Starting phenix.real_space_refine on Thu Mar 14 20:03:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/03_2024/7whm_32504.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/03_2024/7whm_32504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/03_2024/7whm_32504.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/03_2024/7whm_32504.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/03_2024/7whm_32504.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whm_32504/03_2024/7whm_32504.pdb" } resolution = 2.7 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= 0.004 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 39 5.16 5 C 6048 2.51 5 N 1706 2.21 5 O 1857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 382": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 471": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 521": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 551": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A GLU 667": "OE1" <-> "OE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A ARG 729": "NH1" <-> "NH2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A ASP 774": "OD1" <-> "OD2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A ARG 890": "NH1" <-> "NH2" Residue "A GLU 896": "OE1" <-> "OE2" Residue "A ARG 925": "NH1" <-> "NH2" Residue "A ARG 960": "NH1" <-> "NH2" Residue "A PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1070": "OE1" <-> "OE2" Residue "A ARG 1080": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1147": "NH1" <-> "NH2" Residue "A PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1198": "NH1" <-> "NH2" Residue "A ARG 1212": "NH1" <-> "NH2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ARG 1220": "NH1" <-> "NH2" Residue "A ARG 1232": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9650 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1214, 9650 Classifications: {'peptide': 1214} Link IDs: {'PCIS': 4, 'PTRANS': 38, 'TRANS': 1171} Time building chain proxies: 5.51, per 1000 atoms: 0.57 Number of scatterers: 9650 At special positions: 0 Unit cell: (110.448, 128.502, 133.812, 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 39 16.00 O 1857 8.00 N 1706 7.00 C 6048 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: 3.42 Conformation dependent library (CDL) restraints added in 1.9 seconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 37.7% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 28 through 53 Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 306 through 338 removed outlier: 3.723A pdb=" N HIS A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 372 removed outlier: 3.534A pdb=" N ARG A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.562A pdb=" N ARG A 631 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 658 removed outlier: 3.734A pdb=" N ASN A 655 " --> pdb=" O MET A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 688 Processing helix chain 'A' and resid 718 through 724 Processing helix chain 'A' and resid 744 through 754 removed outlier: 4.324A pdb=" N ARG A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 769 Processing helix chain 'A' and resid 773 through 777 Processing helix chain 'A' and resid 778 through 796 Processing helix chain 'A' and resid 800 through 814 removed outlier: 3.739A pdb=" N ILE A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 835 Processing helix chain 'A' and resid 835 through 850 Processing helix chain 'A' and resid 852 through 861 removed outlier: 4.174A pdb=" N GLY A 861 " --> pdb=" O THR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 885 Processing helix chain 'A' and resid 887 through 892 Processing helix chain 'A' and resid 897 through 901 Processing helix chain 'A' and resid 904 through 909 Processing helix chain 'A' and resid 909 through 923 Processing helix chain 'A' and resid 924 through 928 Processing helix chain 'A' and resid 932 through 937 Processing helix chain 'A' and resid 979 through 994 Processing helix chain 'A' and resid 1074 through 1087 Processing helix chain 'A' and resid 1094 through 1105 Processing helix chain 'A' and resid 1123 through 1136 removed outlier: 3.692A pdb=" N LEU A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'A' and resid 1148 through 1161 removed outlier: 4.027A pdb=" N PHE A1152 " --> pdb=" O ASN A1148 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A1153 " --> pdb=" O CYS A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1193 removed outlier: 4.154A pdb=" N ALA A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1220 removed outlier: 3.522A pdb=" N ARG A1220 " --> pdb=" O LYS A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1236 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.934A pdb=" N ASN A 105 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL A 235 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLN A 260 