Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 4 15:33:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/07_2023/7nur_12600.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/07_2023/7nur_12600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.125 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/07_2023/7nur_12600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/07_2023/7nur_12600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/07_2023/7nur_12600.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/07_2023/7nur_12600.pdb" } resolution = 3.125 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 ------------------------------------------------------------------------------- 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= 0.003 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 31 5.16 5 C 5307 2.51 5 N 1417 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 648": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A ARG 1017": "NH1" <-> "NH2" Residue "A TYR 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A ARG 1080": "NH1" <-> "NH2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A ASP 1225": "OD1" <-> "OD2" Residue "A PHE 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1251": "NH1" <-> "NH2" Residue "A PHE 1288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1298": "OD1" <-> "OD2" Residue "A PHE 1304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1307": "OE1" <-> "OE2" Residue "A ASP 1338": "OD1" <-> "OD2" Residue "A ASP 1346": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 8245 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8245 Classifications: {'peptide': 1044} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 61, 'TRANS': 982} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 4.40, per 1000 atoms: 0.53 Number of scatterers: 8245 At special positions: 0 Unit cell: (89.712, 98.256, 120.47, 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 31 16.00 O 1490 8.00 N 1417 7.00 C 5307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 727 " distance=2.03 Simple disulfide: pdb=" SG CYS A1301 " - pdb=" SG CYS A1359 " distance=2.03 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: 3.09 Conformation dependent library (CDL) restraints added in 1.2 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 54.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 308 through 317 removed outlier: 4.288A pdb=" N GLN A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.610A pdb=" N GLY A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 4.007A pdb=" N ARG A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.810A pdb=" N ARG A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 4.000A pdb=" N ILE A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 479 removed outlier: 4.058A pdb=" N THR A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 470 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 477 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.671A pdb=" N SER A 484 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.969A pdb=" N TYR A 498 " --> pdb=" O GLN A 494 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 removed outlier: 4.193A pdb=" N LEU A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 removed outlier: 3.697A pdb=" N LEU A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 576 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.674A pdb=" N GLU A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 removed outlier: 3.969A pdb=" N TYR A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 663 " --> pdb=" O TYR A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.884A pdb=" N TYR A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 763 through 783 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 824 through 834 removed outlier: 3.561A pdb=" N LEU A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 849 removed outlier: 3.582A pdb=" N TYR A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 860 removed outlier: 3.521A pdb=" N PHE A 860 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 891 Processing helix chain 'A' and resid 896 through 908 Processing helix chain 'A' and resid 914 through 928 removed outlier: 3.890A pdb=" N VAL A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 920 " --> pdb=" O ARG A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 941 through 950 removed outlier: 3.562A pdb=" N TYR A 947 " --> pdb=" O VAL A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 982 through 1012 removed outlier: 3.814A pdb=" N SER A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 996 " --> pdb=" O LYS A 992 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1028 removed outlier: 3.738A pdb=" N GLY A1028 " --> pdb=" O GLN A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1052 removed outlier: 4.123A pdb=" N SER A1048 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1074 Processing helix chain 'A' and resid 1075 through 1082 removed outlier: 3.879A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1086 Processing helix chain 'A' and resid 1092 through 1111 removed outlier: 3.655A