Starting phenix.real_space_refine (version: dev) on Sun Feb 19 14:29:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/02_2023/3jd8_6640_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/02_2023/3jd8_6640.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/02_2023/3jd8_6640.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/02_2023/3jd8_6640.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/02_2023/3jd8_6640_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd8_6640/02_2023/3jd8_6640_updated.pdb" } resolution = 4.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 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 2193 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 GLU 30": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A GLU 1188": "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: 8050 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7695 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1133, 7694 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 56, 'TRANS': 1068} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1271 Unresolved non-hydrogen angles: 1643 Unresolved non-hydrogen dihedrals: 1110 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 9, 'ASP:plan': 20, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 716 Conformer: "B" Number of residues, atoms: 1133, 7694 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'CIS': 5, 'PCIS': 3, 'PTRANS': 56, 'TRANS': 1068} Chain breaks: 2 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1271 Unresolved non-hydrogen angles: 1643 Unresolved non-hydrogen dihedrals: 1110 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 6, 'TYR:plan': 15, 'ASN:plan1': 14, 'TRP:plan': 9, 'ASP:plan': 20, 'PHE:plan': 37, 'GLU:plan': 10, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 716 bond proxies already assigned to first conformer: 7835 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 182 Unusual residues: {'CLR': 1, 'NAG': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 8.80, per 1000 atoms: 1.09 Number of scatterers: 8050 At special positions: 0 Unit cell: (84.9251, 97.9905, 169.85, 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 42 16.00 O 1597 8.00 N 1336 7.00 C 5075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.05 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.05 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.06 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.04 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.08 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=1.91 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=1.79 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.10 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.07 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 Links applied ALPHA1-6 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG A1318 " - " NAG A1319 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A1303 " - " ASN A 158 " " NAG A1309 " - " ASN A 572 " " NAG A1316 " - " ASN A 122 " " NAG A1317 " - " ASN A 70 " " NAG A1319 " - " ASN A 185 " " NAG A1320 " - " ASN A1064 " " NAG A1322 " - " ASN A 135 " " NAG A1324 " - " ASN A 459 " " NAG B 1 " - " ASN A 222 " " NAG C 1 " - " ASN A 524 " " NAG D 1 " - " ASN A 557 " " NAG E 1 " - " ASN A 598 " Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 4 sheets defined 52.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 53 through 62 removed outlier: 5.026A pdb=" N ASP A 57 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 77 through 94 removed outlier: 4.508A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 261 through 287 Processing helix chain 'A' and resid 331 through 349 removed outlier: 4.173A pdb=" N ASN A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 369 Processing helix chain 'A' and resid 388 through 399 Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 437 through 451 Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 484 through 488 Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 574 through 593 removed outlier: 3.534A pdb=" N ARG A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 616 removed outlier: 4.051A pdb=" N LEU A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 614 " --> pdb=" O GLU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 637 removed outlier: 3.882A pdb=" N THR A 623 " --> pdb=" O SER A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 665 Processing helix chain 'A' and resid 676 through 697 Proline residue: A 681 - end of helix removed outlier: 4.523A pdb=" N LEU A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) Proline residue: A 691 - end of helix removed outlier: 3.797A pdb=" N VAL A 694 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 713 removed outlier: 3.869A pdb=" N ASP A 712 " --> pdb=" O ALA A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 733 removed outlier: 3.514A pdb=" N ARG A 726 " --> pdb=" O GLN A 722 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 731 " --> pdb=" O VAL A 727 " (cutoff:3.500A) Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 742 through 771 removed outlier: 3.521A pdb=" N VAL A 753 " --> pdb=" O GLY A 749 " (cutoff:3.500A) Proline residue: A 755 - end of helix removed outlier: 4.352A pdb=" N SER A 761 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 764 " --> pdb=" O PHE A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 829 Proline residue: A 827 - end of helix Processing helix chain 'A' and resid 832 through 