Starting phenix.real_space_refine on Fri Mar 15 14:24:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/03_2024/8w41_37260_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/03_2024/8w41_37260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/03_2024/8w41_37260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/03_2024/8w41_37260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/03_2024/8w41_37260_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w41_37260/03_2024/8w41_37260_updated.pdb" } resolution = 3.54 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 28 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 68 5.16 5 C 7417 2.51 5 N 2071 2.21 5 O 2295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 48": "OE1" <-> "OE2" Residue "I GLU 8": "OE1" <-> "OE2" Residue "I GLU 68": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ARG 136": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A ARG 572": "NH1" <-> "NH2" Residue "A ARG 580": "NH1" <-> "NH2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A ARG 613": "NH1" <-> "NH2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "A ARG 825": "NH1" <-> "NH2" Residue "A ARG 832": "NH1" <-> "NH2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ARG 849": "NH1" <-> "NH2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A ARG 939": "NH1" <-> "NH2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "A GLU 941": "OE1" <-> "OE2" Residue "A GLU 944": "OE1" <-> "OE2" Residue "A GLU 975": "OE1" <-> "OE2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A GLU 986": "OE1" <-> "OE2" Residue "A GLU 1004": "OE1" <-> "OE2" Residue "A ARG 1007": "NH1" <-> "NH2" Residue "A GLU 1020": "OE1" <-> "OE2" Residue "A TYR 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A ARG 1102": "NH1" <-> "NH2" Residue "A GLU 1104": "OE1" <-> "OE2" Residue "A ARG 1172": "NH1" <-> "NH2" Residue "A ARG 1177": "NH1" <-> "NH2" Residue "A ARG 1204": "NH1" <-> "NH2" Residue "A GLU 1232": "OE1" <-> "OE2" Residue "A ARG 1240": "NH1" <-> "NH2" Residue "A GLU 1254": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11859 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1156 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "I" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1151 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 2, 'TRANS': 143} Chain: "A" Number of atoms: 9515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1162, 9515 Classifications: {'peptide': 1162} Link IDs: {'PTRANS': 37, 'TRANS': 1124} Chain breaks: 4 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.85, per 1000 atoms: 0.49 Number of scatterers: 11859 At special positions: 0 Unit cell: (74.43, 102.548, 186.075, 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) Ca 4 19.99 S 68 16.00 P 3 15.00 Mg 1 11.99 O 2295 8.00 N 2071 7.00 C 7417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.02 Conformation dependent library (CDL) restraints added in 2.4 seconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 6 sheets defined 56.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'B' and resid 7 through 20 Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 79 through 93 removed outlier: 4.621A pdb=" N GLU B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 113 Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.661A pdb=" N ASP B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'I' and resid 7 through 19 Processing helix chain 'I' and resid 30 through 39 removed outlier: 4.180A pdb=" N THR I 35 " --> pdb=" O LYS I 31 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER I 39 " --> pdb=" O THR I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 59 removed outlier: 4.569A pdb=" N ASP I 59 " --> pdb=" O GLU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 Processing helix chain 'I' and resid 83 through 92 Processing helix chain 'I' and resid 103 through 112 Processing helix chain 'I' and resid 119 through 128 Processing helix chain 'I' and resid 139 through 147 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 70 through 83 removed outlier: 3.520A pdb=" N SER A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 removed outlier: 3.517A pdb=" N TYR A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 177 through 184 removed outlier: 3.761A pdb=" N VAL A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 246 through 254 removed outlier: 3.692A pdb=" N ARG A 250 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU A 251 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 253 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 272 through 275 No H-bonds generated for 'chain 'A' and resid 272 through 275' Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'A' and resid 331 through 349 removed outlier: 3.665A pdb=" N GLY A 348 " --> pdb=" O VAL A 344 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 378 removed outlier: 3.967A pdb=" N SER A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 413 through 443 removed outlier: 3.769A pdb=" N PHE A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 488 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 525 through 533 Processing helix chain 'A' and resid 540 through 550 Processing helix chain 'A' and resid 560 through 562 No H-bonds generated for 'chain 'A' and resid 560 through 562' Processing helix chain 'A' and resid 566 through 570 removed outlier: 3.914A pdb=" N ASN A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 570' Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 593 through 596 No H-bonds generated for 'chain 'A' and resid 593 through 596' Processing helix chain 'A' and resid 603 through 610 Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 643 through 660 Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 694 through 701 Processing helix chain 'A' and resid 711 through 719 Processing helix chain 'A' and resid 724 through 728 removed outlier: 3.666A pdb=" N ARG A 728 " --> pdb=" O ASP A 724 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 724 through 728' Processing helix chain 'A' and resid 731 through 741 removed outlier: 3.561A pdb=" N PHE A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A 740 " --> pdb=" O LYS A 736 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 769 removed outlier: 3.750A pdb=" N GLN A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 828 removed outlier: 3.994A pdb=" N VAL A 796 " --> pdb=" O ARG A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 859 removed outlier: 3.982A pdb=" N GLU A 855 " --> pdb=" O ASP A 851 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 887 Processing helix chain 'A' and resid 892 through 919 removed outlier: 3.558A pdb=" N LYS A 904 " --> pdb=" O ASP A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 978 removed outlier: 3.935A pdb=" N ARG A 928 " --> pdb=" O GLU A 924 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS A 963 " --> pdb=" O GLU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1020 removed outlier: 3.605A pdb=" N ARG A 991 " --> pdb=" O ALA A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 Processing helix chain 'A' and resid 1095 through 1118 removed outlier: 3.864A pdb=" N CYS A1101 " --> pdb=" O LEU A1098 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG A1102 " --> pdb=" O ALA A1099 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A1105 " --> pdb=" O ARG A1102 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A1106 " --> pdb=" O GLU A1103 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A1108 " --> pdb=" O PHE A1105 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A1118 " --> pdb=" O TRP A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1137 Processing helix chain 'A' and resid 1178 through 1180 No H-bonds generated for 'chain 'A' and resid 1178 through 1180' Processing helix chain 'A' and resid 1231 through 1234 No H-bonds generated for 'chain 'A' and resid 1231 through 1234' Processing helix chain 'A' and resid 1246 through 1256 removed outlier: 3.569A pdb=" N GLU A1250 " --> pdb=" O PRO A1246 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS A1256 " --> pdb=" O ILE A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1267 Processing sheet with id= A, first strand: chain 'A' and resid 7 through 10 removed outlier: 3.678A pdb=" N ASN A 20 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 90 removed outlier: 3.663A pdb=" N ILE A 666 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 226 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 352 through 354 Processing sheet with id= D, first strand: chain 'A' and resid 576 through 580 Processing sheet with id= E, first strand: chain 'A' and resid 707 through 710 removed outlier: 3.588A pdb=" N SER A 707 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1168 through 1174 removed outlier: 5.241A pdb=" N ASP A1198 " --> pdb=" O ILE A1202 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE A1202 " --> pdb=" O ASP A1198 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1674 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: 4.32 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2139 1.31 - 1.44: 2999 1.44 - 1.56: 6802 1.56 - 1.69: 3 1.69 - 1.81: 112 Bond restraints: 12055 Sorted by residual: bond pdb=" CA ILE A1244 " pdb=" C ILE A1244 " ideal model delta sigma weight residual 1.526 1.415 0.111 1.16e-02 7.43e+03 9.11e+01 bond pdb=" CA MET A1224 " pdb=" C MET A1224 " ideal model delta sigma weight residual 1.523 1.430 0.093 1.34e-02 5.57e+03 4.85e+01 bond pdb=" CA GLU A 152 " pdb=" C GLU A 152 " ideal model delta sigma weight residual 1.528 1.435 0.092 1.33e-02 5.65e+03 4.83e+01 bond pdb=" CA LYS A1221 " pdb=" C LYS A1221 " ideal model delta sigma weight residual 1.530 1.469 0.060 9.10e-03 1.21e+04 4.41e+01 bond pdb=" CA GLU A1104 " pdb=" C GLU A1104 " ideal model delta sigma weight residual 1.524 1.441 0.083 1.29e-02 6.01e+03 4.16e+01 ... (remaining 12050 not shown) Histogram of bond angle deviations from ideal: 89.98 - 99.18: 10 99.18 - 108.38: 504 108.38 - 117.59: 8228 117.59 - 126.79: 7337 126.79 - 135.99: 105 Bond angle restraints: 16184 Sorted by residual: angle pdb=" N ILE A1089 " pdb=" CA ILE A1089 " pdb=" C ILE A1089 " ideal model delta sigma weight residual 113.53 94.41 19.12 9.80e-01 1.04e+00 3.81e+02 angle pdb=" N LYS A1221 " pdb=" CA LYS A1221 " pdb=" C LYS A1221 " ideal model delta sigma weight residual 108.49 89.98 18.51 1.15e+00 7.56e-01 2.59e+02 angle pdb=" N ARG A1102 " pdb=" CA ARG A1102 " pdb=" C ARG A1102 " ideal model delta sigma weight residual 111.82 101.33 10.49 1.16e+00 7.43e-01 8.17e+01 angle pdb=" N GLU I 105 " pdb=" CA GLU I 105 " pdb=" C GLU I 105 " ideal model delta sigma weight residual 111.36 102.39 8.97 1.09e+00 8.42e-01 6.77e+01 angle pdb=" N PHE A1249 " pdb=" CA PHE A1249 " pdb=" C PHE A1249 " ideal model delta sigma weight residual 111.14 102.90 8.24 1.08e+00 8.57e-01 5.82e+01 ... (remaining 16179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.25: 7170 31.25 - 62.51: 247 62.51 - 93.76: 15 93.76 - 125.01: 0 125.01 - 156.27: 3 Dihedral angle restraints: 7435 sinusoidal: 3188 harmonic: 4247 Sorted by residual: dihedral pdb=" N GLU A1103 " pdb=" C GLU A1103 " pdb=" CA GLU A1103 " pdb=" CB GLU A1103 " ideal model delta harmonic sigma weight residual 122.80 140.00 -17.20 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" C5' ADP A2001 " pdb=" O5' ADP A2001 " pdb=" PA ADP A2001 " pdb=" O2A ADP A2001 " ideal model delta sinusoidal sigma weight residual -60.00 96.27 -156.27 1 2.00e+01 2.50e-03 4.60e+01 dihedral pdb=" C GLU A1103 " pdb=" N GLU A1103 " pdb=" CA GLU A1103 " pdb=" CB GLU A1103 " ideal model delta harmonic sigma weight residual -122.60 -138.75 16.15 0 2.50e+00 1.60e-01 4.18e+01 ... (remaining 7432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1685 0.145 - 0.289: 33 0.289 - 0.434: 7 0.434 - 0.579: 0 0.579 - 0.724: 1 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA GLU A1103 " pdb=" N GLU A1103 " pdb=" C GLU A1103 " pdb=" CB GLU A1103 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ILE A1244 " pdb=" N ILE A1244 " pdb=" C ILE A1244 " pdb=" CB ILE A1244 " both_signs ideal model delta sigma weight residual False 2.43 2.04 0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CA GLU A1254 " pdb=" N GLU A1254 " pdb=" C GLU A1254 " pdb=" CB GLU A1254 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 1723 not shown) Planarity restraints: 2127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 705 " -0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 706 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 706 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 706 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1082 " -0.033 2.00e-02 2.50e+03 2.08e-02 8.66e+00 pdb=" CG TYR A1082 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A1082 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A1082 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A1082 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A1082 