Starting phenix.real_space_refine (version: dev) on Wed Feb 22 23:44:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/02_2023/7bwm_30233.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/02_2023/7bwm_30233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/02_2023/7bwm_30233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/02_2023/7bwm_30233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/02_2023/7bwm_30233.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/02_2023/7bwm_30233.pdb" } resolution = 2.9 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9352 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "A ASP 826": "OD1" <-> "OD2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A PHE 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 909": "OD1" <-> "OD2" Residue "A PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1010": "NH1" <-> "NH2" Residue "A PHE 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1205": "OE1" <-> "OE2" Residue "A ARG 1272": "NH1" <-> "NH2" Residue "A ASP 1362": "OD1" <-> "OD2" Residue "A ARG 1368": "NH1" <-> "NH2" Residue "A GLU 1371": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 9532 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9532 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1219, 9473 Classifications: {'peptide': 1219} Link IDs: {'PCIS': 2, 'PTRANS': 75, 'TRANS': 1141} Chain breaks: 12 Conformer: "B" Number of residues, atoms: 1219, 9473 Classifications: {'peptide': 1219} Link IDs: {'PCIS': 2, 'PTRANS': 75, 'TRANS': 1141} Chain breaks: 12 bond proxies already assigned to first conformer: 9640 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG A 385 " occ=0.70 ... (20 atoms not shown) pdb=" NH2BARG A 385 " occ=0.30 residue: pdb=" N AASN A 911 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 911 " occ=0.50 residue: pdb=" N ATRP A1025 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A1025 " occ=0.50 residue: pdb=" N AGLN A1188 " occ=0.70 ... (16 atoms not shown) pdb=" NE2BGLN A1188 " occ=0.30 residue: pdb=" N AASP A1257 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A1257 " occ=0.50 residue: pdb=" N AGLU A1371 " occ=0.70 ... (16 atoms not shown) pdb=" OE2BGLU A1371 " occ=0.30 Time building chain proxies: 9.78, per 1000 atoms: 1.03 Number of scatterers: 9532 At special positions: 0 Unit cell: (80.04, 100.05, 120.06, 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 8 16.00 O 1853 8.00 N 1674 7.00 C 5997 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: 3.49 Conformation dependent library (CDL) restraints added in 2.5 seconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 15 sheets defined 25.6% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.619A pdb=" N VAL A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.835A pdb=" N VAL A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 209' Processing helix chain 'A' and resid 210 through 213 Processing helix chain 'A' and resid 248 through 254 removed outlier: 3.607A pdb=" N SER A 251 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASN A 252 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 254 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.744A pdb=" N PHE A 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 removed outlier: 3.556A pdb=" N ILE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.899A pdb=" N MET A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.777A pdb=" N THR A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 426 removed outlier: 4.105A pdb=" N ASP A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.821A pdb=" N TRP A 441 " --> pdb=" O HIS A 438 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 442' Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 607 through 610 removed outlier: 3.572A pdb=" N SER A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 611 through 619 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.894A pdb=" N GLY A 633 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 634 " --> pdb=" O PRO A 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 662 through 666 removed outlier: 3.772A pdb=" N GLN A 666 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 753 through 757 removed outlier: 3.511A pdb=" N ASN A 756 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 757 " --> pdb=" O LYS A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 753 through 757' Processing helix chain 'A' and resid 761 through 767 removed outlier: 3.676A pdb=" N ARG A 765 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 767 " --> pdb=" O TYR A 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 767' Processing helix chain 'A' and resid 779 through 785 removed outlier: 3.932A pdb=" N PHE A 783 " --> pdb=" O TRP A 780 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 784 " --> pdb=" O SER A 781 " (cutoff:3.500A) Proline residue: A 785 - end of helix Processing helix chain 'A' and resid 797 through 808 removed outlier: 3.624A pdb=" N ASP A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 804 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 removed outlier: 3.557A pdb=" N ASP A 826 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 981 through 985 removed outlier: 3.524A pdb=" N PHE A 984 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1002 removed outlier: 3.929A pdb=" N GLN A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1023 removed outlier: 3.605A pdb=" N GLN A1023 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1031 Processing helix chain 'A' and resid 1049 through 1059 Processing helix chain 'A' and resid 1067 through 1071 removed outlier: 4.354A pdb=" N THR A1071 " --> pdb=" O SER A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1179 