Starting phenix.real_space_refine on Thu Feb 15 07:21:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/02_2024/7dok_30795_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/02_2024/7dok_30795.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/02_2024/7dok_30795_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/02_2024/7dok_30795_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/02_2024/7dok_30795_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/02_2024/7dok_30795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/02_2024/7dok_30795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/02_2024/7dok_30795_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dok_30795/02_2024/7dok_30795_updated.pdb" } resolution = 2.73 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= 0.006 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 49 5.49 5 Mg 4 5.21 5 S 81 5.16 5 C 7141 2.51 5 N 1942 2.21 5 O 2315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A TYR 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ASP 740": "OD1" <-> "OD2" Residue "A ASP 760": "OD1" <-> "OD2" Residue "A TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 851": "OD1" <-> "OD2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 889": "NH1" <-> "NH2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B ASP 112": "OD1" <-> "OD2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 60": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 143": "OD1" <-> "OD2" Residue "G ASP 163": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11534 Number of models: 1 Model: "" Number of chains: 8 Chain: "P" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 427 Classifications: {'RNA': 20} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 9} Link IDs: {'rna3p': 19} Chain: "T" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 499 Classifications: {'RNA': 24} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 15} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 7457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 7457 Classifications: {'peptide': 925} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 894} Chain: "B" Number of atoms: 1214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1214 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 149} Chain: "C" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 530 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "G" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1360 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain breaks: 1 Chain: "P" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'HCU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 25 Unusual residues: {' MG': 3, ' ZN': 2, 'POP': 2} Classifications: {'undetermined': 7, 'water': 2} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3367 SG CYS A 301 90.773 66.447 46.517 1.00 23.11 S ATOM 3408 SG CYS A 306 90.854 65.667 42.318 1.00 23.19 S ATOM 3440 SG CYS A 310 94.122 65.636 44.859 1.00 20.66 S ATOM 4848 SG CYS A 487 72.617 61.166 54.936 1.00 29.89 S ATOM 6101 SG CYS A 645 71.622 60.925 50.803 1.00 32.78 S ATOM 6107 SG CYS A 646 74.723 63.422 52.381 1.00 31.19 S Time building chain proxies: 7.01, per 1000 atoms: 0.61 Number of scatterers: 11534 At special positions: 0 Unit cell: (150.729, 94.072, 131.487, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 81 16.00 P 49 15.00 Mg 4 11.99 O 2315 8.00 N 1942 7.00 C 7141 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: 4.67 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " 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 ZN A1001 " - pdb=" ND1 HIS A 295 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 3 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2546 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 9 sheets defined 46.0% alpha, 11.0% beta 20 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 5.56 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.533A pdb=" N ARG A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 removed outlier: 3.638A pdb=" N GLN A 81 " --> pdb=" O PHE A 77 " (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 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 169 through 198 removed outlier: 3.526A pdb=" N LEU A 172 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (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: 