Starting phenix.real_space_refine on Wed Feb 4 04:23:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9laa_62923/02_2026/9laa_62923.cif Found real_map, /net/cci-nas-00/data/ceres_data/9laa_62923/02_2026/9laa_62923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9laa_62923/02_2026/9laa_62923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9laa_62923/02_2026/9laa_62923.map" model { file = "/net/cci-nas-00/data/ceres_data/9laa_62923/02_2026/9laa_62923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9laa_62923/02_2026/9laa_62923.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5500 2.51 5 N 1410 2.21 5 O 1820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8790 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 879 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Restraints were copied for chains: B, C, D, E, F, G, H, I, K Time building chain proxies: 0.90, per 1000 atoms: 0.10 Number of scatterers: 8790 At special positions: 0 Unit cell: (68.06, 68.06, 198.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1820 8.00 N 1410 7.00 C 5500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 178 " - pdb=" SG CYS B 185 " distance=2.03 Simple disulfide: pdb=" SG CYS C 305 " - pdb=" SG CYS C 312 " distance=2.03 Simple disulfide: pdb=" SG CYS D 432 " - pdb=" SG CYS D 439 " distance=2.03 Simple disulfide: pdb=" SG CYS E 559 " - pdb=" SG CYS E 566 " distance=2.03 Simple disulfide: pdb=" SG CYS F 686 " - pdb=" SG CYS F 693 " distance=2.03 Simple disulfide: pdb=" SG CYS G 813 " - pdb=" SG CYS G 820 " distance=2.03 Simple disulfide: pdb=" SG CYS H 940 " - pdb=" SG CYS H 947 " distance=2.03 Simple disulfide: pdb=" SG CYS I1067 " - pdb=" SG CYS I1074 " distance=2.03 Simple disulfide: pdb=" SG CYS K1321 " - pdb=" SG CYS K1328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 219 " - pdb=" SG CYS B 248 " distance=2.03 Simple disulfide: pdb=" SG CYS C 346 " - pdb=" SG CYS C 375 " distance=2.03 Simple disulfide: pdb=" SG CYS D 473 " - pdb=" SG CYS D 502 " distance=2.03 Simple disulfide: pdb=" SG CYS E 600 " - pdb=" SG CYS E 629 " distance=2.03 Simple disulfide: pdb=" SG CYS F 727 " - pdb=" SG CYS F 756 " distance=2.03 Simple disulfide: pdb=" SG CYS G 854 " - pdb=" SG CYS G 883 " distance=2.03 Simple disulfide: pdb=" SG CYS H 981 " - pdb=" SG CYS H1010 " distance=2.03 Simple disulfide: pdb=" SG CYS I1108 " - pdb=" SG CYS I1137 " distance=2.03 Simple disulfide: pdb=" SG CYS K1362 " - pdb=" SG CYS K1391 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.81 Conformation dependent library (CDL) restraints added in 374.8 milliseconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 52.8% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 removed outlier: 3.844A pdb=" N ALA A 19 " --> pdb=" O GLY A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 54 removed outlier: 3.808A pdb=" N VAL A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 68 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'B' and resid 130 through 146 removed outlier: 3.844A pdb=" N ALA B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 181 removed outlier: 3.808A pdb=" N VAL B 156 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 195 Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'C' and resid 257 through 273 removed outlier: 3.844A pdb=" N ALA C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 308 removed outlier: 3.808A pdb=" N VAL C 283 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 322 Processing helix chain 'C' and resid 371 through 379 Processing helix chain 'D' and resid 384 through 400 removed outlier: 3.844A pdb=" N ALA D 400 " --> pdb=" O GLY D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 435 removed outlier: 3.809A pdb=" N VAL D 410 " --> pdb=" O TYR D 406 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR D 425 " --> pdb=" O GLY D 421 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS D 428 " --> pdb=" O GLY D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 449 Processing helix chain 'D' and resid 498 through 506 Processing helix chain 'E' and resid 511 through 527 removed outlier: 3.844A pdb=" N ALA E 527 " --> pdb=" O GLY E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 562 removed outlier: 3.808A pdb=" N VAL E 537 " --> pdb=" O TYR E 533 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY E 542 " --> pdb=" O ALA E 538 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY E 551 " --> pdb=" O LYS E 547 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS