Starting phenix.real_space_refine on Mon Mar 11 14:59:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/03_2024/7pq5_13587.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/03_2024/7pq5_13587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/03_2024/7pq5_13587.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/03_2024/7pq5_13587.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/03_2024/7pq5_13587.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pq5_13587/03_2024/7pq5_13587.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 5317 2.51 5 N 1557 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 278": "NH1" <-> "NH2" Residue "L ARG 316": "NH1" <-> "NH2" Residue "L GLU 321": "OE1" <-> "OE2" Residue "L ASP 332": "OD1" <-> "OD2" Residue "L ASP 373": "OD1" <-> "OD2" Residue "L GLU 416": "OE1" <-> "OE2" Residue "L TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 458": "OE1" <-> "OE2" Residue "L GLU 468": "OE1" <-> "OE2" Residue "L GLU 495": "OE1" <-> "OE2" Residue "L ARG 516": "NH1" <-> "NH2" Residue "L TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 592": "OE1" <-> "OE2" Residue "L ASP 603": "OD1" <-> "OD2" Residue "L ARG 606": "NH1" <-> "NH2" Residue "L GLU 612": "OE1" <-> "OE2" Residue "L GLU 623": "OE1" <-> "OE2" Residue "L ASP 625": "OD1" <-> "OD2" Residue "L PHE 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 682": "NH1" <-> "NH2" Residue "L ASP 740": "OD1" <-> "OD2" Residue "L ARG 761": "NH1" <-> "NH2" Residue "L GLU 821": "OE1" <-> "OE2" Residue "L ASP 823": "OD1" <-> "OD2" Residue "L ASP 834": "OD1" <-> "OD2" Residue "L ASP 875": "OD1" <-> "OD2" Residue "L GLU 893": "OE1" <-> "OE2" Residue "L ASP 986": "OD1" <-> "OD2" Residue "L ARG 992": "NH1" <-> "NH2" Residue "L ARG 1005": "NH1" <-> "NH2" Residue "L ARG 1031": "NH1" <-> "NH2" Residue "L ARG 1032": "NH1" <-> "NH2" Residue "L ASP 1046": "OD1" <-> "OD2" Residue "L TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 1085": "NH1" <-> "NH2" Residue "L PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1087": "OD1" <-> "OD2" Residue "L GLU 1122": "OE1" <-> "OE2" Residue "L GLU 1168": "OE1" <-> "OE2" Residue "L GLU 1189": "OE1" <-> "OE2" Residue "L ARG 1197": "NH1" <-> "NH2" Residue "L ARG 1202": "NH1" <-> "NH2" Residue "L ASP 1207": "OD1" <-> "OD2" Residue "L ASP 1224": "OD1" <-> "OD2" Residue "L GLU 1294": "OE1" <-> "OE2" Residue "L ASP 1316": "OD1" <-> "OD2" Residue "L PHE 1336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1345": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8512 Number of models: 1 Model: "" Number of chains: 1 Chain: "L" Number of atoms: 8512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 8512 Classifications: {'peptide': 1047} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 998} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.60, per 1000 atoms: 0.54 Number of scatterers: 8512 At special positions: 0 Unit cell: (84.63, 98.58, 122.76, 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 16 16.00 O 1622 8.00 N 1557 7.00 C 5317 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: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 1.1% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'L' and resid 530 through 532 No H-bonds generated for 'chain 'L' and resid 530 through 532' Processing helix chain 'L' and resid 646 through 648 No H-bonds generated for 'chain 'L' and resid 646 through 648' Processing helix chain 'L' and resid 1277 through 1281 Processing sheet with id=AA1, first strand: chain 'L' and resid 300 through 306 removed outlier: 6.600A pdb=" N PHE L 314 " --> pdb=" O ASP L 303 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR L 305 " --> pdb=" O LEU L 312 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU L 312 " --> pdb=" O THR L 305 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLY L 329 " --> pdb=" O VAL L 319 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N GLU L 321 " --> pdb=" O GLY L 327 " (cutoff:3.500A) removed outlier: 11.547A pdb=" N GLY L 327 " --> pdb=" O GLU L 321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 354 through 358 removed outlier: 4.150A pdb=" N CYS L 337 " --> pdb=" O ARG L 348 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU L 398 " --> pdb=" O LEU L 413 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 365 through 366 removed outlier: 4.633A pdb=" N HIS L 387 " --> pdb=" O VAL L 392 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL L 392 " --> pdb=" O HIS L 387 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU L 416 " --> pdb=" O TYR L 395 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR L 436 " --> pdb=" O LEU L 448 