4.078A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.382A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A) 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: 3.700A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.138A 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 375 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 448 through 455 removed outlier: 4.177A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.772A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (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 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 581 removed outlier: 3.688A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.676A 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 687 through 708 Processing helix chain 'A' and resid 718 through 732 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 847 through 850 Processing helix chain 'A' and resid 856 through 871 removed outlier: 3.528A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Proline residue: A 868 - end of helix removed outlier: 4.903A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 4.206A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 removed outlier: 4.120A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 97 removed outlier: 3.584A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.533A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 135 through 141 removed outlier: 3.826A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 48 through 61 removed outlier: 3.772A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 20 Processing helix chain 'G' and resid 36 through 98 removed outlier: 3.657A pdb=" N LYS G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER G 41 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N THR G 84 " --> pdb=" O ARG G 80 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N SER G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 112 removed outlier: 3.820A pdb=" N ILE G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 139 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 6.799A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS A 73 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER A 115 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 31 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= D, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= E, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.487A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= G, first strand: chain 'A' and resid 815 through 822 Processing sheet with id= H, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.245A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.693A pdb=" N GLN G 158 " --> pdb=" O THR G 187 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU G 189 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE G 156 " --> pdb=" O LEU G 189 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2573 1.33 - 1.45: 2813 1.45 - 1.57: 6254 1.57 - 1.69: 90 1.69 - 1.81: 127 Bond restraints: 11857 Sorted by residual: bond pdb=" O3 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.650 1.429 0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C1 HCU P1201 " pdb=" O1 HCU P1201 " ideal model delta sigma weight residual 1.184 1.401 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C9 HCU P1201 " pdb=" O3 HCU P1201 " ideal model delta sigma weight residual 1.400 1.222 0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" O4 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.510 1.338 0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " ideal model delta sigma weight residual 1.527 1.375 0.152 2.00e-02 2.50e+03 5.74e+01 ... (remaining 11852 not shown) Histogram of bond angle deviations from ideal: 95.75 - 104.20: 319 104.20 - 112.64: 6244 112.64 - 121.09: 6635 121.09 - 129.54: 2988 129.54 - 137.98: 89 Bond angle restraints: 16275 Sorted by residual: angle pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " pdb=" C9 HCU P1201 " ideal model delta sigma weight residual 109.47 132.79 -23.32 3.00e+00 1.11e-01 6.04e+01 angle pdb=" C4' U P 20 " pdb=" C3' U P 20 " pdb=" O3' U P 20 " ideal model delta sigma weight residual 113.00 123.86 -10.86 1.50e+00 4.44e-01 5.24e+01 angle pdb=" C2' G P 8 " pdb=" C1' G P 8 " pdb=" N9 G P 8 " ideal model delta sigma weight residual 112.00 101.41 10.59 1.50e+00 4.44e-01 4.98e+01 angle pdb=" O3' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " ideal