Starting phenix.real_space_refine (version: dev) on Tue Mar 14 01:24:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/03_2023/7myo_24082_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/03_2023/7myo_24082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/03_2023/7myo_24082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/03_2023/7myo_24082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/03_2023/7myo_24082_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7myo_24082/03_2023/7myo_24082_updated.pdb" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 Process input model Symmetric amino acids flipped Residue "B ASP 330": "OD1" <-> "OD2" Residue "B GLU 469": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 939": "OD1" <-> "OD2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1045": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 10634 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2412 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 281} Chain: "A" Number of atoms: 8222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 993, 8137 Unusual residues: {'1LT': 1} Classifications: {'peptide': 992, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945, None: 1} Not linked: pdbres="GLY A1050 " pdbres="1LT A1101 " Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 993, 8137 Unusual residues: {'1LT': 1} Classifications: {'peptide': 992, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 945, None: 1} Not linked: pdbres="GLY A1050 " pdbres="1LT A1101 " Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 8225 Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N AARG A 617 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 617 " occ=0.50 residue: pdb=" N ALYS A 621 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 621 " occ=0.50 residue: pdb=" N AARG A 662 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 662 " occ=0.50 residue: pdb=" N AARG A 899 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 899 " occ=0.50 residue: pdb=" N AARG A 951 " occ=0.63 ... (20 atoms not shown) pdb=" NH2BARG A 951 " occ=0.37 residue: pdb=" N AVAL A 952 " occ=0.63 ... (12 atoms not shown) pdb=" CG2BVAL A 952 " occ=0.37 residue: pdb=" N APRO A 953 " occ=0.63 ... (12 atoms not shown) pdb=" CD BPRO A 953 " occ=0.37 residue: pdb=" N APHE A 954 " occ=0.63 ... (20 atoms not shown) pdb=" CZ BPHE A 954 " occ=0.37 residue: pdb=" N AVAL A 955 " occ=0.63 ... (12 atoms not shown) pdb=" CG2BVAL A 955 " occ=0.37 Time building chain proxies: 10.07, per 1000 atoms: 0.95 Number of scatterers: 10634 At special positions: 0 Unit cell: (89.87, 108.68, 135.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 F 3 9.00 O 1943 8.00 N 1848 7.00 C 6763 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: 4.68 Conformation dependent library (CDL) restraints added in 2.5 seconds 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2466 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 7 sheets defined 44.9% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'B' and resid 340 through 347 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 433 through 435 No H-bonds generated for 'chain 'B' and resid 433 through 435' Processing helix chain 'B' and resid 442 through 507 removed outlier: 4.909A pdb=" N GLU B 507 " --> pdb=" O ARG B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 514 Processing helix chain 'B' and resid 519 through 587 removed outlier: 3.927A pdb=" N LEU B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 532 " --> pdb=" O TYR B 528 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Proline residue: B 568 - end of helix Processing helix chain 'B' and resid 594 through 598 removed outlier: 3.673A pdb=" N LEU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 594 through 598' Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.605A pdb=" N HIS A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 134 through 154 removed outlier: 4.196A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 179 through 182 No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 271 through 279 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 489 through 501 removed outlier: 3.548A pdb=" N VAL A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 535 Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 563 through 570 Proline residue: A 566 - end of helix Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.533A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 602 removed outlier: 4.452A pdb=" N GLU A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A 601 " --> pdb=" O GLN A 597 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 625 through 630 Processing helix chain 'A' and resid 632 through 641 removed outlier: 3.902A pdb=" N LYS A 640 