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N SER A 237 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL A 258 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N HIS A 239 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL A 256 " --> pdb=" O HIS A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.761A pdb=" N VAL A 296 " --> pdb=" O LYS A1109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 181 removed outlier: 6.390A pdb=" N ASP A 155 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR A 149 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU A 157 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 139 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN A 124 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG A 125 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE A 284 " --> pdb=" O ARG A 125 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE A 127 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 206 removed outlier: 4.176A pdb=" N ASN A1053 " --> pdb=" O ILE A1062 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE A1062 " --> pdb=" O ASN A1053 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 300 " --> pdb=" O ILE A1063 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ARG A1065 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 206 removed outlier: 6.697A pdb=" N SER A1016 " --> pdb=" O GLU A1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 380 through 395 removed outlier: 5.516A pdb=" N ARG A 382 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE A 738 " --> pdb=" O ARG A 382 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLU A 384 " --> pdb=" O ALA A 736 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA A 736 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ARG A 386 " --> pdb=" O TRP A 734 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N TRP A 734 " --> pdb=" O ARG A 386 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP A 388 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLY A 732 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR A 725 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N TYR A 570 " --> pdb=" O THR A 725 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL A 727 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU A 568 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 729 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 566 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N HIS A 731 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU A 564 " --> pdb=" O HIS A 731 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 733 " --> pdb=" O GLY A 562 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY A 562 " --> pdb=" O ASN A 733 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER A 735 " --> pdb=" O THR A 560 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR A 560 " --> pdb=" O SER A 735 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 573 " --> pdb=" O TYR A 570 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 409 removed outlier: 6.814A pdb=" N GLN A 435 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE A 676 " --> pdb=" O GLN A 435 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG A 437 " --> pdb=" O PHE A 676 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL A 678 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 439 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N THR A 673 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU A 667 " --> pdb=" O THR A 673 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 458 removed outlier: 5.587A pdb=" N ASN A 449 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN A 472 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER A 451 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR A 470 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N PHE A 453 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N PHE A 468 " --> pdb=" O PHE A 453 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASN A 455 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU A 466 " --> pdb=" O ASN A 455 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 545 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N SER A 469 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL A 543 " --> pdb=" O SER A 469 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ARG A 471 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ILE A 541 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 604 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 545 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE A 602 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU A 547 " --> pdb=" O CYS A 600 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N CYS A 600 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY A 549 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 598 " --> pdb=" O GLY A 549 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY A 593 " --> pdb=" O THR A 589 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 498 through 502 removed outlier: 6.989A pdb=" N THR A 510 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 529 through 531 Processing sheet with id=AB2, first strand: chain 'A' and resid 864 through 865 removed outlier: 6.561A pdb=" N ASN A 864 " --> pdb=" O GLU A1119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 462 hydrogen bonds defined for protein. 