through 1187 Processing helix chain 'A' and resid 1195 through 1201 Processing helix chain 'A' and resid 1218 through 1223 removed outlier: 3.580A pdb=" N LYS A1223 " --> pdb=" O SER A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1263 through 1275 removed outlier: 3.780A pdb=" N VAL A1267 " --> pdb=" O ASP A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1307 removed outlier: 3.534A pdb=" N SER A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1338 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 removed outlier: 3.574A pdb=" N VAL A 92 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 128 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP A 140 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG A 130 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.577A pdb=" N LEU A 201 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 188 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 199 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN A 190 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ARG A 197 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR A 196 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 390 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 377 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE A 388 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA6, first strand: chain 'A' and resid 257 through 259 removed outlier: 5.857A pdb=" N ALA A 286 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 257 through 259 removed outlier: 5.857A pdb=" N ALA A 286 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 319 through 320 removed outlier: 3.681A pdb=" N GLN A 323 " --> pdb=" O GLU A 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 497 Processing sheet with id=AB1, first strand: chain 'A' and resid 574 through 582 removed outlier: 5.110A pdb=" N VAL A 576 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 591 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 578 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 586 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 789 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AB3, first strand: chain 'A' and resid 913 through 914 Processing sheet with id=AB4, first strand: chain 'A' and resid 1006 through 1008 Processing sheet with id=AB5, first strand: chain 'A' and resid 1107 through 1109 removed outlier: 8.658A pdb=" N GLY A1367 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU A1139 " --> pdb=" O GLY A1367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1162 through 1167 removed outlier: 5.466A pdb=" N VAL A1176 " --> pdb=" O ARG A1163 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A1165 " --> pdb=" O GLU A1174 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU A1174 " --> pdb=" O SER A1165 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A1287 " --> pdb=" O MET A1377 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 567 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: 3.22 Time building geometry restraints manager: 3.80 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: 3173 1.34 - 1.46: 1638 1.46 - 1.57: 4947 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 9774 Sorted by residual: bond pdb=" C PHE A 850 " pdb=" N LEU A 851 " ideal model delta sigma weight residual 1.329 1.270 0.059 1.86e-02 2.89e+03 1.01e+01 bond pdb=" C PHE A 722 " pdb=" N VAL A 723 " ideal model delta sigma weight residual 1.329 1.301 0.028 1.31e-02 5.83e+03 4.42e+00 bond pdb=" C SER A 784 " pdb=" N PRO A 785 " ideal model delta sigma weight residual 1.334 1.351 -0.017 8.40e-03 1.42e+04 4.27e+00 bond pdb=" CA SER A 799 " pdb=" C SER A 799 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.35e-02 5.49e+03 2.99e+00 bond pdb=" N HIS A 653 " pdb=" CA HIS A 653 " ideal model delta sigma weight residual 1.456 1.476 -0.020 1.25e-02 6.40e+03 2.65e+00 ... (remaining 9769 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 378 106.99 - 113.75: 5345 113.75 - 120.52: 3610 120.52 - 127.28: 3841 127.28 - 134.04: 157 Bond angle restraints: 13331 Sorted by residual: angle pdb=" N VAL A1363 " pdb=" CA VAL A1363 " pdb=" C VAL A1363 " ideal model delta sigma weight residual 113.71 107.50 6.21 9.50e-01 1.11e+00 4.27e+01 angle pdb=" C THR A 950 " pdb=" CA THR A 950 " pdb=" CB THR A 950 " ideal model delta sigma weight residual 109.83 105.02 4.81 9.90e-01 1.02e+00 2.36e+01 angle pdb=" C SER A 948 " pdb=" N LEU A 949 " pdb=" CA LEU A 949 " ideal model delta sigma weight residual 121.54 130.73 -9.19 1.91e+00 2.74e-01 2.32e+01 angle pdb=" N THR A 950 " pdb=" CA THR A 950 " pdb=" C THR A 950 " ideal model delta sigma weight residual 113.51 120.67 -7.16 1.52e+00 4.33e-01 2.22e+01 angle pdb=" C ASP A 667 " pdb=" N ARG A 668 " pdb=" CA ARG A 668 " ideal model delta sigma weight residual 122.21 111.72 10.49 2.87e+00 1.21e-01 1.34e+01 ... (remaining 13326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5288 16.96 - 33.91: 327 33.91 - 50.87: 107 50.87 - 67.83: 40 67.83 - 84.78: 11 Dihedral angle restraints: 5773 sinusoidal: 2261 harmonic: 3512 Sorted by residual: dihedral pdb=" CA GLN A1282 " pdb=" C GLN A1282 " pdb=" N PRO A1283 " pdb=" CA PRO A1283 " ideal model delta harmonic sigma weight residual 0.00 34.48 -34.48 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA THR A 951 " pdb=" C THR A 951 " pdb=" N GLN A 952 " pdb=" CA GLN A 952 " ideal model delta harmonic sigma weight residual 180.00 146.58 33.42 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA THR A 950 " pdb=" C THR A 950 " pdb=" N THR A 951 " pdb=" CA THR A 951 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 ... (remaining 5770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1005 