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU L 458 " --> pdb=" O LEU L 449 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR L 457 " --> pdb=" O ARG L 472 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG L 472 " --> pdb=" O THR L 457 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE L 459 " --> pdb=" O MET L 470 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS L 474 " --> pdb=" O GLU L 483 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ALA L 482 " --> pdb=" O TYR L 494 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR L 493 " --> pdb=" O TRP L 505 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP L 505 " --> pdb=" O TYR L 493 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU L 495 " --> pdb=" O SER L 503 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER L 503 " --> pdb=" O TYR L 515 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP L 505 " --> pdb=" O VAL L 513 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP L 525 " --> pdb=" O ARG L 516 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N THR L 524 " --> pdb=" O LEU L 537 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR L 544 " --> pdb=" O GLY L 556 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR L 555 " --> pdb=" O ILE L 567 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE L 567 " --> pdb=" O THR L 555 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS L 557 " --> pdb=" O THR L 565 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR L 565 " --> pdb=" O TYR L 577 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL L 586 " --> pdb=" O LEU L 598 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER L 609 " --> pdb=" O THR L 599 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N THR L 608 " --> pdb=" O TYR L 620 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N THR L 630 " --> pdb=" O PRO L 642 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY L 652 " --> pdb=" O GLN L 643 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA L 651 " --> pdb=" O LEU L 663 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU L 663 " --> pdb=" O ALA L 651 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER L 673 " --> pdb=" O THR L 664 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N THR L 672 " --> pdb=" O GLN L 684 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG L 694 " --> pdb=" O GLU L 685 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL L 693 " --> pdb=" O LEU L 705 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG L 714 " --> pdb=" O TRP L 725 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG L 724 " --> pdb=" O SER L 736 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N SER L 736 " --> pdb=" O ARG L 724 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG L 726 " --> pdb=" O ALA L 734 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ALA L 734 " --> pdb=" O PHE L 746 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR L 755 " --> pdb=" O VAL L 767 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA L 777 " --> pdb=" O GLU L 768 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL L 776 " --> pdb=" O TYR L 788 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN L 787 " --> pdb=" O VAL L 800 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL L 800 " --> pdb=" O GLN L 787 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG L 789 " --> pdb=" O THR L 798 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N THR L 798 " --> pdb=" O TYR L 810 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR L 820 " --> pdb=" O THR L 811 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE L 819 " --> pdb=" O TYR L 831 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU L 841 " --> pdb=" O ARG L 832 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE L 840 " --> pdb=" O TYR L 852 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N THR L 861 " --> pdb=" O TYR L 872 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR L 882 " --> pdb=" O HIS L 873 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU L 881 " --> pdb=" O PHE L 892 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER L 888 " --> pdb=" O SER L 885 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR L 889 " --> pdb=" O GLN L 905 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN L 905 " --> pdb=" O THR L 889 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS L 891 " --> pdb=" O GLU L 903 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU L 903 " --> pdb=" O HIS L 891 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU L 893 " --> pdb=" O VAL L 901 