model delta sigma weight residual 113.70 103.30 10.40 1.50e+00 4.44e-01 4.80e+01 angle pdb=" C9 HCU P1201 " pdb=" O3 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 118.46 137.98 -19.52 3.00e+00 1.11e-01 4.23e+01 ... (remaining 16270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.47: 6586 21.47 - 42.94: 463 42.94 - 64.41: 73 64.41 - 85.89: 20 85.89 - 107.36: 3 Dihedral angle restraints: 7145 sinusoidal: 3213 harmonic: 3932 Sorted by residual: dihedral pdb=" O4 POP A1007 " pdb=" O POP A1007 " pdb=" P2 POP A1007 " pdb=" P1 POP A1007 " ideal model delta sinusoidal sigma weight residual -57.41 -164.77 107.36 1 2.00e+01 2.50e-03 3.12e+01 dihedral pdb=" C4' U P 7 " pdb=" C3' U P 7 " pdb=" C2' U P 7 " pdb=" C1' U P 7 " ideal model delta sinusoidal sigma weight residual 36.00 3.53 32.47 1 8.00e+00 1.56e-02 2.35e+01 dihedral pdb=" O4 POP A1003 " pdb=" O POP A1003 " pdb=" P2 POP A1003 " pdb=" P1 POP A1003 " ideal model delta sinusoidal sigma weight residual -57.41 28.41 -85.82 1 2.00e+01 2.50e-03 2.23e+01 ... (remaining 7142 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 1861 0.316 - 0.631: 0 0.631 - 0.947: 0 0.947 - 1.262: 0 1.262 - 1.578: 1 Chirality restraints: 1862 Sorted by residual: chirality pdb=" C8 HCU P1201 " pdb=" C10 HCU P1201 " pdb=" C7 HCU P1201 " pdb=" C9 HCU P1201 " both_signs ideal model delta sigma weight residual False -2.74 -1.16 -1.58 2.00e-01 2.50e+01 6.22e+01 chirality pdb=" C3' G P 8 " pdb=" C4' G P 8 " pdb=" O3' G P 8 " pdb=" C2' G P 8 " both_signs ideal model delta sigma weight residual False -2.48 -2.21 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C1' G P 8 " pdb=" O4' G P 8 " pdb=" C2' G P 8 " pdb=" N9 G P 8 " both_signs ideal model delta sigma weight residual False 2.46 2.72 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1859 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 155 " 0.021 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ASP A 155 " -0.070 2.00e-02 2.50e+03 pdb=" O ASP A 155 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR A 156 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G P 8 " 0.011 2.00e-02 2.50e+03 2.18e-02 1.43e+01 pdb=" N9 G P 8 " -0.056 2.00e-02 2.50e+03 pdb=" C8 G P 8 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G P 8 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G P 8 " 0.008 2.00e-02 2.50e+03 pdb=" C6 G P 8 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G P 8 " 0.000 2.00e-02 2.50e+03 pdb=" N1 G P 8 " -0.016 2.00e-02 2.50e+03 pdb=" C2 G P 8 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G P 8 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G P 8 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G P 8 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 177 " -0.044 5.00e-02 4.00e+02 6.49e-02 6.75e+00 pdb=" N PRO B 178 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 178 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 178 " -0.037 5.00e-02 4.00e+02 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 19 2.34 - 2.98: 5204 2.98 - 3.62: 17240 3.62 - 4.26: 28629 4.26 - 4.90: 45728 Nonbonded interactions: 96820 Sorted by model distance: nonbonded pdb=" O4 POP A1003 " pdb=" O HOH A1101 " model vdw 1.695 2.440 nonbonded pdb="MG MG A1005 " pdb=" O6 POP A1007 " model vdw 1.731 2.170 nonbonded pdb="MG MG A1006 " pdb=" O2 POP A1007 " model vdw 1.950 2.170 nonbonded pdb=" O PHE A 77 " pdb=" OE1 GLN A 81 " model vdw 2.035 3.040 nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1005 " model vdw 2.052 2.170 ... (remaining 96815 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' selection = (chain 'G' and resid 37 through 191) } 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: 1.430 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: 0.000 Extract box with map and model: 7.670 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 39.360 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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:13.