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A 641 " --> pdb=" O GLN A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 658 Processing helix chain 'A' and resid 661 through 674 removed outlier: 3.923A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 694 Processing helix chain 'A' and resid 696 through 720 Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 742 through 748 removed outlier: 3.935A pdb=" N ALA A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 removed outlier: 4.438A pdb=" N GLU A 791 " --> pdb=" O ILE A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 827 Processing helix chain 'A' and resid 857 through 866 Processing helix chain 'A' and resid 876 through 884 Processing helix chain 'A' and resid 887 through 910 removed outlier: 4.448A pdb=" N ASP A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER A 900 " --> pdb=" O PHE A 897 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N CYS A 905 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 906 " --> pdb=" O GLY A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 975 through 1005 removed outlier: 3.987A pdb=" N ARG A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ASN A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 997 " --> pdb=" O GLN A 993 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1026 Processing helix chain 'A' and resid 1032 through 1044 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 36 removed outlier: 3.615A pdb=" N VAL A 32 " --> pdb=" O CYS A 24 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 70 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER A 72 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 207 through 212 removed outlier: 3.531A pdb=" N LYS A 253 " --> pdb=" O MET A 286 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 335 through 338 Processing sheet with id= D, first strand: chain 'A' and resid 353 through 355 removed outlier: 4.391A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 409 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 440 through 444 Processing sheet with id= F, first strand: chain 'A' and resid 779 through 784 Processing sheet with id= G, first strand: chain 'A' and resid 854 through 856 425 hydrogen bonds defined for protein. 1130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1774 1.32 - 1.44: 2816 1.44 - 1.56: 6146 1.56 - 1.69: 2 1.69 - 1.81: 121 Bond restraints: 10859 Sorted by residual: bond pdb=" C3 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 1.391 1.485 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C2 1LT A1101 " pdb=" N1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.458 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C3 1LT A1101 " pdb=" N2 1LT A1101 " ideal model delta sigma weight residual 1.348 1.435 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" N 1LT A1101 " pdb=" C1 1LT A1101 " ideal model delta sigma weight residual 1.368 1.445 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C7 1LT A1101 " pdb=" N2 1LT A1101 " ideal model delta sigma weight residual 1.444 1.520 -0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 10854 not shown) Histogram of bond angle deviations from ideal: 94.34 - 102.38: 54 102.38 - 110.43: 2476 110.43 - 118.47: 5952 118.47 - 126.52: 6006 126.52 - 134.56: 163 Bond angle restraints: 14651 Sorted by residual: angle pdb=" N ASP A1017 " pdb=" CA ASP A1017 " pdb=" C ASP A1017 " ideal model delta sigma weight residual 114.31 108.20 6.11 1.29e+00 6.01e-01 2.25e+01 angle pdb=" C ASP A 939 " pdb=" N HIS A 940 " pdb=" CA HIS A 940 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 angle pdb=" N GLU B 537 " pdb=" CA GLU B 537 " pdb=" CB GLU B 537 " ideal model delta sigma weight residual 110.30 117.00 -6.70 1.54e+00 4.22e-01 1.90e+01 angle pdb=" CB MET A1040 " pdb=" CG MET A1040 " pdb=" SD MET A1040 " ideal model delta sigma weight residual 112.70 125.56 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CG1 ILE A 211 " pdb=" CB ILE A 211 " pdb=" CG2 ILE A 211 " ideal model delta sigma weight residual 110.70 99.90 10.80 3.00e+00 1.11e-01 1.30e+01 ... (remaining 14646 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5879 17.47 - 34.95: 614 34.95 - 52.42: 113 52.42 - 69.89: 29 69.89 - 87.36: 13 Dihedral angle restraints: 6648 sinusoidal: 2845 harmonic: 3803 Sorted by residual: dihedral pdb=" CA LEU A 209 " pdb=" C LEU A 209 " pdb=" N LYS A 210 " pdb=" CA LYS A 210 " ideal model delta harmonic sigma weight residual -180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PHE B 512 " pdb=" C PHE B 512 " pdb=" N LYS B 513 " pdb=" CA LYS B 513 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 262 " pdb=" C LEU A 262 " pdb=" N GLU A 263 " pdb=" CA GLU A 263 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 6645 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1062 