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1082 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A1082 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A1212 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO A1213 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A1213 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1213 " 0.035 5.00e-02 4.00e+02 ... (remaining 2124 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 135 2.51 - 3.11: 9573 3.11 - 3.71: 19604 3.71 - 4.30: 26853 4.30 - 4.90: 43013 Nonbonded interactions: 99178 Sorted by model distance: nonbonded pdb=" O1B ADP A2001 " pdb="MG MG A2002 " model vdw 1.918 2.170 nonbonded pdb="MG MG A2002 " pdb=" O2 PO4 A2003 " model vdw 1.976 2.170 nonbonded pdb=" OG SER A 204 " pdb="MG MG A2002 " model vdw 2.008 2.170 nonbonded pdb=" N LYS A1221 " pdb=" O LYS A1221 " model vdw 2.105 2.496 nonbonded pdb=" O LEU A1231 " pdb=" OG1 THR A1234 " model vdw 2.127 2.440 ... (remaining 99173 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 3 through 148) selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 24.550 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 37.980 Find NCS groups from input model: 0.420 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 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 : 0.008 0.111 12055 Z= 0.516 Angle : 0.912 19.118 16184 Z= 0.565 Chirality : 0.060 0.724 1726 Planarity : 0.005 0.096 2127 Dihedral : 15.405 156.268 4677 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 1.63 % Allowed : 1.32 % Favored : 97.05 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1441 helix: -0.00 (0.17), residues: 837 sheet: -2.39 (0.47), residues: 107 loop : -1.32 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A1253 HIS 0.009 0.001 HIS A 833 PHE 0.039 0.003 PHE I 66 TYR 0.047 0.002 TYR A1082 ARG 0.022 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 311 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6807 (pmm) cc_final: 0.6389 (pmm) REVERT: B 83 GLU cc_start: 0.7060 (tp30) cc_final: 0.6599 (tp30) REVERT: I 38 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6616 (ttm110) REVERT: I 42 GLN cc_start: 0.5856 (pp30) cc_final: 0.5120 (pp30) REVERT: I 50 GLN cc_start: 0.7381 (tm-30) cc_final: 0.6981 (tm-30) REVERT: I 72 MET cc_start: 0.7568 (mmp) cc_final: 0.7363 (mmp) REVERT: I 73 MET cc_start: 0.7331 (tpt) cc_final: 0.6782 (tpt) REVERT: I 108 HIS cc_start: 0.7393 (m170) cc_final: 0.7191 (m170) REVERT: I 124 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7247 (mm-30) REVERT: I 141 GLU cc_start: 0.4241 (mm-30) cc_final: 0.3843 (mm-30) REVERT: A 5 LYS cc_start: 0.8495 (mtmm) cc_final: 0.8251 (ptpp) REVERT: A 46 ASN cc_start: 0.7613 (p0) cc_final: 0.7408 (p0) REVERT: A 132 ASP cc_start: 0.6276 (t70) cc_final: 0.5795 (t0) REVERT: A 135 PHE cc_start: 0.7674 (t80) cc_final: 0.7359 (t80) REVERT: A 138 MET cc_start: 0.7230 (tmm) cc_final: 0.6970 (tmm) REVERT: A 176 GLN cc_start: 0.7550 (pm20) cc_final: 0.7230 (pm20) REVERT: A 180 ASP cc_start: 0.7355 (m-30) cc_final: 0.7017 (m-30) REVERT: A 196 LYS cc_start: 0.8249 (tttm) cc_final: 0.7905 (tttm) REVERT: A 264 HIS cc_start: 0.7727 (m170) cc_final: 0.7376 (m170) REVERT: A 327 ILE cc_start: 0.7967 (pt) cc_final: 0.7226 (pt) REVERT: A 377 GLU cc_start: 0.7785 (tt0) cc_final: 0.7583 (tt0) REVERT: A 387 ARG cc_start: 0.7443 (pmt170) cc_final: 0.6936 (pmt170) REVERT: A 491 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7343 (tm-30) REVERT: A 575 GLU cc_start: 0.6287 (mp0) cc_final: 0.6029 (mp0) REVERT: A 596 LYS cc_start: 0.8142 (mptt) cc_final: 0.7883 (mptt) REVERT: A 609 ILE cc_start: 0.8229 (tp) cc_final: 0.7966 (tp) REVERT: A 611 GLU cc_start: 0.6973 (mp0) cc_final: 0.6766 (mp0) REVERT: A 617 ILE cc_start: 0.8336 (mm) cc_final: 0.8065 (mm) REVERT: A 619 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6555 (mt-10) REVERT: A 701 MET cc_start: 0.7078 (mmt) cc_final: 0.6789 (mmt) REVERT: A 732 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7778 (ttp80) REVERT: A 765 GLU cc_start: 0.6707 (mp0) cc_final: 0.6396 (mp0) REVERT: A 799 CYS cc_start: 0.6902 (t) cc_final: 0.6629 (t) REVERT: A 802 SER cc_start: 0.7427 (t) cc_final: 0.7073 (p) REVERT: A 956 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7416 (tmm) REVERT: A 959 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7500 (tm-30) REVERT: A 961 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: A 1104 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7577 (mm-30) REVERT: A 1105 PHE cc_start: 0.8186 (t80) cc_final: 0.7926 (t80) REVERT: A 1193 TRP cc_start: 0.8375 (t60) cc_final: 0.8087 (t60) REVERT: A 1223 ASP cc_start: 0.7276 (t0) cc_final: 0.6716 (t0) outliers start: 21 outliers final: 5 residues processed: 323 average time/residue: 0.2941 time to fit residues: 128.0196 Evaluate side-chains 305 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 297 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 956 MET Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1090 ASN Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1095 ILE Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1222 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 73 optimal weight: 0.1980 chunk 58 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 68 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12055 Z= 0.229 Angle : 0.623 10.097 16184 Z= 0.326 Chirality : 0.042 0.167 1726 Planarity : 0.005 0.063 2127 Dihedral : 8.930 151.543 1611 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.19 % Favored : 96.67 % Rotamer: Outliers : 1.63 % Allowed : 8.45 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1441 helix: 0.63 (0.18), residues: 820 sheet: -2.01 (0.49), residues: 107 loop : -1.01 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A1253 HIS 0.004 0.001 HIS A 833 PHE 0.035 0.002 PHE A 853 TYR 0.015 0.002 TYR A1082 ARG 0.007 0.001 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 302 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.8220 (mtp) cc_final: 0.7837 (mtm) REVERT: B 73 MET cc_start: 0.6675 (mmt) cc_final: 0.6237 (mmp) REVERT: B 77 MET cc_start: 0.6738 (pmm) cc_final: 0.6455 (pmm) REVERT: B 83 GLU cc_start: 0.6982 (tp30) cc_final: 0.6541 (tp30) REVERT: B 110 MET cc_start: 0.7343 (mmp) cc_final: 0.7117 (mmp) REVERT: B 128 GLU cc_start: 0.6738 (tm-30) cc_final: 0.6448 (tm-30) REVERT: I 50 GLN cc_start: 0.7481 (tm-30) cc_final: 0.7105 (tm-30) REVERT: I 73 MET cc_start: 0.7162 (tpt) cc_final: 0.5726 (tpt) REVERT: I 77 MET cc_start: 0.7588 (ptp) cc_final: 