E 555 " --> pdb=" O GLY E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 576 Processing helix chain 'E' and resid 625 through 633 Processing helix chain 'F' and resid 638 through 654 removed outlier: 3.843A pdb=" N ALA F 654 " --> pdb=" O GLY F 650 " (cutoff:3.500A) Processing helix chain 'F' and resid 660 through 689 removed outlier: 3.809A pdb=" N VAL F 664 " --> pdb=" O TYR F 660 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY F 669 " --> pdb=" O ALA F 665 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY F 678 " --> pdb=" O LYS F 674 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR F 679 " --> pdb=" O GLY F 675 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR F 681 " --> pdb=" O ALA F 677 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS F 682 " --> pdb=" O GLY F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 703 Processing helix chain 'F' and resid 752 through 760 Processing helix chain 'G' and resid 765 through 781 removed outlier: 3.844A pdb=" N ALA G 781 " --> pdb=" O GLY G 777 " (cutoff:3.500A) Processing helix chain 'G' and resid 787 through 816 removed outlier: 3.809A pdb=" N VAL G 791 " --> pdb=" O TYR G 787 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY G 796 " --> pdb=" O ALA G 792 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY G 805 " --> pdb=" O LYS G 801 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR G 806 " --> pdb=" O GLY G 802 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR G 808 " --> pdb=" O ALA G 804 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS G 809 " --> pdb=" O GLY G 805 " (cutoff:3.500A) Processing helix chain 'G' and resid 820 through 830 Processing helix chain 'G' and resid 879 through 887 Processing helix chain 'H' and resid 892 through 908 removed outlier: 3.843A pdb=" N ALA H 908 " --> pdb=" O GLY H 904 " (cutoff:3.500A) Processing helix chain 'H' and resid 914 through 943 removed outlier: 3.808A pdb=" N VAL H 918 " --> pdb=" O TYR H 914 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY H 923 " --> pdb=" O ALA H 919 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY H 932 " --> pdb=" O LYS H 928 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR H 933 " --> pdb=" O GLY H 929 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR H 935 " --> pdb=" O ALA H 931 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS H 936 " --> pdb=" O GLY H 932 " (cutoff:3.500A) Processing helix chain 'H' and resid 947 through 957 Processing helix chain 'H' and resid 1006 through 1014 Processing helix chain 'I' and resid 1019 through 1035 removed outlier: 3.845A pdb=" N ALA I1035 " --> pdb=" O GLY I1031 " (cutoff:3.500A) Processing helix chain 'I' and resid 1041 through 1070 removed outlier: 3.809A pdb=" N VAL I1045 " --> pdb=" O TYR I1041 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY I1050 " --> pdb=" O ALA I1046 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY I1059 " --> pdb=" O LYS I1055 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR I1060 " --> pdb=" O GLY I1056 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR I1062 " --> pdb=" O ALA I1058 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS I1063 " --> pdb=" O GLY I1059 " (cutoff:3.500A) Processing helix chain 'I' and resid 1074 through 1084 Processing helix chain 'I' and resid 1133 through 1141 Processing helix chain 'K' and resid 1273 through 1289 removed outlier: 3.845A pdb=" N ALA K1289 " --> pdb=" O GLY K1285 " (cutoff:3.500A) Processing helix chain 'K' and resid 1295 through 1324 removed outlier: 3.809A pdb=" N VAL K1299 " --> pdb=" O TYR K1295 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY K1304 " --> pdb=" O ALA K1300 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY K1313 " --> pdb=" O LYS K1309 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR K1314 " --> pdb=" O GLY K1310 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR K1316 " --> pdb=" O ALA K1312 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS K1317 " --> pdb=" O GLY K1313 " (cutoff:3.500A) Processing helix chain 'K' and resid 1328 through 1338 Processing helix chain 'K' and resid 1387 through 1395 Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 73 removed outlier: 3.537A pdb=" N VAL A 94 " --> pdb=" O TYR A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 198 through 200 removed outlier: 3.536A pdb=" N VAL B 221 " --> pdb=" O TYR B 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.536A