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.009 0.221 11857 Z= 0.542 Angle : 1.015 23.323 16275 Z= 0.648 Chirality : 0.072 1.578 1862 Planarity : 0.006 0.065 1914 Dihedral : 14.968 107.357 4599 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.60 % Allowed : 4.29 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -2.40 (0.20), residues: 1313 helix: -1.65 (0.17), residues: 651 sheet: -0.82 (0.41), residues: 148 loop : -1.51 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 916 HIS 0.004 0.001 HIS C 36 PHE 0.025 0.003 PHE C 49 TYR 0.022 0.002 TYR A 831 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 1.357 Fit side-chains REVERT: A 72 VAL cc_start: 0.7956 (m) cc_final: 0.7654 (t) REVERT: A 924 MET cc_start: 0.8554 (mmm) cc_final: 0.8286 (mmt) REVERT: B 67 MET cc_start: 0.6169 (ptp) cc_final: 0.5968 (ptp) REVERT: B 171 GLU cc_start: 0.7385 (tt0) cc_final: 0.7078 (tt0) REVERT: C 23 GLU cc_start: 0.8336 (pt0) cc_final: 0.8080 (pt0) REVERT: G 55 MET cc_start: 0.7340 (mtp) cc_final: 0.6286 (pp-130) REVERT: G 59 LEU cc_start: 0.8204 (mt) cc_final: 0.7927 (mp) REVERT: G 75 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7610 (mmm-85) outliers start: 7 outliers final: 2 residues processed: 204 average time/residue: 1.0861 time to fit residues: 242.5236 Evaluate side-chains 143 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 906 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 ASN A 75 HIS A 117 GLN A 541 GLN A 691 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN B 105 ASN B 136 ASN B 158 GLN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 100 ASN G 179 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11857 Z= 0.145 Angle : 0.494 6.328 16275 Z= 0.263 Chirality : 0.038 0.141 1862 Planarity : 0.004 0.051 1914 Dihedral : 12.209 128.320 2112 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.40 % Allowed : 10.72 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.84 (0.21), residues: 1313 helix: -0.20 (0.19), residues: 649 sheet: -0.53 (0.44), residues: 127 loop : -0.84 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.015 0.001 PHE A 652 TYR 0.016 0.001 TYR A 87 ARG 0.003 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 1.302 Fit side-chains REVERT: A 57 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.6282 (tm-30) REVERT: A 372 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8166 (tp) REVERT: A 714 LYS cc_start: 0.8252 (mmmm) cc_final: 0.7848 (mtpt) REVERT: A 755 MET cc_start: 0.9057 (mtm) cc_final: 0.8468 (mtp) REVERT: A 758 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8206 (tp) REVERT: B 55 MET cc_start: 0.2837 (mmt) cc_final: 0.2515 (mtm) REVERT: B 67 MET cc_start: 0.5754 (ptp) cc_final: 0.5526 (ptm) REVERT: B 171 GLU cc_start: 0.7411 (tt0) cc_final: 0.7034 (tt0) REVERT: C 23 GLU cc_start: 0.8344 (pt0) cc_final: 0.8082 (pt0) REVERT: G 55 MET cc_start: 0.7235 (mtp) cc_final: 0.6274 (pp-130) REVERT: G 59 LEU cc_start: 0.8192 (mt) cc_final: 0.7896 (mp) REVERT: G 99 ASP cc_start: 0.6818 (t0) cc_final: 0.6577 (t70) REVERT: G 136 ASN cc_start: 0.6203 (p0) cc_final: 0.5769 (p0) outliers start: 28 outliers final: 11 residues processed: 172 average time/residue: 0.9845 time to fit residues: 187.3832 Evaluate side-chains 157 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain B residue 94 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 403 ASN A 541 GLN A 642 HIS ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 ASN B 136 ASN B 158 GLN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11857 Z= 0.345 Angle : 0.567 10.337 16275 Z= 0.297 Chirality : 0.043 0.149 1862 Planarity : 0.004 0.043 1914 Dihedral : 12.252 124.989 2109 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.86 % Allowed : 11.92 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.55 (0.22), residues: 1313 helix: 0.08 (0.20), residues: 649 sheet: -0.61 (0.42), residues: 136 loop : -0.69 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 290 HIS 0.007 0.001 HIS C 36 PHE 0.017 0.002 PHE A 652 TYR 0.016 0.002 TYR A 788 ARG 0.003 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 135 time to evaluate : 1.202 Fit side-chains revert: symmetry clash REVERT: A 57 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.5932 (tm-30) REVERT: A 291 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7522 (p0) REVERT: A 436 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6674 (mt-10) REVERT: A 666 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8066 (mtt) REVERT: A 892 HIS cc_start: 0.7461 (t-90) cc_final: 0.7250 (t70) REVERT: B 95 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6757 (pp) REVERT: B 171 GLU cc_start: 0.7500 (tt0) cc_final: 0.7161 (tt0) REVERT: G 55 MET cc_start: 0.7273 (mtp) cc_final: 0.6423 (pp-130) REVERT: G 99 ASP cc_start: 0.6960 (t0) cc_final: 0.6557 (t0) REVERT: G 