0.043 - 0.086: 324 0.086 - 0.128: 108 0.128 - 0.171: 6 0.171 - 0.214: 3 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA GLN A 960 " pdb=" N GLN A 960 " pdb=" C GLN A 960 " pdb=" CB GLN A 960 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA THR A 950 " pdb=" N THR A 950 " pdb=" C THR A 950 " pdb=" CB THR A 950 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO A1283 " pdb=" N PRO A1283 " pdb=" C PRO A1283 " pdb=" CB PRO A1283 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 1443 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 973 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 974 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 974 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 974 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1099 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO A1100 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1100 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1100 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 478 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 479 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.020 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 139 2.62 - 3.19: 8094 3.19 - 3.76: 14707 3.76 - 4.33: 22272 4.33 - 4.90: 35629 Nonbonded interactions: 80841 Sorted by model distance: nonbonded pdb=" O THR A 950 " pdb=" OG1 THR A 951 " model vdw 2.048 2.440 nonbonded pdb=" OH TYR A 139 " pdb=" OD1 ASP A 378 " model vdw 2.102 2.440 nonbonded pdb=" O LEU A1271 " pdb=" OG SER A1274 " model vdw 2.150 2.440 nonbonded pdb=" O LEU A 120 " pdb=" OG1 THR A 124 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASP A 142 " pdb=" OG SER A 144 " model vdw 2.193 2.440 ... (remaining 80836 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 5997 2.51 5 N 1674 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 5.170 Check model and map are aligned: 0.150 Process input model: 32.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:13.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.005 0.059 9774 Z= 0.328 Angle : 0.784 10.810 13331 Z= 0.467 Chirality : 0.046 0.214 1446 Planarity : 0.005 0.042 1761 Dihedral : 14.209 84.783 3515 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.78 % Favored : 93.96 % Rotamer Outliers : 7.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.18 % 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: -3.28 (0.20), residues: 1211 helix: -2.75 (0.26), residues: 213 sheet: -1.23 (0.36), residues: 169 loop : -2.38 (0.18), residues: 829 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 118 time to evaluate : 1.075 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 23 residues processed: 183 average time/residue: 1.1487 time to fit residues: 226.0351 Evaluate side-chains 100 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.1271 time to fit residues: 2.1397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 274 GLN A 469 GLN A 490 ASN A 661 ASN A 685 ASN A 716 GLN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 GLN A1279 HIS A1352 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9774 Z= 0.163 Angle : 0.592 10.300 13331 Z= 0.302 Chirality : 0.043 0.210 1446 Planarity : 0.004 0.049 1761 Dihedral : 5.243 33.011 1308 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.05 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.09 % 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: -2.17 (0.22), residues: 1211 helix: -1.48 (0.31), residues: 218 sheet: -0.64 (0.38), residues: 158 loop : -1.68 (0.19), residues: 835 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 84 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 114 average time/residue: 1.1504 time to fit residues: 142.1083 Evaluate side-chains 93 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 1.166 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 2 average time/residue: 0.0880 time to fit residues: 1.8538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 GLN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 9774 Z= 0.299 Angle : 0.651 10.760 13331 Z= 0.331 Chirality : 0.046 0.214 1446 Planarity : 0.005 0.041 1761 Dihedral : 5.340 33.782 1308 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.62 % Favored : 93.29 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.09 % 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: -1.87 (0.22), residues: 1211 helix: -1.16 (0.32), residues: 216 sheet: -0.39 (0.40), residues: 158 loop : -1.51 (0.20), residues: 837 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 80 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 110 average time/residue: 1.1247 time to fit residues: 134.2080 Evaluate side-chains 97 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.0848 time to fit residues: 1.8694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 9774 Z= 0.156 Angle : 0.564 9.316 13331 Z= 0.286 Chirality : 0.043 0.196 1446 Planarity : 0.004 0.063 1761 Dihedral : 4.923 30.540 1308 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.09 % 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: -1.48 (0.22), residues: 1211 helix: -0.69 (0.34), residues: 216 sheet: -0.17 (0.41), residues: 156 loop : -1.28 (0.20), residues: 839 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 1.111 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 104 average time/residue: 1.0680 time to fit residues: 120.5496 Evaluate side-chains 92 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 73 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.0847 time to fit residues: 1.4901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 29 optimal weight: 0.0060 chunk 39 optimal weight: 0.8980 