pdb=" N VAL C 348 " --> pdb=" O TYR C 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 452 through 454 removed outlier: 3.536A pdb=" N VAL D 475 " --> pdb=" O TYR D 468 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 579 through 581 removed outlier: 3.535A pdb=" N VAL E 602 " --> pdb=" O TYR E 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 706 through 708 removed outlier: 3.537A pdb=" N VAL F 729 " --> pdb=" O TYR F 722 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 833 through 835 removed outlier: 3.536A pdb=" N VAL G 856 " --> pdb=" O TYR G 849 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 960 through 962 removed outlier: 3.536A pdb=" N VAL H 983 " --> pdb=" O TYR H 976 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 1087 through 1089 removed outlier: 3.536A pdb=" N VAL I1110 " --> pdb=" O TYR I1103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 1341 through 1343 removed outlier: 3.536A pdb=" N VAL K1364 " --> pdb=" O TYR K1357 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1650 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: 1.53 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2870 1.34 - 1.46: 1709 1.46 - 1.57: 4221 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 8880 Sorted by residual: bond pdb=" CG1 ILE D 390 " pdb=" CD1 ILE D 390 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.53e+00 bond pdb=" CG1 ILE H 898 " pdb=" CD1 ILE H 898 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.48e+00 bond pdb=" CG1 ILE I1025 " pdb=" CD1 ILE I1025 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.48e+00 bond pdb=" CG1 ILE C 263 " pdb=" CD1 ILE C 263 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.47e+00 bond pdb=" CG1 ILE F 644 " pdb=" CD1 ILE F 644 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.47e+00 ... (remaining 8875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 11499 1.33 - 2.67: 506 2.67 - 4.00: 85 4.00 - 5.33: 20 5.33 - 6.67: 10 Bond angle restraints: 12120 Sorted by residual: angle pdb=" C TYR A 25 " pdb=" CA TYR A 25 " pdb=" CB TYR A 25 " ideal model delta sigma weight residual 110.64 107.35 3.29 1.72e+00 3.38e-01 3.65e+00 angle pdb=" C TYR E 533 " pdb=" CA TYR E 533 " pdb=" CB TYR E 533 " ideal model delta sigma weight residual 110.64 107.36 3.28 1.72e+00 3.38e-01 3.63e+00 angle pdb=" CA LEU C 276 " pdb=" CB LEU C 276 " pdb=" CG LEU C 276 " ideal model delta sigma weight residual 116.30 109.63 6.67 3.50e+00 8.16e-02 3.63e+00 angle pdb=" CA LEU H 911 " pdb=" CB LEU H 911 " pdb=" CG LEU H 911 " ideal model delta sigma weight residual 116.30 109.63 6.67 3.50e+00 8.16e-02 3.63e+00 angle pdb=" C TYR I1041 " pdb=" CA TYR I1041 " pdb=" CB TYR I1041 " ideal model delta sigma weight residual 110.64 107.36 3.28 1.72e+00 3.38e-01 3.63e+00 ... (remaining 12115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.92: 4584 12.92 - 25.84: 526 25.84 - 38.76: 120 38.76 - 51.68: 30 51.68 - 64.60: 30 Dihedral angle restraints: 5290 sinusoidal: 1740 harmonic: 3550 Sorted by residual: dihedral pdb=" CB CYS G 813 " pdb=" SG CYS G 813 " pdb=" SG CYS G 820 " pdb=" CB CYS G 820 " ideal model delta sinusoidal sigma weight residual 93.00 28.40 64.60 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CB CYS B 178 " pdb=" SG CYS B 178 " pdb=" SG CYS B 185 " pdb=" CB CYS B 185 " ideal model delta sinusoidal sigma weight residual 93.00 28.42 64.58 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CB CYS F 686 " pdb=" SG CYS F 686 " pdb=" SG CYS F 693 " pdb=" CB CYS F 693 " ideal model delta sinusoidal sigma weight residual 93.00 28.42 64.58 1 1.00e+01 1.00e-02 5.48e+01 ... (remaining 5287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 583 0.026 - 0.051: 702 0.051 - 0.077: 209 0.077 - 0.103: 59 0.103 - 0.128: 27 Chirality restraints: 1580 Sorted by residual: chirality pdb=" CA CYS C 312 " pdb=" N CYS C 312 " pdb=" C CYS C 312 " pdb=" CB CYS C 312 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA CYS G 820 " pdb=" N CYS G 820 " pdb=" C CYS G 820 " pdb=" CB CYS G 820 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA CYS A 58 " pdb=" N CYS A 58 " pdb=" C CYS A 58 " pdb=" CB CYS A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1577 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 836 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO G 837 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 837 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 837 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 