Starting phenix.real_space_refine on Thu Jan 18 08:00:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/01_2024/7nur_12600.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/01_2024/7nur_12600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.125 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/01_2024/7nur_12600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/01_2024/7nur_12600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/01_2024/7nur_12600.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nur_12600/01_2024/7nur_12600.pdb" } resolution = 3.125 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5307 2.51 5 N 1417 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A ASP 392": "OD1" <-> "OD2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A ASP 434": "OD1" <-> "OD2" Residue "A GLU 444": "OE1" <-> "OE2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 609": "OE1" <-> "OE2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 648": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A GLU 686": "OE1" <-> "OE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A ARG 761": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A PHE 949": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "A GLU 1015": "OE1" <-> "OE2" Residue "A ARG 1017": "NH1" <-> "NH2" Residue "A TYR 1022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A ARG 1080": "NH1" <-> "NH2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A ASP 1225": "OD1" <-> "OD2" Residue "A PHE 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1251": "NH1" <-> "NH2" Residue "A PHE 1288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1298": "OD1" <-> "OD2" Residue "A PHE 1304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1307": "OE1" <-> "OE2" Residue "A ASP 1338": "OD1" <-> "OD2" Residue "A ASP 1346": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8245 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8245 Classifications: {'peptide': 1044} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 61, 'TRANS': 982} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 4.80, per 1000 atoms: 0.58 Number of scatterers: 8245 At special positions: 0 Unit cell: (89.712, 98.256, 120.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1490 8.00 N 1417 7.00 C 5307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 727 " distance=2.03 Simple disulfide: pdb=" SG CYS A1301 " - pdb=" SG CYS A1359 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 54.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 308 through 317 removed outlier: 4.288A pdb=" N GLN A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.610A pdb=" N GLY A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 4.007A pdb=" N ARG A 404 " --> pdb=" O LYS A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 421 removed outlier: 3.810A pdb=" N ARG A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 4.000A pdb=" N ILE A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 479 removed outlier: 4.058A pdb=" N THR A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 464 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN A 470 " --> pdb=" O THR A 466 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA A 477 " --> pdb=" O LYS A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.671A pdb=" N SER A 484 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.969A pdb=" N TYR A 498 " --> pdb=" O GLN A 494 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 565 removed outlier: 4.193A pdb=" N LEU A 561 " --> pdb=" O GLY A 557 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU A 563 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 578 removed outlier: 3.697A pdb=" N LEU A 571 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 576 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.674A pdb=" N GLU A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 removed outlier: 3.969A pdb=" N TYR A 662 " --> pdb=" O SER A 658 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 663 " --> pdb=" O TYR A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 703 through 709 Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.884A pdb=" N TYR A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE A 728 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 743 through 754 Processing helix chain 