136 ASN cc_start: 0.6267 (p0) cc_final: 0.5977 (p0) outliers start: 45 outliers final: 20 residues processed: 157 average time/residue: 1.0471 time to fit residues: 181.3572 Evaluate side-chains 156 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 160 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 58 optimal weight: 0.0010 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN A 541 GLN A 543 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 158 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11857 Z= 0.177 Angle : 0.480 8.905 16275 Z= 0.252 Chirality : 0.039 0.138 1862 Planarity : 0.003 0.042 1914 Dihedral : 11.989 120.503 2109 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.43 % Allowed : 13.29 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: -0.18 (0.23), residues: 1313 helix: 0.39 (0.20), residues: 655 sheet: -0.58 (0.42), residues: 134 loop : -0.48 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.015 0.001 PHE A 652 TYR 0.013 0.001 TYR A 788 ARG 0.001 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 148 time to evaluate : 1.405 Fit side-chains revert: symmetry clash REVERT: A 57 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.6072 (tm-30) REVERT: A 372 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7949 (mp) REVERT: A 666 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8019 (mtt) REVERT: A 892 HIS cc_start: 0.7482 (t-90) cc_final: 0.7268 (t-90) REVERT: B 55 MET cc_start: 0.2816 (mmt) cc_final: 0.2517 (mtm) REVERT: B 95 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6747 (pp) REVERT: B 171 GLU cc_start: 0.7620 (tt0) cc_final: 0.7262 (tt0) REVERT: G 55 MET cc_start: 0.7252 (mtp) cc_final: 0.6330 (pp-130) REVERT: G 59 LEU cc_start: 0.8005 (mt) cc_final: 0.7584 (mp) REVERT: G 99 ASP cc_start: 0.6980 (t0) cc_final: 0.6594 (t0) REVERT: G 136 ASN cc_start: 0.6324 (p0) cc_final: 0.6039 (p0) outliers start: 40 outliers final: 17 residues processed: 175 average time/residue: 0.9821 time to fit residues: 189.8859 Evaluate side-chains 158 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN B 104 ASN B 136 ASN B 158 GLN C 31 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11857 Z= 0.265 Angle : 0.525 8.579 16275 Z= 0.274 Chirality : 0.041 0.136 1862 Planarity : 0.004 0.041 1914 Dihedral : 12.053 119.188 2109 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.34 % Allowed : 14.32 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 (0.23), residues: 1313 helix: 0.40 (0.20), residues: 657 sheet: -0.65 (0.41), residues: 136 loop : -0.45 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 290 HIS 0.007 0.001 HIS C 36 PHE 0.016 0.002 PHE A 652 TYR 0.018 0.002 TYR G 138 ARG 0.005 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 133 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 57 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.5907 (tm-30) REVERT: A 666 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8130 (mtt) REVERT: A 758 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8256 (tp) REVERT: A 892 HIS cc_start: 0.7488 (t-90) cc_final: 0.7260 (t-90) REVERT: B 55 MET cc_start: 0.2418 (mmt) cc_final: 0.2206 (mtm) REVERT: B 95 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6773 (pp) REVERT: B 171 GLU cc_start: 0.7604 (tt0) cc_final: 0.7191 (tt0) REVERT: G 55 MET cc_start: 0.7225 (mtp) cc_final: 0.6436 (pp-130) REVERT: G 70 MET cc_start: 0.7035 (ptt) cc_final: 0.6768 (ttp) REVERT: G 99 ASP cc_start: 0.6887 (t0) cc_final: 0.6497 (t0) REVERT: G 136 ASN cc_start: 0.6215 (p0) cc_final: 0.5921 (p0) outliers start: 39 outliers final: 23 residues processed: 155 average time/residue: 0.9952 time to fit residues: 170.7419 Evaluate side-chains 163 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 160 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 31 optimal weight: 0.0980 chunk 129 optimal weight: 20.0000 chunk 107 optimal weight: 0.0970 chunk 60 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN B 104 ASN B 136 ASN B 158 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11857 Z= 0.155 Angle : 0.476 7.968 16275 Z= 0.247 Chirality : 0.038 0.159 1862 Planarity : 0.003 0.049 1914 Dihedral : 11.871 115.977 2109 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.32 % Allowed : 15.95 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.09 (0.23), residues: 1313 helix: 0.61 (0.21), residues: 658 sheet: -0.54 (0.41), residues: 