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG L 899 " --> pdb=" O ASP L 895 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL L 901 " --> pdb=" O ARG L 912 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY L 908 " --> pdb=" O GLN L 905 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR L 961 " --> pdb=" O GLU L 952 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ILE L 960 " --> pdb=" O ILE L 972 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY L 982 " --> pdb=" O GLU L 973 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR L 981 " --> pdb=" O GLN L 993 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L1003 " --> pdb=" O GLN L 994 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N THR L1002 " --> pdb=" O TYR L1033 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR L1042 " --> pdb=" O TYR L1053 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP L1046 " --> pdb=" O GLN L1049 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER L1063 " --> pdb=" O LEU L1054 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU L1066 " --> pdb=" O LEU L1070 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LEU L1070 " --> pdb=" O GLU L1066 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 1086 through 1087 Processing sheet with id=AA5, first strand: chain 'L' and resid 1098 through 1099 removed outlier: 3.720A pdb=" N ARG L1103 " --> pdb=" O GLN L1099 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 1106 through 1107 removed outlier: 6.066A pdb=" N GLN L1121 " --> pdb=" O TYR L1137 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG L1159 " --> pdb=" O GLU L1168 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR L1167 " --> pdb=" O TYR L1180 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA L1188 " --> pdb=" O HIS L1203 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS L1203 " --> pdb=" O ALA L1188 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE L1190 " --> pdb=" O ILE L1201 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE L1201 " --> pdb=" O ILE L1190 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU L1192 " --> pdb=" O LYS L1199 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL L1212 " --> pdb=" O ALA L1239 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N TYR L1238 " --> pdb=" O LEU L1250 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU L1250 " --> pdb=" O TYR L1238 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL L1240 " --> pdb=" O LEU L1248 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU L1248 " --> pdb=" O ARG L1260 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG L1260 " --> pdb=" O LEU L1248 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU L1250 " --> pdb=" O VAL L1258 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 1290 through 1291 removed outlier: 3.500A pdb=" N CYS L1311 " --> pdb=" O LEU L1306 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 1336 through 1337 272 hydrogen bonds defined for protein. 753 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: 4.23 Time building geometry restraints manager: 2.98 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: 2924 1.34 - 1.46: 1753 1.46 - 1.58: 4029 1.58 - 1.69: 0 1.69 - 1.81: 23 Bond restraints: 8729 Sorted by residual: bond pdb=" N ALA L 602 " pdb=" CA ALA L 602 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.59e+00 bond pdb=" CA ASP L 509 " pdb=" C ASP L 509 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.34e-02 5.57e+03 1.11e+00 bond pdb=" N SER L1083 " pdb=" CA SER L1083 " ideal model delta sigma weight residual 1.459 1.446 0.013 1.22e-02 6.72e+03 1.07e+00 bond pdb=" CA ASP L 509 " pdb=" CB ASP L 509 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 1.00e+00 bond pdb=" CA PHE L1086 " pdb=" CB PHE L1086 " ideal model delta sigma weight residual 1.535 1.555 -0.020 2.09e-02 2.29e+03 9.16e-01 ... (remaining 8724 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.64: 170 105.64 - 112.76: 4227 112.76 - 119.87: 3122 119.87 - 126.99: 4207 126.99 - 134.10: 131 Bond angle restraints: 11857 Sorted by residual: angle pdb=" N LEU L 601 " pdb=" CA LEU L 601 " pdb=" C LEU L 601 " ideal model delta sigma weight residual 108.41 98.53 9.88 1.61e+00 3.86e-01 3.77e+01 angle pdb=" C ALA L 602 " pdb=" N ASP L 603 " pdb=" CA ASP L 603 " ideal model delta sigma weight residual 122.60 113.15 9.45 1.56e+00 4.11e-01 3.67e+01 angle pdb=" N ARG L1084 " pdb=" CA ARG L1084 " pdb=" C ARG L1084 " ideal model delta sigma weight residual 110.80 98.91 11.89 2.13e+00 2.20e-01 3.11e+01 angle pdb=" C LEU L 601 " pdb=" N ALA L 602 " pdb=" CA ALA L 602 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.98e+01 