0.044 - 0.088: 374 0.088 - 0.132: 117 0.132 - 0.175: 19 0.175 - 0.219: 9 Chirality restraints: 1581 Sorted by residual: chirality pdb=" CB ILE A 921 " pdb=" CA ILE A 921 " pdb=" CG1 ILE A 921 " pdb=" CG2 ILE A 921 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASN A 202 " pdb=" N ASN A 202 " pdb=" C ASN A 202 " pdb=" CB ASN A 202 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1578 not shown) Planarity restraints: 1883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 426 " 0.082 5.00e-02 4.00e+02 1.24e-01 2.44e+01 pdb=" N PRO B 427 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO B 427 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 427 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO A 178 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 457 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO A 458 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " -0.056 5.00e-02 4.00e+02 ... (remaining 1880 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1521 2.76 - 3.29: 10734 3.29 - 3.83: 18443 3.83 - 4.36: 21491 4.36 - 4.90: 35236 Nonbonded interactions: 87425 Sorted by model distance: nonbonded pdb=" O TYR A1038 " pdb=" OE1 GLN A1042 " model vdw 2.225 3.040 nonbonded pdb=" OH TYR A 988 " pdb=" O LEU A1026 " model vdw 2.247 2.440 nonbonded pdb=" OG SER A 499 " pdb=" OE1 GLN A 582 " model vdw 2.253 2.440 nonbonded pdb=" O ASP A 895 " pdb=" OG1 THR A 898 " model vdw 2.257 2.440 nonbonded pdb=" OE2 GLU B 332 " pdb=" OH TYR B 431 " model vdw 2.268 2.440 ... (remaining 87420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 77 5.16 5 C 6763 2.51 5 N 1848 2.21 5 O 1943 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.37 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.290 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: 2.680 Check model and map are aligned: 0.150 Process input model: 35.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 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 0.094 10859 Z= 0.309 Angle : 0.894 12.856 14651 Z= 0.455 Chirality : 0.051 0.219 1581 Planarity : 0.008 0.124 1883 Dihedral : 15.077 87.363 4182 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.22), residues: 1281 helix: -0.71 (0.19), residues: 593 sheet: -1.80 (0.43), residues: 137 loop : -1.73 (0.26), residues: 551 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 1.391 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 305 average time/residue: 1.0752 time to fit residues: 357.6360 Evaluate side-chains 211 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.0020 chunk 32 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 74 optimal weight: 0.0170 chunk 115 optimal weight: 0.9980 overall best weight: 0.3826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS A 661 GLN A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN A 749 GLN A 785 ASN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10859 Z= 0.197 Angle : 0.709 12.005 14651 Z= 0.351 Chirality : 0.043 0.166 1581 Planarity : 0.006 0.084 1883 Dihedral : 5.116 56.910 1423 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 2.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.22), residues: 1281 helix: -0.24 (0.20), residues: 603 sheet: -1.35 (0.46), residues: 123 loop : -1.75 (0.26), residues: 555 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 241 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 250 average time/residue: 0.9597 time to fit residues: 263.5703 Evaluate side-chains 215 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 210 time to evaluate : 1.230 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1223 time to fit residues: 2.2335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.0010 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN A 59 HIS A 170 ASN A 202 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 10859 Z= 0.230 Angle : 0.700 10.592 14651 Z= 0.348 Chirality : 0.044 0.278 1581 Planarity : 0.005 0.074 1883 Dihedral : 4.890 55.741 1423 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1281 helix: 0.08 (0.21), residues: 597 sheet: -1.74 (0.43), residues: 141 loop : -1.59 (0.27), residues: 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 238 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 17 residues processed: 253 average time/residue: 0.9982 time to fit residues: 277.0986 Evaluate side-chains 227 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 210 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 7 residues processed: 10 average time/residue: 0.3589 time to fit residues: 6.3792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 10859 Z= 0.213 Angle : 0.692 10.196 14651 Z= 0.342 Chirality : 0.043 0.217 1581 Planarity : 0.005 0.068 1883 Dihedral : 4.782 55.054 1423 