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9774 Z= 0.271 Angle : 0.616 10.121 13331 Z= 0.312 Chirality : 0.045 0.194 1446 Planarity : 0.004 0.049 1761 Dihedral : 5.117 30.929 1308 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.29 % Favored : 93.63 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.48 (0.22), residues: 1211 helix: -0.76 (0.33), residues: 217 sheet: -0.18 (0.41), residues: 158 loop : -1.27 (0.20), residues: 836 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 74 time to evaluate : 1.126 Fit side-chains outliers start: 35 outliers final: 25 residues processed: 103 average time/residue: 1.0944 time to fit residues: 122.9069 Evaluate side-chains 95 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 70 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 0.1290 time to fit residues: 2.4393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9774 Z= 0.166 Angle : 0.567 9.306 13331 Z= 0.287 Chirality : 0.043 0.193 1446 Planarity : 0.004 0.053 1761 Dihedral : 4.874 29.869 1308 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.80 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.26 (0.23), residues: 1211 helix: -0.47 (0.35), residues: 216 sheet: -0.08 (0.41), residues: 156 loop : -1.13 (0.20), residues: 839 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 71 time to evaluate : 1.091 Fit side-chains outliers start: 31 outliers final: 23 residues processed: 98 average time/residue: 1.1297 time to fit residues: 120.5088 Evaluate side-chains 94 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 2 average time/residue: 0.1711 time to fit residues: 2.0455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9774 Z= 0.275 Angle : 0.613 9.925 13331 Z= 0.311 Chirality : 0.045 0.190 1446 Planarity : 0.004 0.054 1761 Dihedral : 5.042 29.496 1308 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.71 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.32 (0.23), residues: 1211 helix: -0.52 (0.34), residues: 216 sheet: -0.14 (0.41), residues: 158 loop : -1.17 (0.20), residues: 837 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 1.059 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 97 average time/residue: 1.0860 time to fit residues: 114.9645 Evaluate side-chains 89 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 0.0940 time to fit residues: 1.6458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 9774 Z= 0.222 Angle : 0.591 9.594 13331 Z= 0.300 Chirality : 0.044 0.191 1446 Planarity : 0.004 0.062 1761 Dihedral : 4.983 29.543 1308 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.23 (0.23), residues: 1211 helix: -0.44 (0.35), residues: 216 sheet: -0.07 (0.41), residues: 156 loop : -1.12 (0.20), residues: 839 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 1.196 Fit side-chains outliers start: 26 outliers final: 21 residues processed: 96 average time/residue: 1.1640 time to fit residues: 121.5034 Evaluate side-chains 90 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 20 residues processed: 1 average time/residue: 0.0944 time to fit residues: 1.6586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 71 optimal weight: 0.0870 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9774 Z= 0.130 Angle : 0.542 8.862 13331 Z= 0.275 Chirality : 0.042 0.190 1446 Planarity : 0.004 0.046 1761 Dihedral : 4.728 29.338 1308 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.03 (0.23), residues: 1211 helix: -0.18 (0.36), residues: 216 sheet: 0.00 (0.41), residues: 156 loop : -0.99 (0.20), residues: 839 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 75 time to evaluate : 1.078 Fit side-chains outliers start: 23 outliers final: 19 residues processed: 96 average time/residue: 1.0752 time to fit residues: 112.8741 Evaluate side-chains 90 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.0915 time to fit residues: 1.6419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.0170 chunk 79 optimal weight: 6.9990 chunk 120 optimal weight: 0.0060 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 9774 Z= 0.243 Angle : 0.594 11.005 13331 Z= 0.300 Chirality : 0.045 0.191 1446 Planarity : 0.004 0.065 1761 Dihedral : 4.878 29.075 1308 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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 (0.23), residues: 1211 helix: -0.29 (0.35), residues: 216 sheet: -0.01 (0.41), residues: 156 loop : -1.04 (0.20), residues: 839 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 1.073 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 88 average time/residue: 1.1293 time to fit residues: 108.8116 Evaluate side-chains 85 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 1.5213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 952 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.163975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127949 restraints weight = 39191.633| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 6.94 r_work: 0.3055 rms_B_bonded: 6.08 restraints_weight: 2.0000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3885 r_free = 0.3885 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3883 r_free = 0.3883 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9774 Z= 0.190 Angle : 0.569 10.807 13331 Z= 0.288 Chirality : 0.044 0.191 1446 Planarity : 0.004 0.041 1761 Dihedral : 4.804 29.199 1308 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -1.07 (0.23), residues: 1211 helix: -0.24 (0.35), residues: 216 sheet: 0.00 (0.41), residues: 156 loop : -1.01 (0.20), residues: 839 =============================================================================== Job complete usr+sys time: 3031.57 seconds wall clock time: 54 minutes 46.00 seconds (3286.00 seconds total)