'A' and resid 763 through 783 Processing helix chain 'A' and resid 792 through 802 Processing helix chain 'A' and resid 804 through 813 Processing helix chain 'A' and resid 824 through 834 removed outlier: 3.561A pdb=" N LEU A 831 " --> pdb=" O SER A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 849 removed outlier: 3.582A pdb=" N TYR A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 860 removed outlier: 3.521A pdb=" N PHE A 860 " --> pdb=" O TYR A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 891 Processing helix chain 'A' and resid 896 through 908 Processing helix chain 'A' and resid 914 through 928 removed outlier: 3.890A pdb=" N VAL A 918 " --> pdb=" O GLY A 914 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR A 920 " --> pdb=" O ARG A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 941 through 950 removed outlier: 3.562A pdb=" N TYR A 947 " --> pdb=" O VAL A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 973 Processing helix chain 'A' and resid 982 through 1012 removed outlier: 3.814A pdb=" N SER A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 996 " --> pdb=" O LYS A 992 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1028 removed outlier: 3.738A pdb=" N GLY A1028 " --> pdb=" O GLN A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1052 removed outlier: 4.123A pdb=" N SER A1048 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1074 Processing helix chain 'A' and resid 1075 through 1082 removed outlier: 3.879A pdb=" N LYS A1081 " --> pdb=" O ALA A1077 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1086 Processing helix chain 'A' and resid 1092 through 1111 removed outlier: 3.655A pdb=" N VAL A1106 " --> pdb=" O ALA A1102 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR A1107 " --> pdb=" O ALA A1103 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A1108 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG A1109 " --> pdb=" O ARG A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1129 through 1134 removed outlier: 3.848A pdb=" N LYS A1133 " --> pdb=" O ALA A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 removed outlier: 3.679A pdb=" N SER A1150 " --> pdb=" O ARG A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1157 through 1185 removed outlier: 3.576A pdb=" N GLU A1163 " --> pdb=" O PRO A1159 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP A1168 " --> pdb=" O MET A1164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1180 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A1181 " --> pdb=" O ALA A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1240 removed outlier: 4.290A pdb=" N ARG A1228 " --> pdb=" O ALA A1224 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP A1236 " --> pdb=" O ARG A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1294 removed outlier: 3.621A pdb=" N GLN A1287 " --> pdb=" O LEU A1283 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A1288 " --> pdb=" O GLN A1284 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A1289 " --> pdb=" O PHE A1285 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A1294 " --> pdb=" O THR A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1303 removed outlier: 3.772A pdb=" N ARG A1302 " --> pdb=" O PRO A1299 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A1303 " --> pdb=" O GLN A1300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1299 through 1303' Processing helix chain 'A' and resid 1328 through 1332 Processing helix chain 'A' and resid 1363 through 1368 Processing sheet with id=AA1, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.993A pdb=" N LEU A 324 " --> pdb=" O LYS A 518 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TRP A 526 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 366 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 528 " --> pdb=" O LYS A 364 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 334 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 591 through 592 Processing sheet with id=AA3, first strand: chain 'A' and resid 601 through 604 Processing sheet with id=AA4, first strand: chain 'A' and resid 1246 through 1256 removed outlier: 5.011A pdb=" N GLU A1268 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1307 through 1309 348 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2649 1.34 - 1.46: 1638 1.46 - 1.58: 