1320 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: 3.56 Time building geometry restraints manager: 3.74 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: 3261 1.34 - 1.45: 1325 1.45 - 1.57: 5168 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9828 Sorted by residual: bond pdb=" CB THR A1007 " pdb=" CG2 THR A1007 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.54e+00 bond pdb=" CG1 ILE A1048 " pdb=" CD1 ILE A1048 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.29e+00 bond pdb=" CA GLY A 204 " pdb=" C GLY A 204 " ideal model delta sigma weight residual 1.520 1.500 0.020 1.39e-02 5.18e+03 2.09e+00 bond pdb=" CB ASP A 182 " pdb=" CG ASP A 182 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.88e+00 bond pdb=" CB ASN A1148 " pdb=" CG ASN A1148 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.74e+00 ... (remaining 9823 not shown) Histogram of bond angle deviations from ideal: 98.93 - 105.94: 165 105.94 - 112.96: 5387 112.96 - 119.98: 3216 119.98 - 127.00: 4469 127.00 - 134.02: 88 Bond angle restraints: 13325 Sorted by residual: angle pdb=" C THR A 133 " pdb=" N THR A 134 " pdb=" CA THR A 134 " ideal model delta sigma weight residual 122.74 129.54 -6.80 2.44e+00 1.68e-01 7.77e+00 angle pdb=" C TYR A 710 " pdb=" N GLN A 711 " pdb=" CA GLN A 711 " ideal model delta sigma weight residual 122.61 126.39 -3.78 1.56e+00 4.11e-01 5.86e+00 angle pdb=" N LEU A 745 " pdb=" CA LEU A 745 " pdb=" C LEU A 745 " ideal model delta sigma weight residual 109.81 115.13 -5.32 2.21e+00 2.05e-01 5.81e+00 angle pdb=" CA MET A 955 " pdb=" CB MET A 955 " pdb=" CG MET A 955 " ideal model delta sigma weight residual 114.10 118.82 -4.72 2.00e+00 2.50e-01 5.57e+00 angle pdb=" C TYR A 615 " pdb=" N LEU A 616 " pdb=" CA LEU A 616 " ideal model delta sigma weight residual 120.28 123.63 -3.35 1.44e+00 4.82e-01 5.42e+00 ... (remaining 13320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5400 17.65 - 35.30: 453 35.30 - 52.96: 78 52.96 - 70.61: 19 70.61 - 88.26: 8 Dihedral angle restraints: 5958 sinusoidal: 2406 harmonic: 3552 Sorted by residual: dihedral pdb=" CA ILE A 692 " pdb=" C ILE A 692 " pdb=" N SER A 693 " pdb=" CA SER A 693 " ideal model delta harmonic sigma weight residual -180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA PRO A 700 " pdb=" C PRO A 700 " pdb=" N VAL A 701 " pdb=" CA VAL A 701 " ideal model delta harmonic sigma weight residual 180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA TYR A 706 " pdb=" C TYR A 706 " pdb=" N ALA A 707 " pdb=" CA ALA A 707 " ideal model delta harmonic sigma weight residual -180.00 -162.22 -17.78 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 969 0.040 - 0.081: 378 0.081 - 0.121: 150 0.121 - 0.161: 18 0.161 - 0.202: 2 Chirality restraints: 1517 Sorted by residual: chirality pdb=" CB VAL A 904 " pdb=" CA VAL A 904 " pdb=" CG1 VAL A 904 " pdb=" CG2 VAL A 904 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB THR A1007 " pdb=" CA THR A1007 " pdb=" OG1 THR A1007 " pdb=" CG2 THR A1007 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA VAL A 113 " pdb=" N VAL A 113 " pdb=" C VAL A 113 " pdb=" CB VAL A 113 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 1514 not shown) Planarity restraints: 1737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 134 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO A 135 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 135 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 135 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 398 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 399 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 149 " -0.009 2.00e-02 2.50e+03 9.94e-03 1.98e+00 pdb=" CG TYR A 149 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 149 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 149 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 149 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 149 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 149 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 149 " 0.000 2.00e-02 2.50e+03 ... (remaining 1734 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 240 2.70 - 3.25: 9086 3.25 - 3.80: 15015 3.80 - 4.35: 19729 4.35 - 4.90: 33490 Nonbonded interactions: 77560 Sorted by model distance: nonbonded pdb=" O THR A 84 " pdb=" NH1 ARG A 960 " model vdw 2.155 2.520 nonbonded pdb=" O LEU A 482 " pdb=" NE2 GLN A 531 " model vdw 2.222 2.520 nonbonded pdb=" OH TYR A 470 " pdb=" OE1 GLN A 472 " model vdw 2.259 2.440 nonbonded pdb=" OD1 ASP A 309 " pdb=" NH2 ARG A 312 " model vdw 2.262 2.520 nonbonded pdb=" O TYR A 72 " pdb=" OG1 THR A 75 " model vdw 2.313 2.440 ... (remaining 77555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.490 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.890 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.006 0.059 9828 Z= 0.414 Angle : 0.637 6.811 13325 Z= 0.364 Chirality : 0.048 0.202 1517 Planarity : 0.004 0.040 1737 Dihedral : 13.847 88.259 3666 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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 (0.23), residues: 1212 helix: 1.29 (0.25), residues: 416 sheet: 0.04 (0.29), residues: 292 loop : -0.82 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1099 HIS 0.008 0.001 HIS A 195 PHE 0.022 0.002 PHE A 101 TYR 0.023 0.002 TYR A 149 ARG 0.010 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.112 Fit side-chains REVERT: A 679 GLU cc_start: 0.7732 (tt0) cc_final: 0.7424 (tt0) REVERT: A 733 ASN cc_start: 0.6813 (p0) cc_final: 0.6593 (p0) REVERT: A 1186 MET cc_start: 0.9029 (tpt) cc_final: 0.8820 (tpt) outliers start: 0 outliers final: 1 residues processed: 155 average time/residue: 1.4800 time to fit residues: 242.9485 Evaluate side-chains 137 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1190 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 260 GLN A1139 GLN A1179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9828 Z= 0.244 Angle : 0.540 6.819 13325 Z= 0.292 Chirality : 0.045 0.160 1517 Planarity : 0.004 0.042 1737 Dihedral : 5.058 52.089 1352 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.32 % Allowed : 7.15 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.72 (0.24), residues: 1212 helix: 2.03 (0.25), residues: 406 sheet: 0.33 (0.30), residues: 277 loop : -0.65 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1099 HIS 0.004 0.001 HIS A 195 PHE 0.013 0.002 PHE A 128 TYR 0.014 0.002 TYR A 72 ARG 0.010 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.105 Fit side-chains REVERT: A 161 LYS cc_start: 0.8587 (tmtp) cc_final: 0.8358 (tmtp) REVERT: A 257 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: A 351 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: A 437 ARG cc_start: 0.6728 (OUTLIER) cc_final: 0.6462 (ptt180) REVERT: A 638 THR cc_start: 0.8900 (t) cc_final: 0.8547 (m) REVERT: A 679 GLU cc_start: 0.7626 (tt0) cc_final: 0.7221 (tt0) REVERT: A 780 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8255 (mptt) REVERT: A 1131 ASP cc_start: 0.8578 (m-30) cc_final: 0.8361 (m-30) REVERT: A 1212 ARG cc_start: 0.7511 (mtm110) cc_final: 0.7259 (mtm-85) outliers start: 25 outliers final: 10 residues processed: 151 average time/residue: 1.4042 time to fit residues: 225.4615 Evaluate side-chains 157 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 673 THR Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 780 LYS Chi-restraints excluded: chain A residue 1040 ASN Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1190 MET Chi-restraints excluded: chain A residue 1216 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 30 optimal weight: 0.0870 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 37 optimal weight: 0.0670 chunk 88 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN A1179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9828 Z= 0.153 Angle : 0.468 5.717 13325 Z= 0.254 Chirality : 0.043 0.152 1517 Planarity : 0.003 0.041 1737 Dihedral : 4.438 22.625 1352 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.95 % Allowed : 9.01 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.08 (0.24), residues: 1212 helix: 2.48 (0.26), residues: 404 sheet: 0.36 (0.30), residues: 287 loop : -0.47 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1099 HIS 0.003 0.001 HIS A 317 PHE 0.012 0.001 PHE A1003 TYR 0.018 0.001 TYR A 462 ARG 0.005 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 1.046 Fit side-chains REVERT: A 89 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 161 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8315 (tmtp) REVERT: A 257 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: A 351 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: A 628 GLU cc_start: 0.4900 (pt0) cc_final: 0.3886 (tp30) REVERT: A 638 THR cc_start: 0.8903 (t) cc_final: 0.8604 (m) REVERT: A 672 MET cc_start: 0.6967 (mmt) cc_final: 0.6746 (mmt) REVERT: A 679 GLU cc_start: 0.7484 (tt0) cc_final: 0.7163 (tt0) REVERT: A 1131 ASP cc_start: 0.8554 (m-30) cc_final: 0.8337 (m-30) outliers start: 21 outliers final: 5 residues processed: 151 average time/residue: 1.3987 time to fit residues: 224.8366 Evaluate side-chains 153 