134 loop : -0.33 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.001 PHE A 652 TYR 0.018 0.001 TYR A 903 ARG 0.001 0.000 ARG G 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.341 Fit side-chains revert: symmetry clash REVERT: A 360 ASN cc_start: 0.6561 (OUTLIER) cc_final: 0.6304 (p0) REVERT: A 666 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8003 (mtt) REVERT: A 758 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8243 (tp) REVERT: B 95 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6879 (pp) REVERT: B 171 GLU cc_start: 0.7606 (tt0) cc_final: 0.7284 (tt0) REVERT: G 55 MET cc_start: 0.7228 (mtp) cc_final: 0.6454 (pp-130) REVERT: G 75 ARG cc_start: 0.7859 (mmm-85) cc_final: 0.7484 (mmm-85) REVERT: G 99 ASP cc_start: 0.6852 (t0) cc_final: 0.6479 (t0) REVERT: G 136 ASN cc_start: 0.6185 (p0) cc_final: 0.5888 (p0) outliers start: 27 outliers final: 17 residues processed: 161 average time/residue: 0.9902 time to fit residues: 176.3462 Evaluate side-chains 154 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 62 MET Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 94 optimal weight: 0.0270 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 129 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 1.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 158 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: 0.8178 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11857 Z= 0.171 Angle : 0.482 7.783 16275 Z= 0.250 Chirality : 0.039 0.148 1862 Planarity : 0.003 0.052 1914 Dihedral : 11.867 115.837 2109 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.74 % Allowed : 16.21 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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 (0.23), residues: 1313 helix: 0.69 (0.21), residues: 655 sheet: -0.47 (0.41), residues: 134 loop : -0.27 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.013 0.001 PHE A 652 TYR 0.020 0.001 TYR G 138 ARG 0.001 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8281 (t80) cc_final: 0.7990 (t80) REVERT: A 360 ASN cc_start: 0.6573 (OUTLIER) cc_final: 0.6312 (p0) REVERT: A 666 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7819 (mtt) REVERT: A 758 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8241 (tp) REVERT: B 95 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6847 (pp) REVERT: B 171 GLU cc_start: 0.7625 (tt0) cc_final: 0.7310 (tt0) REVERT: C 44 ASP cc_start: 0.7709 (p0) cc_final: 0.7484 (p0) REVERT: G 55 MET cc_start: 0.7214 (mtp) cc_final: 0.6454 (pp-130) REVERT: G 75 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7572 (mmm-85) REVERT: G 99 ASP cc_start: 0.6906 (t0) cc_final: 0.6546 (t0) outliers start: 32 outliers final: 19 residues processed: 152 average time/residue: 1.0349 time to fit residues: 173.3718 Evaluate side-chains 160 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 117 optimal weight: 0.0170 chunk 123 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN ** A 734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11857 Z= 0.148 Angle : 0.484 11.849 16275 Z= 0.247 Chirality : 0.038 0.141 1862 Planarity : 0.003 0.051 1914 Dihedral : 11.805 114.409 2109 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.66 % Allowed : 16.64 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.33 (0.23), residues: 1313 helix: 0.81 (0.21), residues: 659 sheet: -0.43 (0.41), residues: 134 loop : -0.21 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.012 0.001 PHE A 652 TYR 0.027 0.001 TYR A 903 ARG 0.001 0.000 ARG G 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 142 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8220 (t80) cc_final: 0.7991 (t80) REVERT: A 360 ASN cc_start: 0.6599 (OUTLIER) cc_final: 0.6323 (p0) REVERT: A 380 MET cc_start: 0.7637 (tpp) cc_final: 0.7403 (ttm) REVERT: A 666 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7794 (mtt) REVERT: A 758 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8310 (tp) REVERT: B 95 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6821 (pp) REVERT: B 171 GLU cc_start: 0.7660 (tt0) cc_final: 0.7348 (tt0) REVERT: G 55 MET cc_start: 0.7189 (mtp) cc_final: 0.6450 (pp-130) REVERT: G 75 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7464 (mmm-85) REVERT: G 99 ASP cc_start: 0.6903 (t0) cc_final: 0.6574 (t0) outliers start: 31 outliers final: 19 residues processed: 159 average time/residue: 1.0353 time to