4093 1.58 - 1.70: 0 1.70 - 1.81: 55 Bond restraints: 8435 Sorted by residual: bond pdb=" CA GLU A 858 " pdb=" C GLU A 858 " ideal model delta sigma weight residual 1.523 1.481 0.043 1.80e-02 3.09e+03 5.59e+00 bond pdb=" CA ARG A 916 " pdb=" C ARG A 916 " ideal model delta sigma weight residual 1.522 1.489 0.032 1.72e-02 3.38e+03 3.55e+00 bond pdb=" CB THR A 881 " pdb=" CG2 THR A 881 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.10e+00 bond pdb=" CB VAL A 919 " pdb=" CG1 VAL A 919 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.77e+00 bond pdb=" N LYS A 940 " pdb=" CA LYS A 940 " ideal model delta sigma weight residual 1.456 1.472 -0.016 1.23e-02 6.61e+03 1.77e+00 ... (remaining 8430 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.47: 280 106.47 - 113.38: 4573 113.38 - 120.28: 3292 120.28 - 127.19: 3182 127.19 - 134.10: 96 Bond angle restraints: 11423 Sorted by residual: angle pdb=" CA PHE A1062 " pdb=" C PHE A1062 " pdb=" N PRO A1063 " ideal model delta sigma weight residual 117.82 120.83 -3.01 7.80e-01 1.64e+00 1.49e+01 angle pdb=" CA ALA A1206 " pdb=" C ALA A1206 " pdb=" N HIS A1207 " ideal model delta sigma weight residual 118.43 123.29 -4.86 1.33e+00 5.65e-01 1.34e+01 angle pdb=" C THR A 953 " pdb=" N GLN A 954 " pdb=" CA GLN A 954 " ideal model delta sigma weight residual 121.54 127.90 -6.36 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N GLY A 621 " pdb=" CA GLY A 621 " pdb=" C GLY A 621 " ideal model delta sigma weight residual 113.18 120.70 -7.52 2.37e+00 1.78e-01 1.01e+01 angle pdb=" N GLU A 958 " pdb=" CA GLU A 958 " pdb=" C GLU A 958 " ideal model delta sigma weight residual 110.80 117.38 -6.58 2.13e+00 2.20e-01 9.55e+00 ... (remaining 11418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4598 17.84 - 35.67: 414 35.67 - 53.51: 85 53.51 - 71.35: 7 71.35 - 89.19: 7 Dihedral angle restraints: 5111 sinusoidal: 2066 harmonic: 3045 Sorted by residual: dihedral pdb=" CA PRO A 817 " pdb=" C PRO A 817 " pdb=" N LEU A 818 " pdb=" CA LEU A 818 " ideal model delta harmonic sigma weight residual -180.00 -149.40 -30.60 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" CA THR A 391 " pdb=" C THR A 391 " pdb=" N ASP A 392 " pdb=" CA ASP A 392 " ideal model delta harmonic sigma weight residual -180.00 -149.59 -30.41 0 5.00e+00 4.00e-02 3.70e+01 dihedral pdb=" CA CYS A1359 " pdb=" C CYS A1359 " pdb=" N PHE A1360 " pdb=" CA PHE A1360 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 5108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 658 0.031 - 0.062: 423 0.062 - 0.094: 133 0.094 - 0.125: 59 0.125 - 0.156: 8 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA VAL A 649 " pdb=" N VAL A 649 " pdb=" C VAL A 649 " pdb=" CB VAL A 649 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ILE A1274 " pdb=" N ILE A1274 " pdb=" C ILE A1274 " pdb=" CB ILE A1274 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA ASP A 392 " pdb=" N ASP A 392 " pdb=" C ASP A 392 " pdb=" CB ASP A 392 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1278 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 855 " 0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 856 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 856 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 856 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 606 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 607 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1204 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A1205 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1205 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1205 " 0.023 5.00e-02 4.00e+02 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 413 2.72 - 3.26: 7972 3.26 - 3.81: 11714 3.81 - 4.35: 15023 4.35 - 4.90: 26119 Nonbonded interactions: 61241 Sorted by model distance: nonbonded pdb=" OH TYR A1022 " pdb=" O MET A1090 " model vdw 2.174 2.440 nonbonded pdb=" OG SER A1150 " pdb=" O ALA A1156 " model vdw 2.217 2.440 nonbonded pdb=" O SER A 975 " pdb=" OG SER A 975 " model vdw 2.300 2.440 nonbonded pdb=" O ALA A 489 " pdb=" OG SER A 490 " model vdw 2.317 2.440 nonbonded pdb=" OD1 ASP A 519 " pdb=" N LYS A 520 " model vdw 2.335 2.520 ... (remaining 61236 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.740 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.520 