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 145 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 1063 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 82 optimal weight: 0.0050 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 31 optimal weight: 0.0000 chunk 97 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN A 260 GLN A 484 GLN A1089 GLN A1139 GLN ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9828 Z= 0.127 Angle : 0.441 5.771 13325 Z= 0.238 Chirality : 0.042 0.149 1517 Planarity : 0.003 0.042 1737 Dihedral : 4.130 19.841 1349 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.04 % Allowed : 10.49 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.33 (0.24), residues: 1212 helix: 2.72 (0.26), residues: 406 sheet: 0.65 (0.30), residues: 281 loop : -0.45 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1099 HIS 0.003 0.001 HIS A 452 PHE 0.014 0.001 PHE A 676 TYR 0.013 0.001 TYR A1011 ARG 0.005 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.134 Fit side-chains REVERT: A 86 ASN cc_start: 0.8990 (p0) cc_final: 0.8644 (p0) REVERT: A 89 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 161 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8273 (tttp) REVERT: A 257 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: A 351 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: A 594 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: A 628 GLU cc_start: 0.4881 (pt0) cc_final: 0.4076 (tm-30) REVERT: A 638 THR cc_start: 0.8900 (t) cc_final: 0.8604 (m) REVERT: A 1131 ASP cc_start: 0.8541 (m-30) cc_final: 0.8329 (m-30) outliers start: 22 outliers final: 5 residues processed: 163 average time/residue: 1.3541 time to fit residues: 235.3193 Evaluate side-chains 156 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 1007 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 484 GLN A1148 ASN A1179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9828 Z= 0.307 Angle : 0.536 7.214 13325 Z= 0.287 Chirality : 0.046 0.164 1517 Planarity : 0.004 0.055 1737 Dihedral : 4.468 21.080 1349 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.69 % Allowed : 11.61 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.12 (0.24), residues: 1212 helix: 2.35 (0.25), residues: 406 sheet: 0.60 (0.30), residues: 281 loop : -0.44 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1099 HIS 0.005 0.001 HIS A 317 PHE 0.014 0.002 PHE A 676 TYR 0.017 0.002 TYR A1125 ARG 0.003 0.000 ARG A1065 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 1.196 Fit side-chains REVERT: A 161 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8231 (tmtp) REVERT: A 257 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: A 351 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: A 594 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7565 (tt0) REVERT: A 628 GLU cc_start: 0.4678 (pt0) cc_final: 0.4054 (tp30) REVERT: A 638 THR cc_start: 0.8885 (t) cc_final: 0.8599 (m) REVERT: A 1089 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: A 1131 ASP cc_start: 0.8498 (m-30) cc_final: 0.8267 (m-30) REVERT: A 1216 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8301 (mtpm) outliers start: 29 outliers final: 12 residues processed: 159 average time/residue: 1.4093 time to fit residues: 238.7091 Evaluate side-chains 167 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1190 MET Chi-restraints excluded: chain A residue 1216 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 0.0170 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.0020 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 484 GLN A1139 GLN A1179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9828 Z= 0.118 Angle : 0.435 5.695 13325 Z= 0.234 Chirality : 0.041 0.147 1517 Planarity : 0.003 0.041 1737 Dihedral : 4.069 19.235 1349 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.49 % Allowed : 13.46 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.44 (0.24), residues: 1212 helix: 2.79 (0.26), residues: 405 sheet: 0.71 (0.30), residues: 281 loop : -0.37 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1099 HIS 0.003 0.000 HIS A 452 PHE 0.014 0.001 PHE A 676 TYR 0.013 0.001 TYR A1011 ARG 0.007 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.122 Fit side-chains REVERT: A 89 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8364 (mt-10) REVERT: A 161 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8110 (tttp) REVERT: A 257 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: A 351 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6936 (tm-30) REVERT: A 594 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7658 (tt0) REVERT: A 628 GLU cc_start: 0.4942 (pt0) cc_final: 0.4360 (tm-30) REVERT: A 638 THR cc_start: 0.8885 (t) cc_final: 0.8606 (m) REVERT: A 651 MET cc_start: 0.8592 (mtt) cc_final: 0.7815 (mtt) REVERT: A 685 MET cc_start: 0.8039 (mtm) cc_final: 0.7814 (mtm) REVERT: A 1131 ASP cc_start: 0.8479 (m-30) cc_final: 0.8278 (m-30) outliers start: 16 outliers final: 6 residues processed: 157 average time/residue: 1.3570 time to fit residues: 227.2219 Evaluate side-chains 158 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 1007 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 46 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 754 HIS A1179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9828 Z= 0.344 Angle : 0.554 7.256 13325 Z= 0.296 Chirality : 0.046 0.165 1517 Planarity : 0.004 0.067 1737 Dihedral : 4.500 19.720 1349 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.69 % Allowed : 13.00 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.24), residues: 1212 helix: 2.30 (0.25), residues: 406 sheet: 0.69 (0.31), residues: 277 loop : -0.45 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1099 HIS 0.005 0.001 HIS A 317 PHE 0.018 0.002 PHE A 676 TYR 0.018 0.002 TYR A1125 ARG 0.009 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 0.878 Fit side-chains REVERT: A 145 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: A 161 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8149 (tttt) REVERT: A 240 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8189 (mt) REVERT: A 257 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: A 351 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7131 (tm-30) REVERT: A 437 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6357 (ptp-170) REVERT: A 461 GLU cc_start: 0.7291 (tt0) cc_final: 0.6772 (tp30) REVERT: A 594 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7620 (tt0) REVERT: A 628 GLU cc_start: 0.4774 (pt0) cc_final: 0.4172 (tp30) REVERT: A 638 THR cc_start: 0.8873 (t) cc_final: 0.8605 (m) REVERT: A 651 MET cc_start: 0.8586 (mtt) cc_final: 0.7742 (mtt) REVERT: A 685 MET cc_start: 0.8151 (mtm) cc_final: 0.7948 (mtm) REVERT: A 689 MET cc_start: 0.8077 (ttm) cc_final: 0.7749 (ttm) REVERT: A 960 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7743 (mtp-110) REVERT: A 1083 ARG cc_start: 0.8548 (tpt90) cc_final: 0.8183 (mmm160) REVERT: A 1089 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: A 1131 ASP cc_start: 0.8502 (m-30) cc_final: 0.8282 (m-30) outliers start: 29 outliers final: 14 residues processed: 158 average time/residue: 1.3616 time to fit residues: 228.9289 Evaluate side-chains 171 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 148 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 104 ASP Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1089 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 754 HIS A1139 GLN A1179 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9828 Z= 0.159 Angle : 0.467 6.223 13325 Z= 0.251 Chirality : 0.042 0.154 1517 Planarity : 0.003 0.042 1737 Dihedral : 4.247 19.736 1349 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.95 % Allowed : 14.02 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.34 (0.24), residues: 1212 helix: 2.61 (0.25), residues: 404 sheet: 0.78 (0.31), residues: 277 loop : -0.40 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1099 HIS 0.005 0.001 HIS A 754 PHE 0.016 0.001 PHE A 676 TYR 0.012 0.001 TYR A1011 ARG 0.010 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.184 Fit side-chains REVERT: A 161 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8235 (tttt) REVERT: A 257 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: A 351 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: A 461 GLU cc_start: 0.7224 (tt0) cc_final: 0.6764 (tp30) REVERT: A 594 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: A 628 GLU cc_start: 0.4923 (pt0) cc_final: 0.4443 (tp30) REVERT: A 638 THR cc_start: 0.8872 (t) cc_final: 0.8613 (m) REVERT: A 651 MET cc_start: 0.8624 (mtt) cc_final: 0.7881 (mtt) REVERT: A 685 MET cc_start: 0.8090 (mtm) cc_final: 0.7820 (mtm) REVERT: A 689 MET cc_start: 0.8001 (ttm) cc_final: 0.7682 (ttm) REVERT: A 841 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7284 (mtp180) REVERT: A 960 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7764 (mtp-110) REVERT: A 1131 ASP cc_start: 0.8486 (m-30) cc_final: 0.8270 (m-30) outliers start: 21 outliers final: 11 residues processed: 158 average time/residue: 1.4041 time to fit residues: 235.8787 Evaluate side-chains 171 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1190 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN A1179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9828 Z= 0.245 Angle : 0.507 6.684 13325 Z= 0.272 Chirality : 0.044 0.159 1517 Planarity : 0.004 0.049 1737 Dihedral : 4.352 19.070 1349 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.95 % Allowed : 14.39 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.27 (0.24), residues: 1212 helix: 2.48 (0.25), residues: 405 sheet: 0.78 (0.31), residues: 277 loop : -0.40 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1099 