0.6376 (ptp) REVERT: I 107 ARG cc_start: 0.7343 (ttt-90) cc_final: 0.7061 (ttt-90) REVERT: I 108 HIS cc_start: 0.7237 (m170) cc_final: 0.7023 (m170) REVERT: I 110 MET cc_start: 0.7195 (mpp) cc_final: 0.6943 (mpp) REVERT: I 120 GLU cc_start: 0.7484 (pm20) cc_final: 0.7061 (pm20) REVERT: I 146 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6672 (mtm) REVERT: A 24 ILE cc_start: 0.7761 (mt) cc_final: 0.7513 (mt) REVERT: A 132 ASP cc_start: 0.6269 (t70) cc_final: 0.5913 (t0) REVERT: A 146 SER cc_start: 0.8082 (p) cc_final: 0.7802 (m) REVERT: A 196 LYS cc_start: 0.8109 (tttm) cc_final: 0.7736 (ttmt) REVERT: A 228 TYR cc_start: 0.8570 (m-80) cc_final: 0.8019 (m-80) REVERT: A 264 HIS cc_start: 0.7638 (m170) cc_final: 0.7336 (m170) REVERT: A 327 ILE cc_start: 0.7974 (pt) cc_final: 0.7647 (pt) REVERT: A 491 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7268 (tm-30) REVERT: A 575 GLU cc_start: 0.5953 (mp0) cc_final: 0.5727 (mp0) REVERT: A 592 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7153 (mp10) REVERT: A 617 ILE cc_start: 0.8308 (mm) cc_final: 0.8048 (mm) REVERT: A 619 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6560 (mt-10) REVERT: A 732 ARG cc_start: 0.8041 (ttp80) cc_final: 0.7112 (ttp80) REVERT: A 733 LEU cc_start: 0.8408 (mt) cc_final: 0.8160 (mt) REVERT: A 736 LYS cc_start: 0.7962 (tppt) cc_final: 0.7516 (ttmm) REVERT: A 765 GLU cc_start: 0.6729 (mp0) cc_final: 0.6518 (mp0) REVERT: A 848 LYS cc_start: 0.7279 (mmtm) cc_final: 0.7048 (mmtm) REVERT: A 870 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7406 (pp30) REVERT: A 956 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7237 (ttp) REVERT: A 959 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: A 1091 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6631 (t) REVERT: A 1104 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7197 (mm-30) REVERT: A 1175 PHE cc_start: 0.8321 (m-80) cc_final: 0.8119 (m-80) REVERT: A 1198 ASP cc_start: 0.6049 (t70) cc_final: 0.5227 (p0) REVERT: A 1222 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.6810 (m-30) outliers start: 21 outliers final: 5 residues processed: 307 average time/residue: 0.2829 time to fit residues: 118.7333 Evaluate side-chains 300 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 290 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 956 MET Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1222 ASP Chi-restraints excluded: chain A residue 1227 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 105 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12055 Z= 0.249 Angle : 0.596 9.469 16184 Z= 0.313 Chirality : 0.041 0.175 1726 Planarity : 0.004 0.046 2127 Dihedral : 8.273 151.567 1604 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 2.02 % Allowed : 12.56 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1441 helix: 0.86 (0.17), residues: 834 sheet: -1.81 (0.48), residues: 107 loop : -0.97 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1253 HIS 0.006 0.001 HIS A 833 PHE 0.026 0.002 PHE I 90 TYR 0.013 0.002 TYR A 300 ARG 0.004 0.000 ARG I 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 299 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.6652 (mmt) cc_final: 0.6280 (mmp) REVERT: B 77 MET cc_start: 0.6719 (pmm) cc_final: 0.6408 (pmm) REVERT: B 83 GLU cc_start: 0.6992 (tp30) cc_final: 0.6586 (tp30) REVERT: B 128 GLU cc_start: 0.6692 (tm-30) cc_final: 0.6421 (tm-30) REVERT: I 12 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7606 (tm-30) REVERT: I 50 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7300 (tm-30) REVERT: I 73 MET cc_start: 0.7095 (tpt) cc_final: 0.5697 (tpt) REVERT: I 77 MET cc_start: 0.7599 (ptp) cc_final: 0.6472 (ptp) REVERT: I 92 VAL cc_start: 0.8375 (t) cc_final: 0.8150 (t) REVERT: I 107 ARG cc_start: 0.7301 (ttt-90) cc_final: 0.7045 (ttt-90) REVERT: I 146 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.6641 (mtm) REVERT: A 16 PHE cc_start: 0.8039 (m-80) cc_final: 0.7510 (m-80) REVERT: A 24 ILE cc_start: 0.7799 (mt) cc_final: 0.7546 (mt) REVERT: A 56 LYS cc_start: 0.8205 (mppt) cc_final: 0.7809 (mppt) REVERT: A 61 ASP cc_start: 0.7109 (t70) cc_final: 0.6723 (t0) REVERT: A 146 SER cc_start: 0.8155 (p) cc_final: 0.7862 (m) REVERT: A 196 LYS cc_start: 0.8215 (tttm) cc_final: 0.7828 (tttm) REVERT: A 238 GLN cc_start: 0.6961 (tp-100) cc_final: 0.6709 (mm-40) REVERT: A 264 HIS cc_start: 0.7676 (m170) cc_final: 0.7364 (m170) REVERT: A 327 ILE cc_start: 0.8102 (pt) cc_final: 0.7872 (pt) REVERT: A 479 LYS cc_start: 0.7804 (mttm) cc_final: 0.7584 (mttp) REVERT: A 575 GLU cc_start: 0.6071 (mp0) cc_final: 0.5779 (mp0) REVERT: A 592 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7133 (mp10) REVERT: A 617 ILE cc_start: 0.8314 (mm) cc_final: 0.8057 (mm) REVERT: A 619 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6549 (mt-10) REVERT: A 701 MET cc_start: 0.7055 (mmt) cc_final: 0.6805 (mmt) REVERT: A 732 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7787 (ttp80) REVERT: A 733 LEU cc_start: 0.8471 (mt) cc_final: 0.8146 (mt) REVERT: A 765 GLU cc_start: 0.6718 (mp0) cc_final: 0.6494 (mp0) REVERT: A 848 LYS cc_start: 0.7347 (mmtm) cc_final: 0.7092 (mmtm) REVERT: A 959 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: A 960 MET cc_start: 0.7747 (mmm) cc_final: 0.7313 (mmm) REVERT: A 1104 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7106 (mm-30) REVERT: A 1171 PHE cc_start: 0.7979 (m-80) cc_final: 0.7736 (m-10) REVERT: A 1198 ASP cc_start: 0.6042 (t70) cc_final: 0.5293 (p0) REVERT: A 1207 GLU cc_start: 0.7409 (pm20) cc_final: 0.6957 (mp0) REVERT: A 1221 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7186 (mttt) outliers start: 26 outliers final: 13 residues processed: 308 average time/residue: 0.2896 time to fit residues: 121.7168 Evaluate side-chains 314 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 298 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1091 THR Chi-restraints excluded: chain A residue 1096 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1221 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 0.9980 chunk 98 optimal weight: 0.0670 chunk 67 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 124 optimal weight: 30.0000 chunk 37 optimal weight: 0.5980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN A 873 ASN A 919 GLN ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12055 Z= 0.199 Angle : 0.574 10.599 16184 Z= 0.298 Chirality : 0.040 0.178 1726 Planarity : 0.004 0.045 2127 Dihedral : 7.886 143.932 1599 