fit residues: 181.7322 Evaluate side-chains 152 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 601 MET Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 0.0980 chunk 79 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN B 136 ASN B 158 GLN C 31 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11857 Z= 0.260 Angle : 0.534 11.631 16275 Z= 0.274 Chirality : 0.041 0.143 1862 Planarity : 0.003 0.051 1914 Dihedral : 11.933 117.351 2109 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.09 % Allowed : 16.55 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.22 (0.23), residues: 1313 helix: 0.71 (0.20), residues: 656 sheet: -0.48 (0.42), residues: 134 loop : -0.24 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 290 HIS 0.007 0.001 HIS C 36 PHE 0.015 0.002 PHE A 694 TYR 0.020 0.002 TYR G 138 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8237 (t80) cc_final: 0.8001 (t80) REVERT: A 360 ASN cc_start: 0.6680 (OUTLIER) cc_final: 0.6378 (p0) REVERT: A 666 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8147 (mtt) REVERT: A 758 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8303 (tp) REVERT: B 95 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6878 (pp) REVERT: B 171 GLU cc_start: 0.7642 (tt0) cc_final: 0.7329 (tt0) REVERT: G 55 MET cc_start: 0.7149 (mtp) cc_final: 0.6376 (pp-130) REVERT: G 99 ASP cc_start: 0.6954 (t0) cc_final: 0.6628 (t0) outliers start: 36 outliers final: 23 residues processed: 149 average time/residue: 1.0508 time to fit residues: 172.0673 Evaluate side-chains 162 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 907 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 148 THR Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 133 optimal weight: 0.4980 chunk 122 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN B 136 ASN B 158 GLN C 19 GLN C 31 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11857 Z= 0.156 Angle : 0.490 11.565 16275 Z= 0.253 Chirality : 0.039 0.165 1862 Planarity : 0.003 0.051 1914 Dihedral : 11.792 114.517 2109 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.40 % Allowed : 17.24 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.33 (0.23), residues: 1313 helix: 0.81 (0.21), residues: 658 sheet: -0.40 (0.42), residues: 134 loop : -0.21 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.013 0.001 PHE A 652 TYR 0.019 0.001 TYR A 903 ARG 0.005 0.000 ARG G 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 1.238 Fit side-chains revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8215 (t80) cc_final: 0.7964 (t80) REVERT: A 360 ASN cc_start: 0.6608 (OUTLIER) cc_final: 0.6313 (p0) REVERT: A 666 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7778 (mtt) REVERT: A 758 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8281 (tp) REVERT: B 95 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6849 (pp) REVERT: B 171 GLU cc_start: 0.7647 (tt0) cc_final: 0.7333 (tt0) REVERT: G 55 MET cc_start: 0.7136 (mtp) cc_final: 0.6366 (pp-130) REVERT: G 99 ASP cc_start: 0.6871 (t0) cc_final: 0.6556 (t0) outliers start: 28 outliers final: 17 residues processed: 158 average time/residue: 0.9737 time to fit residues: 170.0085 Evaluate side-chains 152 residues out of total 1166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 555 ARG Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 29 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 0.0970 chunk 93 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN B 136 ASN B 158 GLN C 19 GLN C 31 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.141530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.101653 restraints weight = 15995.393| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.65 r_work: 0.3103 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11857 Z= 0.217 Angle : 0.514 11.457 16275 Z= 0.264 Chirality : 0.040 0.138 1862 Planarity : 0.003 0.051 1914 Dihedral : 11.837 115.165 2109 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.49 % Allowed : 16.72 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.29 (0.23), residues: 1313 helix: 0.79 (0.21), residues: 656 sheet: -0.43 (0.42), residues: 134 loop : -0.25 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.014 0.002 PHE A 652 TYR 0.021 0.002 TYR G 138 ARG 0.005 0.000 ARG G 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.06 seconds wall clock time: 69 minutes 30.49 seconds (4170.49 seconds total)