582 " -0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO E 583 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 583 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 583 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K1344 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO K1345 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO K1345 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO K1345 " -0.028 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 103 2.64 - 3.21: 8473 3.21 - 3.77: 13086 3.77 - 4.34: 18402 4.34 - 4.90: 29502 Nonbonded interactions: 69566 Sorted by model distance: nonbonded pdb=" O ALA A 24 " pdb=" NZ LYS B 174 " model vdw 2.075 3.120 nonbonded pdb=" NZ LYS D 428 " pdb=" O ALA E 532 " model vdw 2.088 3.120 nonbonded pdb=" NZ LYS H 936 " pdb=" O ALA I1040 " model vdw 2.088 3.120 nonbonded pdb=" O ALA B 151 " pdb=" NZ LYS G 809 " model vdw 2.089 3.120 nonbonded pdb=" O ALA C 278 " pdb=" NZ LYS I1063 " model vdw 2.091 3.120 ... (remaining 69561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 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 0.073 8900 Z= 0.353 Angle : 0.684 6.668 12160 Z= 0.369 Chirality : 0.042 0.128 1580 Planarity : 0.005 0.049 1520 Dihedral : 12.692 55.033 2990 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.30 % Allowed : 6.90 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.19), residues: 1250 helix: -1.17 (0.15), residues: 650 sheet: -3.29 (0.27), residues: 180 loop : -3.35 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 153 TYR 0.016 0.002 TYR G 787 PHE 0.007 0.003 PHE F 637 HIS 0.002 0.001 HIS H 922 Details of bonding type rmsd covalent geometry : bond 0.00843 ( 8880) covalent geometry : angle 0.67955 (12120) SS BOND : bond 0.00334 ( 20) SS BOND : angle 1.45730 ( 40) hydrogen bonds : bond 0.16485 ( 550) hydrogen bonds : angle 5.94467 ( 1650) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8377 (t0) cc_final: 0.8169 (t70) REVERT: A 118 LYS cc_start: 0.9044 (tttt) cc_final: 0.8797 (tttm) REVERT: C 315 ILE cc_start: 0.8708 (mm) cc_final: 0.8318 (tt) REVERT: C 372 LYS cc_start: 0.8906 (tttt) cc_final: 0.8688 (tttp) REVERT: E 555 LYS cc_start: 0.8764 (mttt) cc_final: 0.8528 (mttm) REVERT: E 626 LYS cc_start: 0.9067 (tttt) cc_final: 0.8853 (tttp) outliers start: 20 outliers final: 6 residues processed: 234 average time/residue: 0.0827 time to fit residues: 27.6747 Evaluate side-chains 168 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain F residue 701 THR Chi-restraints excluded: chain G residue 825 THR Chi-restraints excluded: chain G residue 828 THR Chi-restraints excluded: chain I residue 1082 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 180 GLN C 307 GLN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 815 GLN K1319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.077790 restraints weight = 17932.086| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.32 r_work: 0.2975 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8900 Z= 0.122 Angle : 0.543 5.969 12160 Z= 0.289 Chirality : 0.040 0.135 1580 Planarity : 0.004 0.043 1520 Dihedral : 4.636 21.589 1326 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.61 % Allowed : 12.07 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.23), residues: 1250 helix: 1.03 (0.19), residues: 660 sheet: -2.33 (0.29), residues: 204 loop : -3.58 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 788 TYR 0.010 0.001 TYR I1041 PHE 0.012 0.001 PHE A 2 HIS 0.002 0.001 HIS A 33 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8880) covalent geometry : angle 0.53700 (12120) SS BOND : bond 0.00139 ( 20) SS BOND : angle 1.49202 ( 40) hydrogen bonds : bond 0.04009 ( 550) hydrogen bonds : angle 3.88895 ( 1650) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8461 (t0) cc_final: 0.7951 (t70) REVERT: C 315 ILE cc_start: 0.8529 (mm) cc_final: 0.8296 (tt) REVERT: E 569 ILE cc_start: 0.8392 (tt) cc_final: 0.8137 (tp) REVERT: G 767 ILE cc_start: 0.8846 (tp) cc_final: 0.8546 (pt) REVERT: G 871 ASP cc_start: 0.8559 (t70) cc_final: 0.8353 (t0) REVERT: H 953 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8683 (mm-30) outliers start: 14 outliers final: 8 residues processed: 219 average time/residue: 0.0785 time to fit residues: 24.7386 Evaluate side-chains 172 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain G residue 826 GLU Chi-restraints excluded: chain I residue 1080 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** D 