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 8435 Z= 0.434 Angle : 0.768 8.580 11423 Z= 0.435 Chirality : 0.045 0.156 1281 Planarity : 0.005 0.057 1456 Dihedral : 14.307 89.187 3125 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.68 % Favored : 92.02 % Rotamer: Outliers : 0.11 % Allowed : 9.81 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.21), residues: 1028 helix: -2.15 (0.19), residues: 520 sheet: -2.95 (0.48), residues: 74 loop : -3.34 (0.24), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 326 HIS 0.007 0.001 HIS A 804 PHE 0.016 0.002 PHE A 457 TYR 0.016 0.002 TYR A 774 ARG 0.008 0.001 ARG A 648 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 0.884 Fit side-chains REVERT: A 399 ILE cc_start: 0.6268 (OUTLIER) cc_final: 0.6013 (mt) REVERT: A 846 GLN cc_start: 0.7513 (tp-100) cc_final: 0.7218 (mt0) REVERT: A 1232 ARG cc_start: 0.7297 (ttm-80) cc_final: 0.7068 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 106 average time/residue: 0.3130 time to fit residues: 41.7333 Evaluate side-chains 77 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 558 ASN A 766 HIS A 801 GLN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 ASN A 954 GLN A 994 HIS A1054 ASN A1083 HIS A1226 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8435 Z= 0.158 Angle : 0.549 6.343 11423 Z= 0.287 Chirality : 0.040 0.146 1281 Planarity : 0.005 0.052 1456 Dihedral : 5.327 33.175 1134 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.03 % Favored : 93.87 % Rotamer: Outliers : 0.91 % Allowed : 13.34 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.24), residues: 1028 helix: -0.70 (0.22), residues: 522 sheet: -2.14 (0.53), residues: 74 loop : -2.73 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1218 HIS 0.004 0.001 HIS A 988 PHE 0.012 0.001 PHE A 808 TYR 0.013 0.001 TYR A 774 ARG 0.002 0.000 ARG A1009 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.985 Fit side-chains REVERT: A 1218 TRP cc_start: 0.8549 (m100) cc_final: 0.8076 (m-10) REVERT: A 1237 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6378 (tm-30) outliers start: 8 outliers final: 5 residues processed: 93 average time/residue: 0.2183 time to fit residues: 28.0574 Evaluate side-chains 79 residues out of total 890 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 382 GLN Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1308 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 58.8782 > 50: distance: 41 - 149: 20.681 distance: 86 - 89: 9.503 distance: 90 - 91: 20.333 distance: 90 - 93: 15.753 distance: 91 - 92: 23.502 distance: 91 - 96: 14.295 distance: 93 - 94: 27.052 distance: 93 - 95: 19.794 distance: 96 - 97: 4.499 distance: 97 - 98: 14.574 distance: 97 - 100: 10.400 distance: 98 - 99: 4.534 distance: 98 - 104: 10.344 distance: 100 - 101: 10.248 distance: 101 - 102: 14.611 distance: 101 - 103: 12.502 distance: 104 - 105: 13.061 distance: 104 - 110: 9.484 distance: 105 - 108: 10.608 distance: 106 - 107: 8.257 distance: 106 - 111: 6.429 distance: 108 - 109: 15.677 distance: 109 - 110: 13.792 distance: 111 - 112: 12.145 distance: 112 - 113: 11.114 distance: 112 - 115: 12.082 distance: 113 - 114: 6.932 distance: 113 - 116: 11.157 distance: 116 - 117: 3.929 distance: 117 - 120: 4.752 distance: 118 - 119: 6.359 distance: 121 - 122: 13.210 distance: 122 - 123: 18.204 distance: 122 - 125: 23.572 distance: 123 - 124: 11.050 distance: 123 - 128: 23.322 distance: 125 - 126: 11.532 distance: 126 - 127: 29.520 distance: 128 - 129: 8.697 distance: 129 - 130: 9.119 distance: 129 - 132: 11.708 distance: 130 - 131: 6.481 distance: 130 - 136: 5.469 distance: 132 - 133: 7.422 distance: 133 - 134: 16.269 distance: 133 - 135: 14.327 distance: 136 - 137: 11.700 distance: 137 - 138: 6.190 distance: 137 - 140: 4.728 distance: 138 - 139: 20.922 distance: 138 - 144: 8.878 distance: 140 - 141: 8.860 distance: 141 - 142: 12.931 distance: 141 - 143: 13.604 distance: 144 - 145: 8.798 distance: 145 - 146: 4.776 distance: 145 - 148: 9.663 distance: 146 - 147: 6.973 distance: 146 - 150: 6.405 distance: 148 - 149: 21.939 distance: 150 - 151: 9.001 distance: 151 - 152: 9.962 distance: 152 - 153: 22.094 distance: 154 - 155: 11.358 distance: 155 - 156: 9.105 distance: 155 - 157: 6.143 distance: 156 - 158: 10.045 distance: 157 - 159: 8.761 distance: 158 - 160: 9.417 distance: 159 - 160: 10.423