angle pdb=" CA PHE L1086 " pdb=" CB PHE L1086 " pdb=" CG PHE L1086 " ideal model delta sigma weight residual 113.80 117.09 -3.29 1.00e+00 1.00e+00 1.08e+01 ... (remaining 11852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 4621 17.82 - 35.64: 348 35.64 - 53.46: 92 53.46 - 71.28: 30 71.28 - 89.10: 20 Dihedral angle restraints: 5111 sinusoidal: 2106 harmonic: 3005 Sorted by residual: dihedral pdb=" CA ASP L 422 " pdb=" C ASP L 422 " pdb=" N ASN L 423 " pdb=" CA ASN L 423 " ideal model delta harmonic sigma weight residual 180.00 153.75 26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ALA L1355 " pdb=" C ALA L1355 " pdb=" N GLY L1356 " pdb=" CA GLY L1356 " ideal model delta harmonic sigma weight residual 180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA GLY L 556 " pdb=" C GLY L 556 " pdb=" N HIS L 557 " pdb=" CA HIS L 557 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 5108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 886 0.052 - 0.105: 259 0.105 - 0.157: 74 0.157 - 0.210: 2 0.210 - 0.262: 1 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CA PHE L1086 " pdb=" N PHE L1086 " pdb=" C PHE L1086 " pdb=" CB PHE L1086 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA HIS L 907 " pdb=" N HIS L 907 " pdb=" C HIS L 907 " pdb=" CB HIS L 907 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA HIS L1102 " pdb=" N HIS L1102 " pdb=" C HIS L1102 " pdb=" CB HIS L1102 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 1219 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L1081 " 0.059 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO L1082 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO L1082 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO L1082 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 832 " 0.078 9.50e-02 1.11e+02 4.58e-02 1.17e+01 pdb=" NE ARG L 832 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG L 832 " 0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG L 832 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG L 832 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L1086 " -0.029 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE L1086 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE L1086 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE L1086 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE L1086 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE L1086 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE L1086 " -0.006 2.00e-02 2.50e+03 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1687 2.78 - 3.31: 6655 3.31 - 3.84: 12598 3.84 - 4.37: 15803 4.37 - 4.90: 28761 Nonbonded interactions: 65504 Sorted by model distance: nonbonded pdb=" O LEU L 456 " pdb=" OH TYR L 475 " model vdw 2.255 2.440 nonbonded pdb=" OD1 ASP L 916 " pdb=" N ASN L 917 " model vdw 2.268 2.520 nonbonded pdb=" OG1 THR L 511 " pdb=" O PRO L 771 " model vdw 2.284 2.440 nonbonded pdb=" OD1 ASP L 509 " pdb=" N GLN L 510 " model vdw 2.313 2.520 nonbonded pdb=" OD1 ASP L 645 " pdb=" N GLU L 646 " model vdw 2.344 2.520 ... (remaining 65499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.040 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 26.290 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 0.039 8729 Z= 0.305 Angle : 0.852 11.886 11857 Z= 0.491 Chirality : 0.052 0.262 1222 Planarity : 0.006 0.088 1580 Dihedral : 15.553 89.105 3213 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.53 % Favored : 95.27 % Rotamer: Outliers : 2.82 % Allowed : 6.98 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1037 helix: None (None), residues: 0 sheet: 1.40 (0.28), residues: 327 loop : -0.88 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 505 HIS 0.006 0.001 HIS L1203 PHE 0.055 0.003 PHE L1086 TYR 0.021 0.003 TYR L 533 ARG 0.057 0.005 ARG L 832 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 411 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7627 (ttm110) REVERT: L 835 ARG cc_start: 0.8383 (mtt90) cc_final: 0.8164 (mtt90) REVERT: L 885 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8788 (p) REVERT: L 1152 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.5662 (m-30) outliers start: 25 outliers final: 11 residues processed: 106 average time/residue: 0.3063 time to fit residues: 41.1791 Evaluate side-chains 61 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 276 ARG Chi-restraints excluded: chain L residue 377 SER Chi-restraints excluded: chain L residue 411 ARG Chi-restraints excluded: chain L residue 509 ASP Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 662 THR Chi-restraints excluded: chain L residue 876 SER Chi-restraints