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1069 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.077555 restraints weight = 17940.384| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.31 r_work: 0.2974 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8900 Z= 0.130 Angle : 0.544 6.726 12160 Z= 0.283 Chirality : 0.040 0.135 1580 Planarity : 0.004 0.041 1520 Dihedral : 4.398 20.700 1320 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.53 % Allowed : 15.40 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.23), residues: 1250 helix: 1.42 (0.20), residues: 658 sheet: -1.94 (0.29), residues: 208 loop : -3.58 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I1042 TYR 0.013 0.001 TYR I1041 PHE 0.006 0.001 PHE A 2 HIS 0.002 0.001 HIS E 541 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8880) covalent geometry : angle 0.53874 (12120) SS BOND : bond 0.00118 ( 20) SS BOND : angle 1.47450 ( 40) hydrogen bonds : bond 0.03723 ( 550) hydrogen bonds : angle 3.62396 ( 1650) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8439 (t0) cc_final: 0.7898 (t70) REVERT: E 576 ASP cc_start: 0.8608 (t0) cc_final: 0.8359 (t0) REVERT: F 651 ILE cc_start: 0.8783 (mt) cc_final: 0.8560 (mt) REVERT: G 851 ASP cc_start: 0.8504 (t70) cc_final: 0.8248 (t0) REVERT: H 953 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8643 (mm-30) outliers start: 22 outliers final: 12 residues processed: 182 average time/residue: 0.0699 time to fit residues: 19.0957 Evaluate side-chains 158 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain F residue 740 SER Chi-restraints excluded: chain G residue 826 GLU Chi-restraints excluded: chain H residue 994 SER Chi-restraints excluded: chain I residue 1105 ASP Chi-restraints excluded: chain I residue 1121 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 557 GLN F 684 GLN ** H 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.092324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.076063 restraints weight = 18245.917| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.27 r_work: 0.2938 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8900 Z= 0.173 Angle : 0.570 7.152 12160 Z= 0.298 Chirality : 0.041 0.122 1580 Planarity : 0.004 0.042 1520 Dihedral : 4.576 21.882 1320 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.33 % Allowed : 16.09 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.23), residues: 1250 helix: 1.45 (0.20), residues: 657 sheet: -1.73 (0.29), residues: 212 loop : -3.57 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 915 TYR 0.015 0.002 TYR B 152 PHE 0.012 0.002 PHE A 2 HIS 0.002 0.001 HIS E 541 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8880) covalent geometry : angle 0.56349 (12120) SS BOND : bond 0.00202 ( 20) SS BOND : angle 1.58794 ( 40) hydrogen bonds : bond 0.03930 ( 550) hydrogen bonds : angle 3.60437 ( 1650) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8492 (t0) cc_final: 0.7907 (t70) REVERT: D 442 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8206 (tp) REVERT: E 576 ASP cc_start: 0.8855 (t0) cc_final: 0.8588 (t0) REVERT: H 953 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8639 (mm-30) REVERT: I 1080 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8172 (mm-30) outliers start: 29 outliers final: 20 residues processed: 182 average time/residue: 0.0722 time to fit residues: 20.0319 Evaluate side-chains 174 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain F residue 740 SER Chi-restraints excluded: chain G residue 771 ILE Chi-restraints excluded: chain G residue 826 GLU Chi-restraints excluded: chain H residue 994 SER Chi-restraints excluded: chain I residue 1025 ILE Chi-restraints excluded: chain I residue 1080 GLU Chi-restraints excluded: chain I residue 1105 ASP Chi-restraints excluded: chain I residue 1121 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 815 GLN ** H 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.074346 restraints weight = 18264.603| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.27 r_work: 0.2910 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 8900 Z= 0.227 Angle : 0.610 7.770 12160 Z= 0.322 Chirality : 0.043 0.132 1580 Planarity : 0.005 0.080 1520 Dihedral : 4.907 22.680 1320 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.68 % Allowed : 17.70 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1250 helix: 1.39 (0.19), residues: 658 sheet: -1.60 (0.30), residues: 215 loop : -3.48 (0.27), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG H 915 TYR 0.017 0.002 TYR B 152 PHE 0.009 0.002 PHE A 2 HIS 0.001 0.000 HIS I1049 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 8880) covalent geometry : angle 0.60217 (12120) SS BOND : bond 0.00300 ( 20) SS BOND : angle 1.78049 ( 40) hydrogen bonds : bond 0.04296 ( 550) hydrogen bonds : angle 3.70511 ( 1650) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8507 (t0) cc_final: 0.7945 (t70) REVERT: D 442 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8301 (tp) REVERT: E 576 ASP cc_start: 0.8897 (t0) cc_final: 0.8554 (t0) REVERT: H 953 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8652 (mm-30) REVERT: I 1021 ILE cc_start: 0.8999 (tp) cc_final: 0.8767 (pt) REVERT: I 1080 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8198 (mm-30) outliers start: 32 outliers final: 27 residues processed: 175 average time/residue: 0.0609 time to fit residues: 16.4661 Evaluate side-chains 175 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 452 ILE Chi-restraints excluded: chain E residue 517 ILE Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 560 ILE Chi-restraints excluded: chain F residue 740 SER Chi-restraints excluded: chain G residue 771 ILE Chi-restraints excluded: chain G residue 826 GLU Chi-restraints excluded: chain H residue 905 ILE Chi-restraints excluded: chain H residue 994 SER Chi-restraints excluded: chain I residue 1025 ILE Chi-restraints excluded: chain I residue 1080 GLU Chi-restraints excluded: chain I residue 1105 ASP Chi-restraints excluded: chain I residue 1121 SER Chi-restraints excluded: chain I residue 1129 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 89 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 88 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 44 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.078908 restraints weight = 17823.000| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.25 r_work: 0.2998 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8900 Z= 0.111 Angle : 0.520 6.798 12160 Z= 0.271 Chirality : 0.039 0.115 1580 Planarity : 0.004 0.078 1520 Dihedral : 4.250 20.540 1320 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.87 % Allowed : 19.20 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.24), residues: 1250 helix: 1.90 (0.20), residues: 656 sheet: -1.26 (0.31), residues: 220 loop : -3.59 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I1042 TYR 0.012 0.001 TYR B 152 PHE 0.010 0.001 PHE A 2 HIS 0.002 0.001 HIS E 541 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8880) covalent geometry : angle 0.51256 (12120) SS BOND : bond 0.00121 ( 20) SS BOND : angle 1.60323 ( 40) hydrogen bonds : bond 0.03376 ( 550) hydrogen bonds : angle 3.39266 ( 1650) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8365 (t0) cc_final: 0.7680 (t70) REVERT: C 315 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7788 (tp) REVERT: E 576 ASP cc_start: 0.8917 (t0) cc_final: 0.8585 (t0) REVERT: F 651 ILE cc_start: 0.8787 (mt) cc_final: 0.8552 (mt) REVERT: H 953 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8573 (mm-30) outliers start: 25 outliers final: 19 residues processed: 177 average time/residue: 0.0645 time to fit residues: 17.4972 Evaluate side-chains 164 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain F residue 740 SER Chi-restraints excluded: chain F residue 748 THR Chi-restraints excluded: chain G residue 863 THR Chi-restraints excluded: chain H residue 994 SER Chi-restraints excluded: chain I residue 1025 ILE Chi-restraints excluded: chain I residue 1105 ASP Chi-restraints excluded: chain I residue 1117 THR Chi-restraints excluded: chain I residue 1121 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN H 942 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078627 restraints weight = 17897.544| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.26 r_work: 0.2991 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8900 Z= 0.125 Angle : 0.556 9.622 12160 Z= 0.285 Chirality : 0.039 0.116 1580 Planarity : 0.004 0.067 1520 Dihedral : 4.188 19.760 1320 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.87 % Allowed : 19.77 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1250 helix: 1.93 (0.20), residues: 657 sheet: -1.10 (0.32), residues: 220 loop : -3.54 (0.27), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I1042 TYR 0.011 0.001 TYR B 152 PHE 0.004 0.001 PHE C 256 HIS 0.002 0.001 HIS G 795 