850 Proline residue: A 836 - end of helix Processing helix chain 'A' and resid 865 through 875 Processing helix chain 'A' and resid 894 through 911 Processing helix chain 'A' and resid 931 through 939 Proline residue: A 939 - end of helix Processing helix chain 'A' and resid 987 through 994 removed outlier: 3.527A pdb=" N GLN A 991 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 Processing helix chain 'A' and resid 1048 through 1068 Processing helix chain 'A' and resid 1085 through 1091 removed outlier: 4.429A pdb=" N GLN A1090 " --> pdb=" O VAL A1086 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N TYR A1091 " --> pdb=" O PHE A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1112 Processing helix chain 'A' and resid 1122 through 1143 removed outlier: 3.595A pdb=" N THR A1130 " --> pdb=" O ILE A1126 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A1132 " --> pdb=" O CYS A1128 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A1135 " --> pdb=" O ILE A1131 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN A1137 " --> pdb=" O MET A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1173 removed outlier: 3.828A pdb=" N VAL A1155 " --> pdb=" O ALA A1151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1212 removed outlier: 3.643A pdb=" N HIS A1193 " --> pdb=" O GLU A1189 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1196 " --> pdb=" O ALA A1192 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL A1211 " --> pdb=" O PHE A1207 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1250 removed outlier: 3.773A pdb=" N TYR A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A1227 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A1229 " --> pdb=" O TYR A1225 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A1230 " --> pdb=" O PHE A1226 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A1241 " --> pdb=" O ALA A1237 " (cutoff:3.500A) Proline residue: A1245 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 126 through 130 Processing sheet with id= B, first strand: chain 'A' and resid 204 through 209 removed outlier: 3.552A pdb=" N LEU A 144 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 561 through 567 Processing sheet with id= D, first strand: chain 'A' and resid 454 through 457 390 hydrogen bonds defined for protein. 1125 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: 2.32 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 3489 1.44 - 1.67: 4645 1.67 - 1.90: 60 1.90 - 2.13: 0 2.13 - 2.36: 1 Bond restraints: 8195 Sorted by residual: bond pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.334 2.360 -1.026 2.34e-02 1.83e+03 1.92e+03 bond pdb=" C SER A 940 " pdb=" N SER A 941 " ideal model delta sigma weight residual 1.332 1.657 -0.325 1.40e-02 5.10e+03 5.38e+02 bond pdb=" C LEU A 469 " pdb=" N ALA A 470 " ideal model delta sigma weight residual 1.334 1.216 0.118 1.26e-02 6.30e+03 8.77e+01 bond pdb=" C LEU A1060 " pdb=" N ILE A1061 " ideal model delta sigma weight residual 1.334 1.441 -0.107 1.25e-02 6.40e+03 7.33e+01 bond pdb=" C GLN A 881 " pdb=" N TYR A 882 " ideal model delta sigma weight residual 1.331 1.221 0.111 1.33e-02 5.65e+03 6.93e+01 ... (remaining 8190 not shown) Histogram of bond angle deviations from ideal: 86.79 - 98.15: 2 98.15 - 109.50: 951 109.50 - 120.86: 7447 120.86 - 132.22: 2814 132.22 - 143.58: 20 Bond angle restraints: 11234 Sorted by residual: angle pdb=" CA VAL A 959 " pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 118.88 86.79 32.09 1.54e+00 4.22e-01 4.34e+02 angle pdb=" O VAL A 959 " pdb=" C VAL A 959 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 121.10 143.58 -22.48 1.14e+00 7.69e-01 3.89e+02 angle pdb=" C VAL A 959 " pdb=" N PRO A 984 " pdb=" CA PRO A 984 " ideal model delta sigma weight residual 119.84 98.82 21.02 1.25e+00 6.40e-01 2.83e+02 angle pdb=" N GLN A 881 " pdb=" CA GLN A 881 " pdb=" C GLN A 881 " ideal model delta sigma weight residual 108.86 123.53 -14.67 1.41e+00 5.03e-01 1.08e+02 angle pdb=" N PHE A 995 " pdb=" CA PHE A 995 " pdb=" C PHE A 995 " ideal model delta sigma weight residual 108.34 121.88 -13.54 1.31e+00 5.83e-01 1.07e+02 ... (remaining 11229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 4488 23.14 - 46.27: 213 46.27 - 69.41: 90 69.41 - 92.55: 17 92.55 - 115.69: 1 Dihedral angle restraints: 4809 sinusoidal: 1526 harmonic: 3283 Sorted by residual: dihedral pdb=" CB CYS A 240 " pdb=" SG CYS A 240 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 13.01 79.99 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" C SER A 602 " pdb=" N SER A 602 " pdb=" CA SER A 602 " pdb=" CB SER A 602 " ideal model delta harmonic sigma weight residual -122.60 -102.74 -19.86 0 2.50e+00 1.60e-01 6.31e+01 dihedral pdb=" CA SER A 602 " pdb=" C SER A 602 " pdb=" N PHE A 603 " pdb=" CA PHE A 603 " ideal model delta harmonic sigma weight residual 180.00 -142.67 -37.33 0 5.00e+00 4.00e-02 5.57e+01 ... (remaining 4806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.409: 1394 0.409 - 0.817: 10 0.817 - 1.226: 4 1.226 - 1.634: 2 1.634 - 2.043: 1 Chirality restraints: 1411 Sorted by residual: chirality pdb=" C1 NAG A1318 " pdb=" C2 NAG A1318 " pdb=" O5 NAG A1318 " pdb=" O4 NAG A1319 " both_signs ideal model delta sigma weight residual False -2.40 -0.84 -1.56 2.00e-02 2.50e+03 6.11e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.87 -1.53 2.00e-02 2.50e+03 5.85e+03 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-02 2.50e+03 4.95e+02 ... (remaining 1408 not