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.64 % Favored : 97.29 % Rotamer: Outliers : 1.94 % Allowed : 14.81 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1441 helix: 1.21 (0.18), residues: 833 sheet: -1.66 (0.48), residues: 109 loop : -0.81 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1253 HIS 0.009 0.001 HIS I 108 PHE 0.039 0.002 PHE A 853 TYR 0.013 0.001 TYR A1082 ARG 0.005 0.000 ARG I 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 297 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 MET cc_start: 0.6617 (mmt) cc_final: 0.6255 (mmp) REVERT: B 77 MET cc_start: 0.6663 (pmm) cc_final: 0.6293 (pmm) REVERT: B 83 GLU cc_start: 0.6963 (tp30) cc_final: 0.6571 (tp30) REVERT: I 50 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7314 (tm-30) REVERT: I 73 MET cc_start: 0.7010 (tpt) cc_final: 0.6641 (tpt) REVERT: I 92 VAL cc_start: 0.8384 (t) cc_final: 0.8162 (t) REVERT: I 107 ARG cc_start: 0.7296 (ttt-90) cc_final: 0.7000 (ttt-90) REVERT: I 146 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6212 (mmm) REVERT: A 24 ILE cc_start: 0.7800 (mt) cc_final: 0.7557 (mt) REVERT: A 61 ASP cc_start: 0.7148 (t70) cc_final: 0.6751 (t0) REVERT: A 146 SER cc_start: 0.8168 (p) cc_final: 0.7878 (m) REVERT: A 180 ASP cc_start: 0.7478 (m-30) cc_final: 0.7136 (m-30) REVERT: A 196 LYS cc_start: 0.8205 (tttm) cc_final: 0.7838 (tttm) REVERT: A 264 HIS cc_start: 0.7641 (m170) cc_final: 0.7373 (m170) REVERT: A 479 LYS cc_start: 0.7828 (mttm) cc_final: 0.7559 (mttp) REVERT: A 575 GLU cc_start: 0.5977 (mp0) cc_final: 0.5681 (mp0) REVERT: A 592 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7112 (mp10) REVERT: A 606 GLU cc_start: 0.7394 (tp30) cc_final: 0.7110 (tp30) REVERT: A 617 ILE cc_start: 0.8321 (mm) cc_final: 0.8067 (mm) REVERT: A 619 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6523 (mt-10) REVERT: A 701 MET cc_start: 0.7070 (mmt) cc_final: 0.6838 (mmt) REVERT: A 732 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7842 (ttm-80) REVERT: A 765 GLU cc_start: 0.6732 (mp0) cc_final: 0.6490 (mp0) REVERT: A 848 LYS cc_start: 0.7367 (mmtm) cc_final: 0.7111 (mmtm) REVERT: A 890 MET cc_start: 0.7088 (mtp) cc_final: 0.6782 (mtp) REVERT: A 956 MET cc_start: 0.7696 (tpp) cc_final: 0.6929 (tpp) REVERT: A 959 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: A 1198 ASP cc_start: 0.5965 (t70) cc_final: 0.5215 (p0) REVERT: A 1207 GLU cc_start: 0.7385 (pm20) cc_final: 0.6906 (mp0) REVERT: A 1221 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6961 (mttt) outliers start: 25 outliers final: 12 residues processed: 305 average time/residue: 0.2979 time to fit residues: 123.6853 Evaluate side-chains 303 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 288 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1132 LYS Chi-restraints excluded: chain A residue 1221 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 50.0000 chunk 35 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12055 Z= 0.328 Angle : 0.622 9.250 16184 Z= 0.326 Chirality : 0.043 0.212 1726 Planarity : 0.004 0.051 2127 Dihedral : 8.003 152.186 1595 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.68 % Favored : 96.25 % Rotamer: Outliers : 2.02 % Allowed : 16.28 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1441 helix: 1.00 (0.18), residues: 834 sheet: -1.78 (0.47), residues: 108 loop : -0.88 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1253 HIS 0.008 0.001 HIS A 833 PHE 0.041 0.003 PHE A 853 TYR 0.016 0.002 TYR A 812 ARG 0.005 0.000 ARG A 732 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 298 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 PHE cc_start: 0.5608 (OUTLIER) cc_final: 0.5344 (m-10) REVERT: B 73 MET cc_start: 0.6780 (mmt) cc_final: 0.6442 (mmp) REVERT: B 77 MET cc_start: 0.6709 (pmm) cc_final: 0.6319 (pmm) REVERT: B 83 GLU cc_start: 0.7001 (tp30) cc_final: 0.6617 (tp30) REVERT: I 50 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7410 (tm-30) REVERT: I 73 MET cc_start: 0.6971 (tpt) cc_final: 0.6680 (tpt) REVERT: I 92 VAL cc_start: 0.8372 (t) cc_final: 0.8139 (t) REVERT: I 107 ARG cc_start: 0.7343 (ttt-90) cc_final: 0.6963 (ttt-90) REVERT: I 110 MET cc_start: 0.7191 (mpp) cc_final: 0.6909 (mpp) REVERT: I 146 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6652 (mtm) REVERT: A 18 MET cc_start: 0.7362 (mmm) cc_final: 0.6962 (tpp) REVERT: A 24 ILE cc_start: 0.7811 (mt) cc_final: 0.7574 (mt) REVERT: A 61 ASP cc_start: 0.7088 (t70) cc_final: 0.6730 (t0) REVERT: A 146 SER cc_start: 0.8224 (p) cc_final: 0.7939 (m) REVERT: A 264 HIS cc_start: 0.7686 (m170) cc_final: 0.7337 (m170) REVERT: A 479 LYS cc_start: 0.7844 (mttm) cc_final: 0.7542 (mttp) REVERT: A 575 GLU cc_start: 0.6140 (mp0) cc_final: 0.5907 (mp0) REVERT: A 592 GLN cc_start: 0.7409 (mm-40) cc_final: 0.7104 (mp10) REVERT: A 606 GLU cc_start: 0.7455 (tp30) cc_final: 0.7079 (tp30) REVERT: A 617 ILE cc_start: 0.8325 (mm) cc_final: 0.8070 (mm) REVERT: A 619 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6520 (mt-10) REVERT: A 701 MET cc_start: 0.7122 (mmt) cc_final: 0.6789 (mmt) REVERT: A 736 LYS cc_start: 0.8188 (mtmt) cc_final: 0.7847 (mtpp) REVERT: A 765 GLU cc_start: 0.6752 (mp0) cc_final: 0.6516 (mp0) REVERT: A 848 LYS cc_start: 0.7391 (mmtm) cc_final: 0.7144 (mmtm) REVERT: A 890 MET cc_start: 0.7165 (mtp) cc_final: 0.6863 (mtp) REVERT: A 956 MET cc_start: 0.7806 (tpp) cc_final: 0.7153 (tpp) REVERT: A 959 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: A 1084 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7175 (tp30) REVERT: A 1104 GLU cc_start: 0.7526 (tp30) cc_final: 0.7147 (tp30) REVERT: A 1171 PHE cc_start: 0.7919 (m-80) cc_final: 0.7707 (m-80) REVERT: A 1198 ASP cc_start: 0.6067 (t70) cc_final: 0.5292 (p0) REVERT: A 1223 ASP cc_start: 0.6936 (t0) cc_final: 0.6676 (t0) outliers start: 26 outliers final: 15 residues processed: 310 average time/residue: 0.2779 time to fit residues: 117.6656 Evaluate side-chains 314 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 295 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1132 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.3980 chunk 125 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 0.0980 chunk 73 optimal weight: 0.0970 chunk 134 optimal weight: 1.