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8880) covalent geometry : angle 0.54945 (12120) SS BOND : bond 0.00133 ( 20) SS BOND : angle 1.56632 ( 40) hydrogen bonds : bond 0.03408 ( 550) hydrogen bonds : angle 3.36767 ( 1650) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8379 (t0) cc_final: 0.7708 (t70) REVERT: C 315 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7819 (tp) REVERT: E 576 ASP cc_start: 0.8897 (t0) cc_final: 0.8556 (t0) REVERT: F 651 ILE cc_start: 0.8797 (mt) cc_final: 0.8577 (mt) REVERT: H 953 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8611 (mm-30) outliers start: 25 outliers final: 23 residues processed: 172 average time/residue: 0.0702 time to fit residues: 18.4275 Evaluate side-chains 173 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 748 THR Chi-restraints excluded: chain G residue 863 THR Chi-restraints excluded: chain G residue 875 THR Chi-restraints excluded: chain H residue 990 THR Chi-restraints excluded: chain H residue 994 SER Chi-restraints excluded: chain I residue 1025 ILE Chi-restraints excluded: chain I residue 1105 ASP Chi-restraints excluded: chain I residue 1117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 59 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076893 restraints weight = 18013.212| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.27 r_work: 0.2959 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8900 Z= 0.161 Angle : 0.587 8.218 12160 Z= 0.302 Chirality : 0.041 0.125 1580 Planarity : 0.005 0.082 1520 Dihedral : 4.410 20.751 1320 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.56 % Allowed : 19.66 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.24), residues: 1250 helix: 1.82 (0.20), residues: 657 sheet: -1.13 (0.32), residues: 220 loop : -3.45 (0.27), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 788 TYR 0.014 0.001 TYR B 152 PHE 0.017 0.002 PHE A 2 HIS 0.002 0.001 HIS K1303 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 8880) covalent geometry : angle 0.57979 (12120) SS BOND : bond 0.00196 ( 20) SS BOND : angle 1.67840 ( 40) hydrogen bonds : bond 0.03747 ( 550) hydrogen bonds : angle 3.45268 ( 1650) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8447 (t0) cc_final: 0.7798 (t70) REVERT: C 315 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7864 (tp) REVERT: E 576 ASP cc_start: 0.8883 (t0) cc_final: 0.8533 (t0) REVERT: F 651 ILE cc_start: 0.8812 (mt) cc_final: 0.8592 (mt) REVERT: H 953 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8644 (mm-30) outliers start: 31 outliers final: 28 residues processed: 169 average time/residue: 0.0666 time to fit residues: 17.3203 Evaluate side-chains 166 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 553 VAL Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 748 THR Chi-restraints excluded: chain G residue 826 GLU Chi-restraints excluded: chain G residue 863 THR Chi-restraints excluded: chain G residue 875 THR Chi-restraints excluded: chain H residue 990 THR Chi-restraints excluded: chain H residue 994 SER Chi-restraints excluded: chain H residue 1002 THR Chi-restraints excluded: chain I residue 1025 ILE Chi-restraints excluded: chain I residue 1105 ASP Chi-restraints excluded: chain I residue 1117 THR Chi-restraints excluded: chain I residue 1129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 0.4980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079716 restraints weight = 17690.799| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.24 r_work: 0.3015 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8900 Z= 0.114 Angle : 0.546 8.674 12160 Z= 0.279 Chirality : 0.039 0.116 1580 Planarity : 0.004 0.075 1520 Dihedral : 4.073 19.655 1320 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.22 % Allowed : 20.00 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.24), residues: 1250 helix: 2.04 (0.20), residues: 656 sheet: -0.94 (0.33), residues: 220 loop : -3.47 (0.27), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I1042 TYR 0.009 0.001 TYR B 152 PHE 0.017 0.001 PHE A 2 HIS 0.002 0.001 HIS K1303 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8880) covalent geometry : angle 0.53986 (12120) SS BOND : bond 0.00145 ( 20) SS BOND : angle 1.52028 ( 40) hydrogen bonds : bond 0.03252 ( 550) hydrogen bonds : angle 3.29890 ( 1650) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8395 (t0) cc_final: 0.7708 (t70) REVERT: C 315 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7588 (tp) REVERT: E 576 ASP