pdb=" N VAL A1106 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A1107 " --> pdb=" O ALA A1103 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A1108 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG A1109 " --> pdb=" O ARG A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1129 through 1134 removed outlier: 3.848A pdb=" N LYS A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 removed outlier: 3.679A pdb=" N SER A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1185 removed outlier: 3.576A pdb=" N GLU A1163 " --> pdb=" O PRO A1159 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A1168 " --> pdb=" O MET A1164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1180 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A1181 " --> pdb=" O ALA A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1240 removed outlier: 4.290A pdb=" N ARG A1228 " --> pdb=" O ALA A1224 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP A1236 " --> pdb=" O ARG A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1294 removed outlier: 3.621A pdb=" N GLN A1287 " --> pdb=" O LEU A1283 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A1288 " --> pdb=" O GLN A1284 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A1289 " --> pdb=" O PHE A1285 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A1294 " --> pdb=" O THR A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1303 removed outlier: 3.772A pdb=" N ARG A1302 " --> pdb=" O PRO A1299 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A1303 " --> pdb=" O GLN A1300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1299 through 1303' Processing helix chain 'A' and resid 1328 through 1332 Processing helix chain 'A' and resid 1363 through 1368 Processing sheet with id=AA1, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.993A pdb=" N LEU A 324 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TRP A 526 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 366 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 528 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 334 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA3, first strand: chain 'A' and resid 601 through 604 Processing sheet with id=AA4, first strand: chain 'A' and resid 1246 through 1256 removed outlier: 5.011A pdb=" N GLU A1268 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1307 through 1309 348 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 3.37 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: 2649 1.34 - 1.46: 1638 1.46 - 1.58: 4093 1.58 - 1.70: 0 1.70 - 1.81: 55 Bond restraints: 8435 Sorted by residual: bond pdb=" CA GLU A 858 " pdb=" C GLU A 858 " ideal model delta sigma weight residual 1.523 1.481 0.043 1.80e-02 3.09e+03 5.59e+00 bond pdb=" CA ARG A 916 " pdb=" C ARG A 916 " ideal model delta sigma weight residual 1.522 1.489 0.032 1.72e-02 3.38e+03 3.55e+00 bond pdb=" CB THR A 881 " pdb=" CG2 THR A 881 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.10e+00 bond pdb=" CB VAL A 919 " pdb=" CG1 VAL A 919 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" N LYS A 940 " pdb=" CA LYS A 940 " ideal model delta sigma weight residual 1.456 1.472 -0.016 1.23e-02 6.61e+03 1.77e+00 ... (remaining 8430 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.47: 280 106.47 - 113.38: 4573 113.38 - 120.28: 3292 120.28 - 127.19: 3182 127.19 - 134.10: 96 Bond angle restraints: 11423 Sorted by residual: angle pdb=" CA PHE A1062 " pdb=" C PHE A1062 " pdb=" N PRO A1063 " ideal model delta sigma weight residual 117.82 120.83 -3.01 7.80e-01 1.64e+00 1.49e+01 angle pdb=" CA ALA A1206 " pdb=" C ALA A1206 " pdb=" N HIS A1207 " ideal model delta sigma weight residual 118.43 123.29 -4.86 1.33e+00 5.65e-01 1.34e+01 angle pdb=" C THR A 953 " pdb=" N GLN A 954 " pdb=" CA GLN A 954 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N GLY A 621 " pdb=" CA GLY A 621 " pdb=" C GLY A 621 " ideal model delta sigma weight residual 113.18 120.70 -7.52 2.37e+00 1.78e-01 1.01e+01 angle pdb=" N GLU A 958 " pdb=" CA GLU A 958 " pdb=" C GLU A 958 " ideal model delta sigma weight residual 110.80 117.38 -6.58 2.13e+00 2.20e-01 9.55e+00 ... (remaining 11418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4598 17.84 - 35.67: 414 35.67 - 53.51: 85 53.51 - 71.35: 7 71.35 - 89.19: 7 Dihedral angle restraints: 5111 sinusoidal: 2066 harmonic: 3045 Sorted by residual: dihedral pdb=" CA PRO A 817 " pdb=" C PRO A 817 " pdb=" N LEU A 818 " pdb=" CA LEU A 818 " ideal model delta harmonic sigma weight residual -180.00 -149.40 -30.60 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CA THR A 391 " pdb=" C THR A 391 " pdb=" N ASP A 392 " pdb=" CA ASP A 392 " ideal model delta harmonic sigma weight residual -180.00 -149.59 -30.41 0 5.00e+00 4.00e-02 3.70e+01 dihedral pdb=" CA CYS A1359 " pdb=" C CYS A1359 " pdb=" N PHE A1360 " pdb=" CA PHE A1360 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 5108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 658 0.031 - 0.062: 423 0.062 - 0.094: 133 0.094 - 0.125: 59 0.125 - 0.156: 8 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA VAL A 649 " pdb=" N VAL A 649 " pdb=" C VAL A 649 " pdb=" CB VAL A 649 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ILE A1274 " pdb=" N ILE A1274 " pdb=" C ILE A1274 " pdb=" CB ILE A1274 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ASP A 392 " pdb=" N ASP A 392 " pdb=" C ASP A 392 " pdb=" CB ASP A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1278 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 855 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 856 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 856 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 856 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 606 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 607 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1204 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A1205 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1205 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1205 " 0.023 5.00e-02 4.00e+02 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 413 2.72 - 3.26: 7972 3.26 - 3.81: 11714 3.81 - 4.35: 15023 4.35 - 4.90: 26119 Nonbonded interactions: 61241 Sorted by model distance: nonbonded pdb=" OH TYR A1022 " pdb=" O MET A1090 " model vdw 2.174 2.440 nonbonded pdb=" OG SER A1150 " pdb=" O ALA A1156 " model vdw 2.217 2.440 nonbonded pdb=" O SER A 975 " pdb=" OG SER A 975 " model vdw 2.300 2.440 nonbonded pdb=" O ALA A 489 " pdb=" OG SER A 490 " model vdw 2.317 2.440 nonbonded pdb=" OD1 ASP A 519 " pdb=" N LYS A 520 " model vdw 2.335 2.520 ... (remaining 61236 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: 2.550 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: 6.090 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 24.620 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.007 0.058 8435 Z= 0.434 Angle : 0.768 8.580 11423 Z= 0.435 Chirality : 0.045 0.156 1281 Planarity : 0.005 0.057 1456 Dihedral : 14.307 89.187 3125 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.68 % Favored : 92.02 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.11 (0.21), residues: 1028 helix: -2.15 (0.19), residues: 520 sheet: -2.95 (0.48), residues: 74 loop : -3.34 (0.24), residues: 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.964 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.3179 time to fit residues: 42.3450 Evaluate side-chains 76 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 ASN A 766 HIS A 801 GLN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN A 954 GLN A 994 HIS A1054 ASN A1083 HIS A1226 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 8435 Z= 0.157 Angle : 0.550 6.358 11423 Z= 0.287 Chirality : 0.040 0.145 1281 Planarity : 0.005 0.053 1456 Dihedral : 5.200 29.477 1132 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.03 % Favored : 93.87 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.24), residues: 1028 helix: -0.69 (0.22), residues: 522 sheet: -2.12 (0.54), residues: 74 loop : -2.72 (0.26), residues: 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.914 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.2268 time to fit residues: 29.3393 Evaluate side-chains 80 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 75 time to evaluate : 1.038 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0955 time to fit residues: 2.2736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN A1024 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8435 Z= 0.208 Angle : 0.541 6.546 11423 Z= 0.279 Chirality : 0.040 0.137 1281 Planarity : 0.005 0.051 1456 Dihedral : 5.025 29.275 1132 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.52 % Favored : 93.39 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.25), residues: 1028 helix: -0.03 (0.23), residues: 521 sheet: -1.67 (0.56), residues: 74 loop : -2.48 (0.27), residues: 433 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.980 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 80 average time/residue: 0.2283 time to fit residues: 25.2483 Evaluate side-chains 77 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0935 time to fit residues: 2.2418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8435 Z= 0.254 Angle : 0.562 7.673 11423 Z= 0.288 Chirality : 0.041 0.137 1281 Planarity : 0.005 0.051 1456 Dihedral : 5.068 29.186 1132 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.25), residues: 1028 helix: 0.22 (0.23), residues: 521 sheet: -1.42 (0.58), residues: 74 loop : -2.30 (0.27), residues: 433 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.981 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 82 average time/residue: 0.2107 time to fit residues: 24.7158 Evaluate side-chains 79 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0816 time to fit residues: 2.5527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 0.0020 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1300 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8435 Z= 0.173 Angle : 0.509 6.987 11423 Z= 0.263 Chirality : 0.039 0.142 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.797 28.432 1132 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.03 % Favored : 93.87 