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN A 602 HIS ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12055 Z= 0.185 Angle : 0.576 9.338 16184 Z= 0.296 Chirality : 0.040 0.166 1726 Planarity : 0.004 0.046 2127 Dihedral : 7.676 139.758 1595 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.50 % Favored : 97.43 % Rotamer: Outliers : 2.17 % Allowed : 17.75 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1441 helix: 1.32 (0.18), residues: 833 sheet: -1.67 (0.48), residues: 104 loop : -0.71 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1253 HIS 0.004 0.001 HIS A 833 PHE 0.039 0.002 PHE A 853 TYR 0.012 0.001 TYR A1082 ARG 0.006 0.000 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 293 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6457 (mtp) REVERT: B 77 MET cc_start: 0.6671 (pmm) cc_final: 0.6302 (pmm) REVERT: B 83 GLU cc_start: 0.6934 (tp30) cc_final: 0.6565 (tp30) REVERT: I 50 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7386 (tm-30) REVERT: I 72 MET cc_start: 0.6605 (mmt) cc_final: 0.5840 (mmt) REVERT: I 73 MET cc_start: 0.7012 (tpt) cc_final: 0.6771 (tpt) REVERT: I 92 VAL cc_start: 0.8392 (t) cc_final: 0.8153 (t) REVERT: I 107 ARG cc_start: 0.7314 (ttt-90) cc_final: 0.6967 (ttt-90) REVERT: I 146 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6267 (mmm) REVERT: A 18 MET cc_start: 0.7388 (mmm) cc_final: 0.7035 (tpp) REVERT: A 23 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.6841 (t70) REVERT: A 24 ILE cc_start: 0.7762 (mt) cc_final: 0.7417 (mt) REVERT: A 57 LYS cc_start: 0.7349 (mtmt) cc_final: 0.7064 (mtmt) REVERT: A 61 ASP cc_start: 0.7114 (t70) cc_final: 0.6758 (t0) REVERT: A 146 SER cc_start: 0.8188 (p) cc_final: 0.7907 (m) REVERT: A 196 LYS cc_start: 0.8196 (tttm) cc_final: 0.7979 (ttpp) REVERT: A 264 HIS cc_start: 0.7618 (m170) cc_final: 0.7352 (m170) REVERT: A 286 GLU cc_start: 0.7718 (mp0) cc_final: 0.7509 (mp0) REVERT: A 319 ARG cc_start: 0.7721 (ptp-110) cc_final: 0.7485 (ptp90) REVERT: A 383 GLN cc_start: 0.8023 (mt0) cc_final: 0.7809 (mt0) REVERT: A 479 LYS cc_start: 0.7849 (mttm) cc_final: 0.7416 (mttm) REVERT: A 575 GLU cc_start: 0.5794 (mp0) cc_final: 0.5538 (mp0) REVERT: A 592 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7187 (mp10) REVERT: A 617 ILE cc_start: 0.8294 (mm) cc_final: 0.8032 (mm) REVERT: A 619 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6512 (mt-10) REVERT: A 701 MET cc_start: 0.7086 (mmt) cc_final: 0.6769 (mmt) REVERT: A 736 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7903 (mtmt) REVERT: A 765 GLU cc_start: 0.6736 (mp0) cc_final: 0.6483 (mp0) REVERT: A 848 LYS cc_start: 0.7348 (mmtm) cc_final: 0.7081 (mmtm) REVERT: A 956 MET cc_start: 0.7751 (tpp) cc_final: 0.7467 (tpp) REVERT: A 959 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: A 1089 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7643 (tt) REVERT: A 1104 GLU cc_start: 0.7558 (tp30) cc_final: 0.7140 (tp30) REVERT: A 1198 ASP cc_start: 0.5852 (t70) cc_final: 0.5052 (p0) REVERT: A 1207 GLU cc_start: 0.7349 (pm20) cc_final: 0.6807 (mp0) outliers start: 28 outliers final: 14 residues processed: 307 average time/residue: 0.3014 time to fit residues: 127.6835 Evaluate side-chains 307 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 288 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain I residue 43 ASN Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1132 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 117 optimal weight: 3.9990 chunk 77 optimal weight: 0.0870 chunk 138 optimal weight: 0.0170 chunk 86 optimal weight: 0.0670 chunk 84 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.1732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 ASN ** A 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1196 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12055 Z= 0.157 Angle : 0.571 10.361 16184 Z= 0.292 Chirality : 0.039 0.159 1726 Planarity : 0.004 0.045 2127 Dihedral : 7.468 142.358 1595 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 2.48 % Allowed : 18.22 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1441 helix: 1.58 (0.18), residues: 827 sheet: -1.53 (0.47), residues: 111 loop : -0.57 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1253 HIS 0.003 0.000 HIS A 581 PHE 0.033 0.002 PHE I 66 TYR 0.013 0.001 TYR A 172 ARG 0.007 0.000 ARG I 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 300 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6628 (pmm) cc_final: 0.6236 (pmm) REVERT: B 83 GLU cc_start: 0.6948 (tp30) cc_final: 0.6550 (tp30) REVERT: I 50 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7379 (tm-30) REVERT: I 70 LEU cc_start: 0.8332 (tt) cc_final: 0.8080 (tt) REVERT: I 73 MET cc_start: 0.7013 (tpt) cc_final: 0.6737 (tpt) REVERT: I 92 VAL cc_start: 0.8378 (t) cc_final: 0.8147 (t) REVERT: I 107 ARG cc_start: 0.7326 (ttt-90) cc_final: 0.6955 (ttt-90) REVERT: I 120 GLU cc_start: 0.7827 (pm20) cc_final: 0.7575 (pm20) REVERT: I 146 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6252 (mtm) REVERT: A 18 MET cc_start: 0.7377 (mmm) cc_final: 0.7004 (tpp) REVERT: A 23 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.6977 (t70) REVERT: A 24 ILE cc_start: 0.7775 (mt) cc_final: 0.7471 (mt) REVERT: A 56 LYS cc_start: 0.8265 (mppt) cc_final: 0.7955 (mmtm) REVERT: A 61 ASP cc_start: 0.7112 (t70) cc_final: 0.6771 (t0) REVERT: A 146 SER cc_start: 0.8156 (p) cc_final: 0.7858 (m) REVERT: A 196 LYS cc_start: 0.8146 (tttm) cc_final: 0.7946 (ttpp) REVERT: A 250 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7776 (mtt180) REVERT: A 264 HIS cc_start: 0.7587 (m170) cc_final: 0.7345 (m170) REVERT: A 387 ARG cc_start: 0.7768 (ptm160) cc_final: 0.7508 (ptm160) REVERT: A 603 MET cc_start: 0.7506 (tpt) cc_final: 0.7060 (tpt) REVERT: A 617 ILE cc_start: 0.8326 (mm) cc_final: 0.8043 (mm) REVERT: A 619 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6529 (mt-10) REVERT: A 701 MET cc_start: 0.7128 (mmt) cc_final: 0.6904 (mmt) REVERT: A 736 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7841 (mtmt) REVERT: A 765 GLU cc_start: 0.6715 (mp0) cc_final: 0.6422 (mp0) REVERT: A 848 LYS cc_start: 0.7336 (mmtm) cc_final: 0.7074 (mmtm) REVERT: A 890 MET cc_start: 0.7108 (mtp) cc_final: 0.6722 (mtp) REVERT: A 956 MET cc_start: 0.7713 (tpp) cc_final: 0.7456 (tpp) REVERT: A 959 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: A 1084 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7146 (tp30) REVERT: A 1089 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7644 (tt) REVERT: A 1104 GLU cc_start: 0.7534 (tp30) cc_final: 0.7057 (tp30) REVERT: A 1198 ASP cc_start: 0.5774 (t70) cc_final: 0.5020 (p0) outliers start: 32 outliers final: 13 residues processed: 314 average time/residue: 0.2752 time to fit