shown) Planarity restraints: 1465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 572 " 0.132 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" CG ASN A 572 " -0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN A 572 " 0.155 2.00e-02 2.50e+03 pdb=" ND2 ASN A 572 " -0.530 2.00e-02 2.50e+03 pdb=" C1 NAG A1309 " 0.323 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.329 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG D 1 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.501 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.308 2.00e-02 2.50e+03 2.59e-01 8.41e+02 pdb=" C7 NAG D 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.446 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.030 2.00e-02 2.50e+03 ... (remaining 1462 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 40 2.05 - 2.76: 1323 2.76 - 3.47: 12474 3.47 - 4.19: 18775 4.19 - 4.90: 31123 Nonbonded interactions: 63735 Sorted by model distance: nonbonded pdb=" O TRP A 942 " pdb=" CB CYS A1011 " model vdw 1.335 3.440 nonbonded pdb=" CD2 LEU A 656 " pdb=" CB PRO A 755 " model vdw 1.371 3.860 nonbonded pdb=" CG1 VAL A 727 " pdb=" CG1 VAL A1165 " model vdw 1.411 3.880 nonbonded pdb=" CD2 LEU A 680 " pdb=" CE2 TYR A1229 " model vdw 1.470 3.760 nonbonded pdb=" O LEU A 656 " pdb=" CD1 LEU A 751 " model vdw 1.483 3.460 ... (remaining 63730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' } 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 42 5.16 5 C 5075 2.51 5 N 1336 2.21 5 O 1597 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 2.500 Check model and map are aligned: 0.130 Process input model: 28.670 Find NCS groups from input model: 0.260 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 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 : 0.015 1.026 8195 Z= 0.992 Angle : 1.544 32.094 11234 Z= 1.044 Chirality : 0.127 2.043 1411 Planarity : 0.016 0.285 1453 Dihedral : 16.743 115.687 2658 Min Nonbonded Distance : 1.335 Molprobity Statistics. All-atom Clashscore : 78.07 Ramachandran Plot: Outliers : 8.36 % Allowed : 11.91 % Favored : 79.73 % Rotamer Outliers : 11.82 % Cbeta Deviations : 0.47 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.27 (0.23), residues: 1125 helix: -1.35 (0.20), residues: 546 sheet: -0.69 (0.56), residues: 85 loop : -3.45 (0.27), residues: 494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 248 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 25 residues processed: 290 average time/residue: 0.2172 time to fit residues: 83.3609 Evaluate side-chains 174 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 149 time to evaluate : 0.880 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 3 residues processed: 25 average time/residue: 0.1308 time to fit residues: 5.9942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 0.3980 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 106 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.093 8195 Z= 0.379 Angle : 1.020 15.383 11234 Z= 0.527 Chirality : 0.067 0.987 1411 Planarity : 0.006 0.073 1453 Dihedral : 7.476 105.764 1349 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 1.77 % Allowed : 9.32 % Favored : 88.91 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.72 (0.25), residues: 1127 helix: 0.19 (0.22), residues: 566 sheet: -0.11 (0.57), residues: 82 loop : -3.09 (0.28), residues: 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 193 average time/residue: 0.1722 time to fit residues: 47.2499 Evaluate side-chains 132 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 85 optimal weight: 30.0000 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN A 150 GLN A 154 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 8195 Z= 0.299 Angle : 0.868 14.116 11234 Z= 0.442 Chirality : 0.059 0.820 1411 Planarity : 0.007 0.159 1453 Dihedral : 6.953 102.736 1349 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 1.42 % Allowed : 9.94 % Favored : 88.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.09 (0.26), residues: 1127 helix: 0.64 (0.23), residues: 584 sheet: -0.32 (0.62), residues: 78 loop : -2.66 (0.29), residues: 465 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1606 time to fit residues: 38.8542 Evaluate side-chains 120 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 90 optimal weight: 40.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8195 Z= 0.276 Angle : 0.798 10.855 11234 Z= 0.409 Chirality : 0.055 0.770 1411 Planarity : 0.005 0.064 1453 Dihedral : 6.755 100.877 1349 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 1.24 % Allowed : 8.61 % Favored : 90.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 1127 helix: 0.76 (0.22), residues: 586 sheet: -0.76 (0.61), residues: 70 loop : -2.55 (0.28), residues: 471 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1729 time to fit residues: 38.6555 Evaluate side-chains 116 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 30.0000 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.6986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.095 8195 Z= 0.401 Angle : 0.881 10.800 11234 Z= 0.458 Chirality : 0.055 0.723 1411 Planarity : 0.006 0.060 1453 Dihedral : 7.041 99.648 1349 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 1.24 % Allowed : 9.32 % Favored : 89.