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.26), residues: 1028 helix: 0.60 (0.23), residues: 520 sheet: -1.15 (0.59), residues: 74 loop : -2.15 (0.28), residues: 434 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 1.018 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 77 average time/residue: 0.2280 time to fit residues: 24.5476 Evaluate side-chains 71 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0800 time to fit residues: 1.6743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1300 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 8435 Z= 0.196 Angle : 0.521 7.386 11423 Z= 0.268 Chirality : 0.040 0.139 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.791 27.799 1132 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1028 helix: 0.80 (0.23), residues: 515 sheet: -0.96 (0.60), residues: 74 loop : -2.09 (0.28), residues: 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.919 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 75 average time/residue: 0.2320 time to fit residues: 24.2063 Evaluate side-chains 74 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0898 time to fit residues: 2.2060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN A1300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8435 Z= 0.166 Angle : 0.499 7.036 11423 Z= 0.257 Chirality : 0.039 0.141 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.645 27.447 1132 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.46 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.26), residues: 1028 helix: 0.98 (0.23), residues: 518 sheet: -0.81 (0.62), residues: 74 loop : -2.00 (0.28), residues: 436 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.949 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 75 average time/residue: 0.2315 time to fit residues: 24.0488 Evaluate side-chains 71 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0763 time to fit residues: 1.6308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.0570 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8435 Z= 0.211 Angle : 0.530 8.119 11423 Z= 0.270 Chirality : 0.040 0.138 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.710 27.021 1132 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.13 % Favored : 93.77 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.26), residues: 1028 helix: 0.93 (0.23), residues: 519 sheet: -0.83 (0.61), residues: 72 loop : -1.97 (0.28), residues: 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.986 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 74 average time/residue: 0.2120 time to fit residues: 22.2334 Evaluate side-chains 71 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0854 time to fit residues: 1.9448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 494 GLN A 525 HIS A1300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 8435 Z= 0.217 Angle : 0.544 8.221 11423 Z= 0.276 Chirality : 0.040 0.138 1281 Planarity : 0.005 0.050 1456 Dihedral : 4.747 26.933 1132 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1028 helix: 0.87 (0.23), residues: 525 sheet: -0.75 (0.62), residues: 74 loop : -1.86 (0.29), residues: 429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 1.022 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.2210 time to fit residues: 22.8400 Evaluate side-chains 72 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.991 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0791 time to fit residues: 1.5340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 103 optimal weight: 0.0270 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 overall best weight: 0.4454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 8435 Z= 0.139 Angle : 0.498 7.248 11423 Z= 0.253 Chirality : 0.038 0.141 1281 Planarity : 0.004 0.049 1456 Dihedral : 4.446 26.516 1132 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.27), residues: 1028 helix: 1.21 (0.23), residues: 524 sheet: -0.61 (0.63), residues: 74 loop : -1.81 (0.29), residues: 430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.984 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 77 average time/residue: 0.2379 time to fit residues: 25.6318 Evaluate side-chains 69 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.924 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN A 494 GLN A1300 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.136402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107101 restraints weight = 10302.440| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.17 r_work: 0.2968 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 8435 Z= 0.384 Angle : 0.647 9.255 11423 Z= 0.329 Chirality : 0.045 0.138 1281 Planarity : 0.005 0.052 1456 Dihedral : 5.108 26.835 1132 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.30 % Favored : 92.61 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1028 helix: 0.64 (0.23), residues: 523 sheet: -0.84 (0.60), residues: 72 loop : -1.90 (0.28), residues: 433 =============================================================================== Job complete usr+sys time: 1814.90 seconds wall clock time: 33 minutes 29.01 seconds (2009.01 seconds total)