cc_start: 0.8897 (t0) cc_final: 0.8570 (t0) REVERT: F 651 ILE cc_start: 0.8774 (mt) cc_final: 0.8556 (mt) REVERT: H 953 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8624 (mm-30) outliers start: 28 outliers final: 25 residues processed: 174 average time/residue: 0.0683 time to fit residues: 18.3779 Evaluate side-chains 172 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 748 THR Chi-restraints excluded: chain G residue 826 GLU Chi-restraints excluded: chain G residue 863 THR Chi-restraints excluded: chain G residue 875 THR Chi-restraints excluded: chain H residue 990 THR Chi-restraints excluded: chain H residue 994 SER Chi-restraints excluded: chain H residue 1002 THR Chi-restraints excluded: chain I residue 1025 ILE Chi-restraints excluded: chain I residue 1105 ASP Chi-restraints excluded: chain I residue 1117 THR Chi-restraints excluded: chain I residue 1129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 0.3980 chunk 14 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.098311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.081849 restraints weight = 17747.960| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.27 r_work: 0.3057 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8900 Z= 0.105 Angle : 0.537 8.818 12160 Z= 0.273 Chirality : 0.038 0.124 1580 Planarity : 0.004 0.067 1520 Dihedral : 3.803 18.073 1320 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.41 % Allowed : 20.57 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.24), residues: 1250 helix: 2.13 (0.20), residues: 659 sheet: -0.72 (0.34), residues: 220 loop : -3.43 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 26 TYR 0.010 0.001 TYR B 152 PHE 0.012 0.001 PHE B 129 HIS 0.002 0.001 HIS K1303 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8880) covalent geometry : angle 0.53254 (12120) SS BOND : bond 0.00121 ( 20) SS BOND : angle 1.32836 ( 40) hydrogen bonds : bond 0.02981 ( 550) hydrogen bonds : angle 3.21317 ( 1650) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8393 (t0) cc_final: 0.7701 (t70) REVERT: C 298 TYR cc_start: 0.7439 (m-80) cc_final: 0.7150 (m-10) REVERT: C 315 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7420 (tp) REVERT: E 630 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7894 (mt-10) REVERT: F 651 ILE cc_start: 0.8677 (mt) cc_final: 0.8440 (mt) REVERT: H 895 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8466 (mt-10) REVERT: H 953 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8610 (mm-30) outliers start: 21 outliers final: 20 residues processed: 184 average time/residue: 0.0690 time to fit residues: 19.7713 Evaluate side-chains 170 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain E residue 621 THR Chi-restraints excluded: chain F residue 736 THR Chi-restraints excluded: chain F residue 748 THR Chi-restraints excluded: chain G residue 863 THR Chi-restraints excluded: chain G residue 875 THR Chi-restraints excluded: chain H residue 990 THR Chi-restraints excluded: chain H residue 994 SER Chi-restraints excluded: chain H residue 1002 THR Chi-restraints excluded: chain I residue 1105 ASP Chi-restraints excluded: chain I residue 1117 THR Chi-restraints excluded: chain I residue 1129 THR Chi-restraints excluded: chain K residue 1383 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 815 GLN ** K1319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.091270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074724 restraints weight = 18020.020| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.24 r_work: 0.2918 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 8900 Z= 0.259 Angle : 0.684 9.689 12160 Z= 0.353 Chirality : 0.044 0.143 1580 Planarity : 0.005 0.070 1520 Dihedral : 4.811 22.749 1320 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.79 % Allowed : 20.92 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.23), residues: 1250 helix: 1.57 (0.19), residues: 657 sheet: -1.23 (0.31), residues: 220 loop : -3.25 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 788 TYR 0.018 0.002 TYR B 152 PHE 0.018 0.003 PHE C 256 HIS 0.003 0.001 HIS K1303 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 8880) covalent geometry : angle 0.67589 (12120) SS BOND : bond 0.00336 ( 20) SS BOND : angle 1.92994 ( 40) hydrogen bonds : bond 0.04423 ( 550) hydrogen bonds : angle 3.69362 ( 1650) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2060.34 seconds wall clock time: 36 minutes 14.85 seconds (2174.85 seconds total)