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.23), residues: 1281 helix: 0.17 (0.21), residues: 597 sheet: -1.48 (0.43), residues: 134 loop : -1.50 (0.27), residues: 550 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 228 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 242 average time/residue: 0.9746 time to fit residues: 259.8118 Evaluate side-chains 223 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 210 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.4779 time to fit residues: 5.2280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 84 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 HIS ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 10859 Z= 0.217 Angle : 0.692 9.969 14651 Z= 0.344 Chirality : 0.043 0.173 1581 Planarity : 0.005 0.065 1883 Dihedral : 4.710 53.050 1423 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.99 (0.23), residues: 1281 helix: 0.28 (0.21), residues: 597 sheet: -1.64 (0.43), residues: 137 loop : -1.37 (0.27), residues: 547 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 231 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 14 residues processed: 247 average time/residue: 0.9260 time to fit residues: 252.9426 Evaluate side-chains 235 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 7 average time/residue: 0.4570 time to fit residues: 5.7204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 HIS ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 GLN ** A 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 10859 Z= 0.261 Angle : 0.732 9.958 14651 Z= 0.363 Chirality : 0.044 0.152 1581 Planarity : 0.005 0.064 1883 Dihedral : 4.784 51.498 1423 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.23), residues: 1281 helix: 0.26 (0.21), residues: 600 sheet: -1.72 (0.42), residues: 137 loop : -1.39 (0.27), residues: 544 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 244 average time/residue: 0.9100 time to fit residues: 245.8898 Evaluate side-chains 236 residues out of total 1165 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 221 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 6 residues processed: 9 average time/residue: 0.3876 time to fit residues: 6.1066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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-4893/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-4893/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/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-4893/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-4893/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-4893/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-4893/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: 70.1007 > 50: distance: 90 - 95: 28.029 distance: 95 - 96: 41.267 distance: 95 - 101: 48.436 distance: 96 - 97: 16.257 distance: 96 - 99: 70.101 distance: 97 - 98: 28.410 distance: 97 - 102: 32.775 distance: 102 - 103: 37.672 distance: 103 - 104: 32.777 distance: 103 - 106: 34.919 distance: 104 - 105: 6.444 distance: 104 - 109: 16.027 distance: 106 - 107: 29.449 distance: 106 - 108: 42.633 distance: 109 - 110: 18.286 distance: 109 - 115: 23.851 distance: 110 - 111: 45.408 distance: 110 - 113: 56.064 distance: 111 - 112: 55.883 distance: 111 - 116: 40.552 distance: 113 - 114: 60.950 distance: 114 - 115: 38.704 distance: 116 - 117: 52.046 distance: 117 - 118: 60.776 distance: 117 - 120: 6.432 distance: 118 - 119: 39.751 distance: 118 - 126: 56.456 distance: 120 - 121: 46.064 distance: 121 - 122: 43.037 distance: 121 - 123: 32.201 distance: 122 - 124: 13.806 distance: 123 - 125: 10.254 distance: 124 - 125: 28.653 distance: 126 - 127: 52.250 distance: 127 - 128: 20.288 distance: 128 - 129: 20.852 distance: 128 - 130: 48.769 distance: 130 - 131: 16.777 distance: 131 - 132: 4.871 distance: 131 - 134: 49.123 distance: 132 - 133: 38.174 distance: 132 - 138: 57.803 distance: 134 - 135: 42.577 distance: 135 - 136: 35.848 distance: 135 - 137: 52.287 distance: 138 - 139: 44.428 distance: 139 - 140: 46.613 distance: 139 - 142: 35.070 distance: 140 - 141: 18.894 distance: 140 - 147: 41.389 distance: 142 - 143: 25.068 distance: 143 - 144: 53.119 distance: 144 - 145: 28.902 distance: 144 - 146: 34.607 distance: 147 - 148: 20.980 distance: 148 - 149: 42.076 distance: 148 - 151: 53.408 distance: 149 - 150: 42.403 distance: 149 - 155: 47.027 distance: 151 - 152: 34.573 distance: 152 - 153: 61.288 distance: 152 - 154: 16.912 distance: 155 - 156: 46.425 distance: 156 - 157: 39.607 distance: 156 - 159: 15.452 distance: 157 - 158: 52.117 distance: 157 - 163: 8.500 distance: 159 - 160: 17.249 distance: 160 - 161: 43.923 distance: 160 - 162: 29.552 distance: 163 - 164: 40.491 distance: 165 - 171: 34.414 distance: 167 - 168: 40.219 distance: 168 - 169: 41.627 distance: 168 - 170: 41.070