222 Evaluate side-chains 145 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 717 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 4.9990 chunk 22 optimal weight: 0.4980 chunk 66 optimal weight: 0.4980 chunk 27 optimal weight: 0.0980 chunk 113 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9750 Z= 0.112 Angle : 0.418 5.521 13252 Z= 0.223 Chirality : 0.040 0.169 1477 Planarity : 0.003 0.048 1682 Dihedral : 7.015 174.477 1299 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.19 % Allowed : 15.55 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.25 (0.24), residues: 1165 helix: 0.68 (0.23), residues: 534 sheet: -0.01 (0.40), residues: 140 loop : -0.20 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 154 HIS 0.008 0.000 HIS C 36 PHE 0.012 0.001 PHE A 652 TYR 0.011 0.001 TYR A 788 ARG 0.006 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: B 78 ASP cc_start: 0.4049 (OUTLIER) cc_final: 0.3683 (p0) REVERT: B 80 ARG cc_start: 0.8052 (ttt90) cc_final: 0.7814 (ttt180) REVERT: B 88 GLN cc_start: 0.8407 (tt0) cc_final: 0.8067 (mt0) REVERT: B 127 LYS cc_start: 0.8795 (ttmm) cc_final: 0.8430 (ttpt) REVERT: C 50 GLU cc_start: 0.5375 (OUTLIER) cc_final: 0.5133 (mp0) REVERT: G 111 ARG cc_start: 0.6161 (ttt180) cc_final: 0.5902 (tpp-160) REVERT: G 129 MET cc_start: 0.7873 (mtm) cc_final: 0.7611 (ttp) REVERT: G 184 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6482 (pp) REVERT: A 104 PHE cc_start: 0.7916 (t80) cc_final: 0.7416 (t80) REVERT: A 110 MET cc_start: 0.6004 (mmm) cc_final: 0.5634 (mmp) REVERT: A 452 ASP cc_start: 0.8400 (t70) cc_final: 0.8144 (t70) REVERT: A 568 ASN cc_start: 0.8087 (m-40) cc_final: 0.7697 (m-40) REVERT: A 714 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8307 (ptpt) outliers start: 23 outliers final: 10 residues processed: 152 average time/residue: 1.1434 time to fit residues: 186.9587 Evaluate side-chains 147 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 133 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 854 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 52 optimal weight: 0.0870 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9750 Z= 0.169 Angle : 0.448 5.509 13252 Z= 0.239 Chirality : 0.041 0.170 1477 Planarity : 0.003 0.043 1682 Dihedral : 7.067 175.073 1299 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.10 % Allowed : 15.84 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.24 (0.24), residues: 1165 helix: 0.67 (0.23), residues: 535 sheet: -0.01 (0.39), residues: 150 loop : -0.20 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 182 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.001 PHE A 652 TYR 0.014 0.001 TYR A 788 ARG 0.005 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: B 78 ASP cc_start: 0.4085 (OUTLIER) cc_final: 0.3749 (p0) REVERT: B 88 GLN cc_start: 0.8383 (tt0) cc_final: 0.8032 (mt0) REVERT: B 127 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8473 (ttpt) REVERT: C 50 GLU cc_start: 0.5400 (OUTLIER) cc_final: 0.5139 (mp0) REVERT: G 111 ARG cc_start: 0.6106 (ttt180) cc_final: 0.5824 (tpp-160) REVERT: G 129 MET cc_start: 0.7918 (mtm) cc_final: 0.7617 (ttp) REVERT: A 104 PHE cc_start: 0.7765 (t80) cc_final: 0.7204 (t80) REVERT: A 110 MET cc_start: 0.6010 (mmm) cc_final: 0.5518 (mmp) REVERT: A 452 ASP cc_start: 0.8464 (t70) cc_final: 0.7847 (t0) REVERT: A 556 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.9003 (p) REVERT: A 568 ASN cc_start: 0.8163 (m-40) cc_final: 0.7790 (m-40) REVERT: A 714 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8373 (ptpt) REVERT: A 857 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7772 (mt-10) outliers start: 22 outliers final: 13 residues processed: 147 average time/residue: 1.2216 time to fit residues: 192.7798 Evaluate side-chains 153 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 854 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 88 optimal weight: 0.3980 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9750 Z= 0.133 Angle : 0.428 5.486 13252 Z= 0.229 Chirality : 0.040 0.169 1477 Planarity : 0.003 0.043 1682 Dihedral : 7.020 175.101 1299 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.91 % Allowed : 15.94 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.37 (0.24), residues: 1165 helix: 0.73 (0.23), residues: 535 sheet: 0.10 (0.40), residues: 140 loop : -0.10 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 182 HIS 0.007 0.001 HIS C 36 PHE 0.014 0.001 PHE A 652 TYR 0.013 0.001 TYR A 788 ARG 0.005 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.122 Fit side-chains revert: symmetry clash REVERT: B 88 GLN cc_start: 0.8383 (tt0) cc_final: 0.8012 (mt0) REVERT: B 127 LYS cc_start: 0.8802 (ttmm) cc_final: 0.8424 (ttpt) REVERT: C 50 GLU cc_start: 0.5415 (OUTLIER) cc_final: 0.5134 (mp0) REVERT: G 111 ARG cc_start: 0.6182 (ttt180) cc_final: 0.5927 (tpp-160) REVERT: G 129 MET cc_start: 0.7874 (mtm) cc_final: 0.7571 (ttp) REVERT: G 184 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6612 (pp) REVERT: A 104 PHE cc_start: 0.7757 (t80) cc_final: 0.7191 (t80) REVERT: A 110 MET cc_start: 