excluded: chain L residue 885 SER Chi-restraints excluded: chain L residue 925 LEU Chi-restraints excluded: chain L residue 1089 VAL Chi-restraints excluded: chain L residue 1097 LEU Chi-restraints excluded: chain L residue 1152 ASP Chi-restraints excluded: chain L residue 1183 ASP Chi-restraints excluded: chain L residue 1320 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 368 ASN L 371 HIS L 387 HIS L 400 HIS L 455 GLN L 488 GLN L 680 ASN L 848 ASN L 897 GLN L 923 GLN L 967 GLN L1058 ASN L1110 HIS L1195 HIS L1225 ASN L1325 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8729 Z= 0.355 Angle : 0.681 8.693 11857 Z= 0.368 Chirality : 0.047 0.162 1222 Planarity : 0.005 0.045 1580 Dihedral : 7.417 58.106 1233 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.91 % Allowed : 9.80 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.09 (0.25), residues: 1037 helix: None (None), residues: 0 sheet: 1.34 (0.27), residues: 341 loop : -0.64 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 505 HIS 0.004 0.001 HIS L 864 PHE 0.032 0.002 PHE L1086 TYR 0.018 0.002 TYR L 533 ARG 0.005 0.000 ARG L1008 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: L 885 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8673 (p) REVERT: L 1152 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5392 (m-30) outliers start: 17 outliers final: 10 residues processed: 67 average time/residue: 0.2675 time to fit residues: 24.2326 Evaluate side-chains 57 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 365 HIS Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 581 ARG Chi-restraints excluded: chain L residue 662 THR Chi-restraints excluded: chain L residue 780 ASP Chi-restraints excluded: chain L residue 885 SER Chi-restraints excluded: chain L residue 1089 VAL Chi-restraints excluded: chain L residue 1097 LEU Chi-restraints excluded: chain L residue 1145 LEU Chi-restraints excluded: chain L residue 1152 ASP Chi-restraints excluded: chain L residue 1183 ASP Chi-restraints excluded: chain L residue 1320 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 0.0270 chunk 93 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 568 HIS L1289 GLN L1300 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8729 Z= 0.142 Angle : 0.536 6.092 11857 Z= 0.289 Chirality : 0.043 0.142 1222 Planarity : 0.004 0.050 1580 Dihedral : 6.076 58.233 1218 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.91 % Allowed : 10.14 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1037 helix: None (None), residues: 0 sheet: 1.33 (0.27), residues: 344 loop : -0.54 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 505 HIS 0.002 0.001 HIS L 748 PHE 0.019 0.001 PHE L1086 TYR 0.011 0.001 TYR L1193 ARG 0.004 0.000 ARG L1085 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: L 885 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8662 (p) REVERT: L 1152 ASP cc_start: 0.6049 (OUTLIER) cc_final: 0.4636 (m-30) outliers start: 17 outliers final: 7 residues processed: 81 average time/residue: 0.2363 time to fit residues: 26.2151 Evaluate side-chains 59 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 662 THR Chi-restraints excluded: chain L residue 885 SER Chi-restraints excluded: chain L residue 1055 LEU Chi-restraints excluded: chain L residue 1089 VAL Chi-restraints excluded: chain L residue 1097 LEU Chi-restraints excluded: chain L residue 1145 LEU Chi-restraints excluded: chain L residue 1152 ASP Chi-restraints excluded: chain L residue 1161 ASP Chi-restraints excluded: chain L residue 1320 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.0020 chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 83 optimal weight: 0.0050 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 751 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8729 Z= 0.116 Angle : 0.510 7.612 11857 Z= 0.274 Chirality : 0.041 0.140 1222 Planarity : 0.004 0.052 1580 Dihedral : 5.339 54.048 1216 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.24 % Allowed : 11.04 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1037 helix: None (None), residues: 0 sheet: 1.40 (0.28), residues: 341 loop : -0.46 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 505 HIS 0.003 0.000 HIS L 751 PHE 0.012 0.001 PHE L1086 TYR 0.009 0.001 TYR L1193 ARG 0.006 0.000 ARG L1068 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: L 1152 ASP cc_start: 0.6016 (OUTLIER) cc_final: 0.4571 (m-30) outliers start: 11 outliers final: 3 residues processed: 63 average time/residue: 0.2828 time to fit residues: 23.7756 Evaluate side-chains 51 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 662 THR Chi-restraints excluded: chain L residue 1145 LEU Chi-restraints excluded: chain L residue 1152 ASP Chi-restraints excluded: chain L residue 1320 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 8729 Z= 0.399 Angle : 0.617 6.666 11857 Z= 0.333 Chirality : 0.046 0.174 1222 Planarity : 0.005 0.052 1580 Dihedral : 5.456 51.685 1212 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.14 % Allowed : 10.02 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1037 helix: None (None), residues: 0 sheet: 1.25 (0.27), residues: 352 loop : -0.66 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 947 HIS 0.004 0.001 HIS L 387 PHE 0.028 0.002 PHE L1086 TYR 0.016 0.002 TYR L1193 ARG 0.008 0.000 ARG L 946 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: L 1152 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.5106 (m-30) outliers start: 19 outliers final: 7 residues processed: 62 average time/residue: 0.2317 time to fit residues: 20.2077 Evaluate side-chains 52 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 546 SER Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 662 THR Chi-restraints excluded: chain L residue 1145 LEU Chi-restraints excluded: chain L residue 1149 ILE Chi-restraints excluded: chain L residue 1152 ASP Chi-restraints excluded: chain L residue 1320 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.0870 chunk 97 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 923 GLN L 948 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8729 Z= 0.139 Angle : 0.512 5.965 11857 Z= 0.275 Chirality : 0.042 0.152 1222 Planarity : 0.004 0.054 1580 Dihedral : 5.005 49.620 1212 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.01 % Allowed : 10.92 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1037 helix: None (None), residues: 0 sheet: 1.29 (0.27), residues: 346 loop : -0.61 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 505 HIS 0.002 0.000 HIS L 748 PHE 0.015 0.001 PHE L1086 TYR 0.010 0.001 TYR L1193 ARG 0.006 0.000 ARG L1068 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 53 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: L 1152 ASP cc_start: 0.6077 (OUTLIER) cc_final: 0.4559 (m-30) outliers start: 9 outliers final: 4 residues processed: 62 average time/residue: 0.2295 time to fit residues: 20.2445 Evaluate side-chains 53 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 662 THR Chi-restraints excluded: chain L residue 1145 LEU Chi-restraints excluded: chain L residue 1152 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.0020 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 365 HIS L 400 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8729 Z= 0.204 Angle : 0.549 11.532 11857 Z= 0.294 Chirality : 0.043 0.194 1222 Planarity : 0.004 0.053 1580 Dihedral : 4.761 34.431 1210 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.79 % Allowed : 11.15 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.25), residues: 1037 helix: None (None), residues: 0 sheet: 1.27 (0.27), residues: 350 loop : -0.68 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 505 HIS 0.007 0.001 HIS L 365 PHE 0.019 0.001 PHE L1086 TYR 0.011 0.001 TYR L1193 ARG 0.007 0.000 ARG L 946 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: L 1152 ASP cc_start: 0.6207 (OUTLIER) cc_final: 0.4806 (m-30) outliers start: 7 outliers final: 5 residues processed: 52 average time/residue: 0.2457 time to fit residues: 17.8856 Evaluate side-chains 52 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 662 THR Chi-restraints excluded: chain L residue 1145 LEU Chi-restraints excluded: chain L residue 1149 ILE Chi-restraints excluded: chain L residue 1152 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 400 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8729 Z= 0.189 Angle : 0.535 11.093 11857 Z= 0.286 Chirality : 0.042 0.166 1222 Planarity : 0.004 0.054 1580 Dihedral : 4.694 34.873 1210 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.13 % Allowed : 10.70 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1037 helix: None (None), residues: 0 sheet: 1.30 (0.27), residues: 349 loop : -0.69 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 505 HIS 0.002 0.001 HIS L1102 PHE 0.018 0.001 PHE L1086 TYR 0.011 0.001 TYR L1193 ARG 0.008 0.000 ARG L1068 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: L 1152 ASP cc_start: 0.6080 (OUTLIER) cc_final: 0.4614 (m-30) outliers start: 10 outliers final: 7 residues processed: 56 average time/residue: 0.2478 time to fit residues: 19.4666 Evaluate side-chains 52 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 332 ASP Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 502 