HIS 0.005 0.001 HIS A 317 PHE 0.018 0.002 PHE A 676 TYR 0.014 0.001 TYR A1125 ARG 0.011 0.000 ARG A1212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.015 Fit side-chains REVERT: A 161 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8176 (tmtp) REVERT: A 257 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: A 351 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: A 461 GLU cc_start: 0.7277 (tt0) cc_final: 0.6807 (tp30) REVERT: A 594 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: A 628 GLU cc_start: 0.4713 (pt0) cc_final: 0.4117 (tm-30) REVERT: A 638 THR cc_start: 0.8866 (t) cc_final: 0.8612 (m) REVERT: A 651 MET cc_start: 0.8627 (mtt) cc_final: 0.7888 (mtt) REVERT: A 689 MET cc_start: 0.8008 (ttm) cc_final: 0.7793 (ttm) REVERT: A 960 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7754 (mtp-110) REVERT: A 1083 ARG cc_start: 0.8535 (tpt90) cc_final: 0.8287 (mmm160) REVERT: A 1089 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.6942 (mp10) REVERT: A 1131 ASP cc_start: 0.8478 (m-30) cc_final: 0.8255 (m-30) outliers start: 21 outliers final: 13 residues processed: 152 average time/residue: 1.3957 time to fit residues: 225.8711 Evaluate side-chains 166 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1190 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN A1179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9828 Z= 0.163 Angle : 0.472 6.752 13325 Z= 0.254 Chirality : 0.043 0.154 1517 Planarity : 0.003 0.052 1737 Dihedral : 4.227 18.960 1349 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.04 % Allowed : 14.48 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.40 (0.24), residues: 1212 helix: 2.65 (0.26), residues: 404 sheet: 0.82 (0.31), residues: 277 loop : -0.37 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1099 HIS 0.004 0.001 HIS A 452 PHE 0.017 0.001 PHE A 676 TYR 0.013 0.001 TYR A1011 ARG 0.011 0.000 ARG A1212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.186 Fit side-chains REVERT: A 89 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8408 (mt-10) REVERT: A 161 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8079 (tmtp) REVERT: A 257 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7457 (m-30) REVERT: A 351 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6998 (tm-30) REVERT: A 437 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6347 (ptp-170) REVERT: A 461 GLU cc_start: 0.7224 (tt0) cc_final: 0.6772 (tp30) REVERT: A 594 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: A 628 GLU cc_start: 0.4765 (pt0) cc_final: 0.4237 (tm-30) REVERT: A 638 THR cc_start: 0.8867 (t) cc_final: 0.8614 (m) REVERT: A 651 MET cc_start: 0.8608 (mtt) cc_final: 0.7901 (mtt) REVERT: A 685 MET cc_start: 0.8114 (mtm) cc_final: 0.7848 (mtm) REVERT: A 689 MET cc_start: 0.7987 (ttm) cc_final: 0.7667 (ttm) REVERT: A 841 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7272 (mtp180) REVERT: A 960 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7747 (mtp-110) REVERT: A 1083 ARG cc_start: 0.8509 (tpt90) cc_final: 0.8174 (mmm160) REVERT: A 1089 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: A 1131 ASP cc_start: 0.8496 (m-30) cc_final: 0.8290 (m-30) outliers start: 22 outliers final: 9 residues processed: 155 average time/residue: 1.4062 time to fit residues: 231.8006 Evaluate side-chains 167 residues out of total 1077 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 150 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 594 GLU Chi-restraints excluded: chain A residue 629 ASP Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 841 ARG Chi-restraints excluded: chain A residue 960 ARG Chi-restraints excluded: chain A residue 1007 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain A residue 1089 GLN Chi-restraints excluded: chain A residue 1190 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN ** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1139 GLN A1179 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.140865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.094381 restraints weight = 11100.960| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.57 r_work: 0.2796 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9828 Z= 0.217 Angle : 0.492 6.551 13325 Z= 0.264 Chirality : 0.044 0.158 1517 Planarity : 0.004 0.052 1737 Dihedral : 4.304 18.446 1349 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 14.30 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.34 (0.24), residues: 1212 helix: 2.55 (0.25), residues: 404 sheet: 0.78 (0.30), residues: 281 loop : -0.35 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1099 HIS 0.005 0.001 HIS A 317 PHE 0.018 0.001 PHE A 676 TYR 0.014 0.001 TYR A1125 ARG 0.011 0.000 ARG A1212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4165.43 seconds wall clock time: 73 minutes 56.59 seconds (4436.59 seconds total)