0.6002 (mmm) cc_final: 0.5510 (mmp) REVERT: A 452 ASP cc_start: 0.8437 (t70) cc_final: 0.7808 (t0) REVERT: A 568 ASN cc_start: 0.8098 (m-40) cc_final: 0.7715 (m-40) REVERT: A 714 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8363 (ptpt) REVERT: A 857 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7760 (mt-10) outliers start: 20 outliers final: 13 residues processed: 145 average time/residue: 1.1775 time to fit residues: 183.5786 Evaluate side-chains 151 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 854 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9750 Z= 0.272 Angle : 0.499 5.591 13252 Z= 0.267 Chirality : 0.044 0.184 1477 Planarity : 0.004 0.037 1682 Dihedral : 7.207 176.482 1299 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.48 % Allowed : 15.94 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.15 (0.24), residues: 1165 helix: 0.58 (0.23), residues: 533 sheet: -0.00 (0.40), residues: 150 loop : -0.25 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 182 HIS 0.007 0.001 HIS C 36 PHE 0.020 0.002 PHE A 652 TYR 0.019 0.002 TYR A 289 ARG 0.004 0.000 ARG A 553 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: B 88 GLN cc_start: 0.8377 (tt0) cc_final: 0.8005 (mt0) REVERT: B 127 LYS cc_start: 0.8884 (ttmm) cc_final: 0.8487 (ttpt) REVERT: C 50 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.4997 (mp0) REVERT: G 111 ARG cc_start: 0.6219 (ttt180) cc_final: 0.5949 (tpp-160) REVERT: G 129 MET cc_start: 0.7954 (mtm) cc_final: 0.7625 (ttp) REVERT: G 184 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6568 (pp) REVERT: A 83 GLU cc_start: 0.6041 (mt-10) cc_final: 0.5801 (tt0) REVERT: A 104 PHE cc_start: 0.7760 (t80) cc_final: 0.7203 (t80) REVERT: A 110 MET cc_start: 0.6040 (mmm) cc_final: 0.5537 (mmp) REVERT: A 452 ASP cc_start: 0.8595 (t70) cc_final: 0.7959 (t0) REVERT: A 568 ASN cc_start: 0.8119 (m-40) cc_final: 0.7769 (m-40) REVERT: A 714 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8443 (ptpt) outliers start: 26 outliers final: 15 residues processed: 148 average time/residue: 1.1824 time to fit residues: 188.1144 Evaluate side-chains 153 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 818 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN B 109 ASN C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9750 Z= 0.169 Angle : 0.453 5.525 13252 Z= 0.241 Chirality : 0.041 0.173 1477 Planarity : 0.003 0.038 1682 Dihedral : 7.106 175.679 1299 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.72 % Allowed : 16.41 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.17 (0.24), residues: 1165 helix: 0.58 (0.23), residues: 539 sheet: -0.01 (0.40), residues: 150 loop : -0.22 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 182 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.001 PHE A 652 TYR 0.014 0.001 TYR A 788 ARG 0.004 0.000 ARG A 553 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: B 88 GLN cc_start: 0.8366 (tt0) cc_final: 0.8020 (mt0) REVERT: B 127 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8464 (ttpt) REVERT: C 50 GLU cc_start: 0.5479 (OUTLIER) cc_final: 0.5079 (mp0) REVERT: G 111 ARG cc_start: 0.6217 (ttt180) cc_final: 0.5932 (tpp-160) REVERT: G 129 MET cc_start: 0.7920 (mtm) cc_final: 0.7607 (ttp) REVERT: G 184 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6621 (pp) REVERT: A 83 GLU cc_start: 0.6021 (mt-10) cc_final: 0.5772 (tt0) REVERT: A 104 PHE cc_start: 0.7757 (t80) cc_final: 0.7192 (t80) REVERT: A 110 MET cc_start: 0.6028 (mmm) cc_final: 0.5526 (mmp) REVERT: A 452 ASP cc_start: 0.8369 (t70) cc_final: 0.7788 (t0) REVERT: A 568 ASN cc_start: 0.8079 (m-40) cc_final: 0.7683 (m-40) REVERT: A 714 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8410 (ptpt) outliers start: 18 outliers final: 14 residues processed: 141 average time/residue: 1.1987 time to fit residues: 182.3433 Evaluate side-chains 148 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 155 GLU Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain A residue 340 PHE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 739 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 92 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.128159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094408 restraints weight = 12357.494| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.85 r_work: 0.3022 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9750 Z= 0.183 Angle : 0.460 5.527 13252 Z= 0.244 Chirality : 0.042 0.172 1477 Planarity : 0.003 0.036 1682 Dihedral : 7.112 175.981 1299 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.53 % Allowed : 16.70 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.19 (0.24), residues: 1165 helix: 0.59 (0.23), residues: 539 sheet: 0.03 (0.40), residues: 150 loop : -0.20 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 182 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.001 PHE A 652 TYR 0.014 0.001 TYR A 788 ARG 0.004 0.000 ARG A 553 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3854.57 seconds wall clock time: 68 minutes 41.44 seconds (4121.44 seconds total)