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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 (0.25), residues: 1127 helix: 0.39 (0.22), residues: 595 sheet: -1.84 (0.51), residues: 89 loop : -2.46 (0.30), residues: 443 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1812 time to fit residues: 34.5392 Evaluate side-chains 104 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 26 optimal weight: 0.0060 chunk 109 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 0.0370 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.0078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.7122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8195 Z= 0.224 Angle : 0.778 11.977 11234 Z= 0.384 Chirality : 0.052 0.715 1411 Planarity : 0.005 0.061 1453 Dihedral : 6.576 96.623 1349 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 1.15 % Allowed : 7.72 % Favored : 91.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.91 (0.26), residues: 1127 helix: 0.81 (0.22), residues: 592 sheet: -1.75 (0.52), residues: 87 loop : -2.34 (0.29), residues: 448 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1696 time to fit residues: 36.1742 Evaluate side-chains 112 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 79 optimal weight: 30.0000 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.7418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 8195 Z= 0.230 Angle : 0.761 10.213 11234 Z= 0.382 Chirality : 0.049 0.607 1411 Planarity : 0.005 0.062 1453 Dihedral : 6.509 97.395 1349 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 1.24 % Allowed : 7.63 % Favored : 91.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 1127 helix: 0.98 (0.22), residues: 591 sheet: -1.91 (0.50), residues: 89 loop : -2.31 (0.30), residues: 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1675 time to fit residues: 32.7070 Evaluate side-chains 106 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 40.0000 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 85 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8195 Z= 0.205 Angle : 0.748 10.933 11234 Z= 0.371 Chirality : 0.047 0.574 1411 Planarity : 0.005 0.063 1453 Dihedral : 6.330 95.944 1349 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 1.06 % Allowed : 7.90 % Favored : 91.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % 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: -0.66 (0.26), residues: 1127 helix: 1.04 (0.22), residues: 596 sheet: -1.99 (0.48), residues: 99 loop : -2.21 (0.31), residues: 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.087 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1669 time to fit residues: 34.7833 Evaluate side-chains 113 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 107 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.7870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 8195 Z= 0.240 Angle : 0.766 10.758 11234 Z= 0.387 Chirality : 0.048 0.578 1411 Planarity : 0.005 0.064 1453 Dihedral : 6.314 96.750 1349 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.16 % Favored : 91.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % 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: -0.61 (0.26), residues: 1127 helix: 1.06 (0.22), residues: 588 sheet: -2.00 (0.50), residues: 90 loop : -2.10 (0.30), residues: 449 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1733 time to fit residues: 33.7451 Evaluate side-chains 103 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.0010 chunk 74 optimal weight: 30.0000 chunk 112 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 89 optimal weight: 0.4980 chunk 9 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 54 optimal weight: 10.0000 chunk 71 optimal weight: 50.0000 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 overall best weight: 2.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.8120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8195 Z= 0.222 Angle : 0.754 9.998 11234 Z= 0.377 Chirality : 0.048 0.563 1411 Planarity : 0.005 0.062 1453 Dihedral : 6.225 95.870 1349 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.90 % Favored : 91.22 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % 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: -0.54 (0.27), residues: 1127 helix: 1.18 (0.23), residues: 587 sheet: -2.11 (0.47), residues: 99 loop : -2.12 (0.31), residues: 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1756 time to fit residues: 34.2701 Evaluate side-chains 106 residues out of total 982 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 0.0050 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 11 optimal weight: 50.0000 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.079951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.065092 restraints weight = 51158.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.066098 restraints weight = 38976.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.066834 restraints weight = 31407.597| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.8369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 8195 Z= 0.227 Angle : 0.744 10.140 11234 Z= 0.376 Chirality : 0.047 0.553 1411 Planarity : 0.005 0.061 1453 Dihedral : 6.228 96.244 1349 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.52 % Favored : 90.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.47 % 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: -0.63 (0.26), residues: 1127 helix: 1.11 (0.22), residues: 594 sheet: -2.31 (0.46), residues: 99 loop : -2.15 (0.31), residues: 434 =============================================================================== Job complete usr+sys time: 1667.71 seconds wall clock time: 31 minutes 33.70 seconds (1893.70 seconds total)