residues: 119.0034 Evaluate side-chains 313 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 295 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain I residue 43 ASN Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 597 ASN Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1132 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.0870 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 126 optimal weight: 10.0000 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN A 597 ASN A 988 GLN ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12055 Z= 0.251 Angle : 0.615 9.025 16184 Z= 0.318 Chirality : 0.042 0.304 1726 Planarity : 0.004 0.049 2127 Dihedral : 7.640 136.923 1595 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.22 % Rotamer: Outliers : 2.40 % Allowed : 19.07 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.22), residues: 1441 helix: 1.40 (0.18), residues: 832 sheet: -1.52 (0.48), residues: 104 loop : -0.61 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1253 HIS 0.006 0.001 HIS A1196 PHE 0.031 0.003 PHE A1105 TYR 0.013 0.001 TYR A1082 ARG 0.008 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 298 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6690 (pmm) cc_final: 0.6285 (pmm) REVERT: B 83 GLU cc_start: 0.6983 (tp30) cc_final: 0.6622 (tp30) REVERT: I 50 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7435 (tm-30) REVERT: I 70 LEU cc_start: 0.8348 (tt) cc_final: 0.8082 (tt) REVERT: I 73 MET cc_start: 0.6985 (tpt) cc_final: 0.6764 (tpt) REVERT: I 92 VAL cc_start: 0.8367 (t) cc_final: 0.8146 (t) REVERT: I 107 ARG cc_start: 0.7375 (ttt-90) cc_final: 0.6990 (ttt-90) REVERT: I 146 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6228 (mtm) REVERT: A 18 MET cc_start: 0.7400 (mmm) cc_final: 0.7030 (tpp) REVERT: A 23 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.6916 (t70) REVERT: A 24 ILE cc_start: 0.7802 (mt) cc_final: 0.7459 (mt) REVERT: A 56 LYS cc_start: 0.8303 (mppt) cc_final: 0.7992 (mmtm) REVERT: A 57 LYS cc_start: 0.7339 (mtmt) cc_final: 0.7061 (mtmt) REVERT: A 61 ASP cc_start: 0.7119 (t70) cc_final: 0.6718 (t0) REVERT: A 88 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7811 (p) REVERT: A 92 ASN cc_start: 0.7606 (t0) cc_final: 0.7350 (t0) REVERT: A 264 HIS cc_start: 0.7583 (m170) cc_final: 0.7285 (m170) REVERT: A 284 ASN cc_start: 0.7387 (m-40) cc_final: 0.7115 (t0) REVERT: A 319 ARG cc_start: 0.7656 (ptp90) cc_final: 0.7339 (mpp80) REVERT: A 387 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7564 (ptm160) REVERT: A 475 TYR cc_start: 0.7570 (t80) cc_final: 0.6942 (t80) REVERT: A 479 LYS cc_start: 0.7861 (mttm) cc_final: 0.7462 (mttm) REVERT: A 572 ARG cc_start: 0.6307 (ptt90) cc_final: 0.5838 (ptt90) REVERT: A 603 MET cc_start: 0.7549 (tpt) cc_final: 0.7101 (tpt) REVERT: A 617 ILE cc_start: 0.8309 (mm) cc_final: 0.8049 (mm) REVERT: A 619 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6533 (mt-10) REVERT: A 701 MET cc_start: 0.7143 (mmt) cc_final: 0.6819 (mmt) REVERT: A 736 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7761 (mtpp) REVERT: A 765 GLU cc_start: 0.6756 (mp0) cc_final: 0.6423 (mp0) REVERT: A 956 MET cc_start: 0.7732 (tpp) cc_final: 0.7453 (tpp) REVERT: A 959 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: A 1084 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: A 1089 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7684 (tt) REVERT: A 1198 ASP cc_start: 0.5887 (t70) cc_final: 0.5073 (p0) REVERT: A 1201 TRP cc_start: 0.7829 (m100) cc_final: 0.7500 (m100) REVERT: A 1207 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: A 1226 MET cc_start: 0.7197 (mtm) cc_final: 0.6938 (mtp) outliers start: 31 outliers final: 16 residues processed: 313 average time/residue: 0.2904 time to fit residues: 124.5104 Evaluate side-chains 315 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 292 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain I residue 43 ASN Chi-restraints excluded: chain I residue 95 LYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1207 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.4980 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 77 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12055 Z= 0.265 Angle : 0.639 8.973 16184 Z= 0.329 Chirality : 0.042 0.249 1726 Planarity : 0.004 0.050 2127 Dihedral : 7.684 136.419 1595 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 2.25 % Allowed : 19.46 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1441 helix: 1.32 (0.18), residues: 821 sheet: -1.58 (0.48), residues: 103 loop : -0.61 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1253 HIS 0.006 0.001 HIS A 833 PHE 0.032 0.003 PHE A1105 TYR 0.016 0.001 TYR A 172 ARG 0.012 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 294 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6714 (pmm) cc_final: 0.6316 (pmm) REVERT: B 83 GLU cc_start: 0.7007 (tp30) cc_final: 0.6648 (tp30) REVERT: I 50 GLN cc_start: 0.7732 (tm-30) cc_final: 0.7469 (tm-30) REVERT: I 70 LEU cc_start: 0.8380 (tt) cc_final: 0.8115 (tt) REVERT: I 73 MET cc_start: 0.6992 (tpt) cc_final: 0.5879 (tpt) REVERT: I 77 MET cc_start: 0.7572 (ptp) cc_final: 0.6588 (ptp) REVERT: I 92 VAL cc_start: 0.8367 (t) cc_final: 0.8138 (t) REVERT: I 107 ARG cc_start: 0.7412 (ttt-90) cc_final: 0.7185 (ttt-90) REVERT: I 146 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.6182 (mtm) REVERT: A 18 MET cc_start: 0.7397 (mmm) cc_final: 0.7096 (tpp) REVERT: A 23 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.6908 (t70) REVERT: A 24 ILE cc_start: 0.7788 (mt) cc_final: 0.7444 (mt) REVERT: A 56 LYS cc_start: 0.8331 (mppt) cc_final: 0.8011 (mmtm) REVERT: A 57 LYS cc_start: 0.7340 (mtmt) cc_final: 0.7016 (mtmt) REVERT: A 61 ASP cc_start: 0.7114 (t70) cc_final: 0.6714 (t0) REVERT: A 88 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7792 (p) REVERT: A 92 ASN cc_start: 0.7610 (t0) cc_final: 0.7371 (t0) REVERT: A 196 LYS cc_start: 0.8250 (tttm) cc_final: 0.7995 (ttpp) REVERT: A 264 HIS cc_start: 0.7580 (m170) cc_final: 0.7251 (m170) REVERT: A 269 ASP cc_start: 0.5928 (p0) cc_final: 0.5715 (p0) REVERT: A 377 GLU cc_start: 0.7674 (tt0) cc_final: 0.7324 (tm-30) REVERT: A 387 ARG cc_start: 0.7804 (ptm160) cc_final: 0.7554 (ptm160) REVERT: A 475 TYR cc_start: 0.7535 (t80) cc_final: 0.6914 (t80) REVERT: A 479 LYS cc_start: 0.7834 (mttm) cc_final: 0.7370 (mttm) REVERT: A 596 LYS cc_start: 0.8186 (mptt) cc_final: 0.7753 (mmtp) REVERT: A 603 MET cc_start: 0.7565 (tpt) cc_final: 0.7130 (tpt) REVERT: A 617 ILE cc_start: 0.8308 (mm) cc_final: 0.8054 (mm) REVERT: A 619 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6528 (mt-10) REVERT: A 701 MET cc_start: 0.7143 (mmt) cc_final: 0.6805 (mmt) REVERT: A 736 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7793 (mtpp) REVERT: A 765 GLU cc_start: 0.6764 (mp0) cc_final: 0.6451 (mp0) REVERT: A 956 MET cc_start: 0.7720 (tpp) cc_final: 0.7471 (tpp) REVERT: A 959 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7269 (tt0) REVERT: A 1084 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: A 1089 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7757 (tt) REVERT: A 1198 ASP cc_start: 0.5894 (t70) cc_final: 0.5090 (p0) REVERT: A 1201 TRP cc_start: 0.7849 (m100) cc_final: 0.7561 (m100) REVERT: A 1206 MET cc_start: 0.7461 (tmm) cc_final: 0.7155 (tmm) REVERT: A 1207 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6934 (mp0) outliers start: 29 outliers final: 15 residues processed: 310 average time/residue: 0.2985 time to fit residues: 126.1227 Evaluate side-chains 312 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 290 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain I residue 43 ASN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1089 ILE Chi-restraints excluded: chain A residue 1207 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 0.0670 chunk 70 optimal weight: 0.3980 chunk 90 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN A1090 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12055 Z= 0.238 Angle : 0.649 9.749 16184 Z= 0.333 Chirality : 0.042 0.222 1726 Planarity : 0.004 0.051 2127 Dihedral : 7.644 137.408 1595 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.22 % Rotamer: Outliers : 2.02 % Allowed : 19.84 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1441 helix: 1.34 (0.18), residues: 822 sheet: -1.45 (0.49), residues: 102 loop : -0.56 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1253 HIS 0.006 0.001 HIS A1196 PHE 0.031 0.002 PHE A1105 TYR 0.018 0.001 TYR A 172 ARG 0.011 0.000 ARG A 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 291 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 MET cc_start: 0.6728 (pmm) cc_final: 0.6322 (pmm) REVERT: B 83 GLU cc_start: 0.6994 (tp30) cc_final: 0.6645 (tp30) REVERT: I 50 GLN cc_start: 0.7729 (tm-30) cc_final: 0.7481 (tm-30) REVERT: I 70 LEU cc_start: 0.8392 (tt) cc_final: 0.8116 (tt) REVERT: I 73 MET cc_start: 0.7037 (tpt) cc_final: 0.6817 (tpt) REVERT: I 92 VAL cc_start: 0.8379 (t) cc_final: 0.8143 (t) REVERT: I 107 ARG cc_start: 0.7444 (ttt-90) cc_final: 0.7241 (ttt-90) REVERT: I 146 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6173 (mtm) REVERT: A 5 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8173 (mtpp) REVERT: A 18 MET cc_start: 0.7395 (mmm) cc_final: 0.7069 (tpp) REVERT: A 23 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.6919 (t70) REVERT: A 24 ILE cc_start: 0.7764 (mt) cc_final: 0.7437 (mt) REVERT: A 56 LYS cc_start: 0.8333 (mppt) cc_final: 0.8013 (mmtm) REVERT: A 57 LYS cc_start: 0.7339 (mtmt) cc_final: 0.7024 (mtmt) REVERT: A 61 ASP cc_start: 0.7103 (t70) cc_final: 0.6709 (t0) REVERT: A 88 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7789 (p) REVERT: A 92 ASN cc_start: 0.7621 (t0) cc_final: 0.7413 (t0) REVERT: A 196 LYS cc_start: 0.8237 (tttm) cc_final: 0.7982 (ttpp) REVERT: A 250 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7803 (mtt180) REVERT: A 264 HIS cc_start: 0.7573 (m170) cc_final: 0.7275 (m170) REVERT: A 308 ASP cc_start: 0.6928 (t0) cc_final: 0.6705 (t0) REVERT: A 319 ARG cc_start: 0.7725 (ptp90) cc_final: 0.7353 (mpp80) REVERT: A 387 ARG cc_start: 0.7796 (ptm160) cc_final: 0.7555 (ptm160) REVERT: A 475 TYR cc_start: 0.7497 (t80) cc_final: 0.6866 (t80) REVERT: A 479 LYS cc_start: 0.7831 (mttm) cc_final: 0.7354 (mttm) REVERT: A 596 LYS cc_start: 0.8190 (mptt) cc_final: 0.7749 (mmtp) REVERT: A 603 MET cc_start: 0.7542 (tpt) cc_final: 0.7043 (tpt) REVERT: A 617 ILE cc_start: 0.8292 (mm) cc_final: 0.8029 (mm) REVERT: A 619 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6522 (mt-10) REVERT: A 701 MET cc_start: 0.7131 (mmt) cc_final: 0.6802 (mmt) REVERT: A 736 LYS cc_start: 0.8176 (mtmt) cc_final: 0.7781 (mtpp) REVERT: A 739 PHE cc_start: 0.7609 (m-10) cc_final: 0.7263 (m-10) REVERT: A 765 GLU cc_start: 0.6758 (mp0) cc_final: 0.6409 (mp0) REVERT: A 956 MET cc_start: 0.7704 (tpp) cc_final: 0.7397 (tpp) REVERT: A 959 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: A 1084 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7217 (tp30) REVERT: A 1089 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7776 (tt) REVERT: A 1198 ASP cc_start: 0.5871 (t70) cc_final: 0.5086 (p0) REVERT: A 1201 TRP cc_start: 0.7819 (m100) cc_final: 0.7546 (m100) outliers start: 26 outliers final: 15 residues processed: 305 average time/residue: 0.3042 time to fit residues: 126.3554 Evaluate side-chains 310 residues out of total 1290 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 289 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain I residue 43 ASN Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 785 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 959 GLU Chi-restraints excluded: chain A residue 1084 GLU Chi-restraints excluded: chain A residue 1089 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 0.0040 chunk 100 optimal weight: 0.3980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 GLN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.162107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138867 restraints weight = 19094.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.143481 restraints weight = 9265.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.146515 restraints weight = 5562.243| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12055 Z= 0.204 Angle : 0.639 9.974 16184 Z= 0.328 Chirality : 0.041 0.211 1726 Planarity : 0.004 0.049 2127 Dihedral : 7.590 139.114 1595 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.64 % Favored : 97.29 % Rotamer: Outliers : 1.71 % Allowed : 20.70 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1441 helix: 1.49 (0.18), residues: 826 sheet: -1.36 (0.49), residues: 102 loop : -0.53 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1253 HIS 0.006 0.001 HIS A1196 PHE 0.031 0.002 PHE A1105 TYR 0.017 0.001 TYR A 172 ARG 0.011 0.000 ARG A 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3134.96 seconds wall clock time: 57 minutes 45.36 seconds (3465.36 seconds total)