ILE Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 1145 LEU Chi-restraints excluded: chain L residue 1149 ILE Chi-restraints excluded: chain L residue 1152 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 400 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8729 Z= 0.261 Angle : 0.570 11.352 11857 Z= 0.307 Chirality : 0.043 0.226 1222 Planarity : 0.004 0.054 1580 Dihedral : 4.757 33.749 1209 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.13 % Allowed : 10.92 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1037 helix: None (None), residues: 0 sheet: 1.21 (0.27), residues: 349 loop : -0.72 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 505 HIS 0.003 0.001 HIS L1102 PHE 0.021 0.001 PHE L1086 TYR 0.013 0.001 TYR L1193 ARG 0.008 0.000 ARG L 946 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: L 1152 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.4850 (m-30) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.2598 time to fit residues: 18.9018 Evaluate side-chains 52 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 332 ASP Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 502 ILE Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 1145 LEU Chi-restraints excluded: chain L residue 1149 ILE Chi-restraints excluded: chain L residue 1152 ASP Chi-restraints excluded: chain L residue 1216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 0.2980 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 400 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8729 Z= 0.183 Angle : 0.540 10.845 11857 Z= 0.289 Chirality : 0.042 0.188 1222 Planarity : 0.004 0.055 1580 Dihedral : 4.625 34.605 1209 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.01 % Allowed : 11.37 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1037 helix: None (None), residues: 0 sheet: 1.23 (0.27), residues: 349 loop : -0.68 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 505 HIS 0.002 0.001 HIS L1203 PHE 0.018 0.001 PHE L1086 TYR 0.011 0.001 TYR L1193 ARG 0.008 0.000 ARG L 946 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2074 Ramachandran restraints generated. 1037 Oldfield, 0 Emsley, 1037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: L 1152 ASP cc_start: 0.6082 (OUTLIER) cc_final: 0.4617 (m-30) outliers start: 9 outliers final: 8 residues processed: 52 average time/residue: 0.2602 time to fit residues: 18.8740 Evaluate side-chains 52 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 332 ASP Chi-restraints excluded: chain L residue 341 THR Chi-restraints excluded: chain L residue 432 HIS Chi-restraints excluded: chain L residue 502 ILE Chi-restraints excluded: chain L residue 569 THR Chi-restraints excluded: chain L residue 1145 LEU Chi-restraints excluded: chain L residue 1149 ILE Chi-restraints excluded: chain L residue 1152 ASP Chi-restraints excluded: chain L residue 1216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.3436 > 50: distance: 50 - 103: 6.623 distance: 53 - 100: 6.712 distance: 75 - 76: 3.360 distance: 76 - 77: 10.318 distance: 76 - 82: 4.046 distance: 79 - 81: 6.303 distance: 82 - 83: 4.029 distance: 83 - 86: 3.156 distance: 86 - 87: 3.507 distance: 87 - 89: 4.799 distance: 88 - 90: 8.449 distance: 89 - 91: 6.180 distance: 91 - 92: 5.316 distance: 93 - 94: 4.310 distance: 93 - 180: 6.042 distance: 95 - 96: 3.884 distance: 95 - 100: 6.149 distance: 97 - 99: 4.702 distance: 101 - 102: 4.449 distance: 101 - 104: 5.015 distance: 102 - 103: 3.087 distance: 102 - 108: 6.206 distance: 104 - 105: 5.461 distance: 105 - 106: 4.758 distance: 105 - 107: 4.009 distance: 108 - 109: 6.636 distance: 108 - 165: 7.177 distance: 109 - 110: 5.116 distance: 109 - 112: 5.992 distance: 110 - 111: 4.226 distance: 112 - 113: 6.832 distance: 115 - 118: 5.906 distance: 116 - 117: 12.675 distance: 116 - 125: 6.609 distance: 118 - 119: 4.392 distance: 119 - 120: 7.783 distance: 120 - 121: 6.635 distance: 121 - 122: 7.882 distance: 122 - 123: 3.727 distance: 125 - 126: 16.746 distance: 126 - 127: 21.565 distance: 127 - 128: 37.959 distance: 127 - 129: 9.587 distance: 129 - 130: 9.339 distance: 130 - 131: 16.385 distance: 130 - 133: 11.253 distance: 131 - 132: 13.721 distance: 131 - 138: 11.590 distance: 133 - 134: 13.157 distance: 134 - 135: 16.389 distance: 135 - 136: 23.010 distance: 135 - 137: 3.896 distance: 138 - 139: 4.610 distance: 139 - 140: 5.349 distance: 139 - 142: 5.127 distance: 140 - 141: 10.021 distance: 140 - 147: 6.631 distance: 143 - 144: 4.746 distance: 144 - 145: 7.693 distance: 144 - 146: 10.226 distance: 147 - 148: 5.715 distance: 148 - 149: 7.199 distance: 149 - 150: 9.136 distance: 149 - 151: 3.926 distance: 151 - 205: 3.066