Starting phenix.real_space_refine on Sat Jul 20 03:56:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/07_2024/8seb_40409.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/07_2024/8seb_40409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/07_2024/8seb_40409.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/07_2024/8seb_40409.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/07_2024/8seb_40409.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8seb_40409/07_2024/8seb_40409.cif" } resolution = 3.24 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= 0.018 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 36 5.16 5 C 6106 2.51 5 N 1687 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9609 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7693 Classifications: {'peptide': 989} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 923} Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 5.73, per 1000 atoms: 0.60 Number of scatterers: 9609 At special positions: 0 Unit cell: (103.317, 96.6512, 112.482, 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 36 16.00 P 1 15.00 O 1779 8.00 N 1687 7.00 C 6106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS C 86 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.85 Conformation dependent library (CDL) restraints added in 1.8 seconds 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 44.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.731A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.696A pdb=" N ASP A 71 " --> pdb=" O CYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.874A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 266 through 273 removed outlier: 3.885A pdb=" N LEU A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 357 through 378 Processing helix chain 'A' and resid 392 through 395 removed outlier: 3.726A pdb=" N LEU A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 423 through 432 Processing helix chain 'A' and resid 441 through 455 Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.725A pdb=" N GLU A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.354A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.219A pdb=" N VAL A 601 " --> pdb=" O PRO A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 623 Processing helix chain 'A' and resid 624 through 630 removed outlier: 4.354A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 4.318A pdb=" N ALA A 636 " --> pdb=" O HIS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 653 removed outlier: 4.042A pdb=" N THR A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 656 No H-bonds generated for 'chain 'A' and resid 654 through 656' Processing helix chain 'A' and resid 669 through 682 removed outlier: 3.915A pdb=" N HIS A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 721 through 740 removed outlier: 3.649A pdb=" N LEU A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 757 removed outlier: 3.634A pdb=" N LEU A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.832A pdb=" N MET A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.981A pdb=" N GLN A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 815 removed outlier: 3.503A pdb=" N ASN A 815 " --> pdb=" O ASP A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 812 through 815' Processing helix chain 'A' and resid 816 through 832 removed outlier: 3.684A pdb=" N GLN A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 843 Processing helix chain 'A' and resid 853 through 872 removed outlier: 3.721A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.594A pdb=" N LYS C 49 " --> pdb=" O TYR C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.619A pdb=" N PHE C 136 " --> pdb=" O ASN C 132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.667A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.667A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.168A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 212 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA A 252 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 214 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY A 250 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY A 216 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 248 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ARG A 249 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS A 183 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 251 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 236 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 509 through 512 removed outlier: 7.052A pdb=" N LEU A 464 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU A 512 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 466 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 436 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA A 538 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 438 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA7, first strand: chain 'A' and resid 917 through 920 removed outlier: 6.154A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 945 " --> pdb=" O SER A 995 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ARG A 944 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 955 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 98 Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 27 removed outlier: 5.718A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1251 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: 3.41 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2854 1.33 - 1.45: 1466 1.45 - 1.57: 5473 1.57 - 1.69: 4 1.69 - 1.81: 54 Bond restraints: 9851 Sorted by residual: bond pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 1.415 1.621 -0.206 1.50e-02 4.44e+03 1.88e+02 bond pdb=" C1' AMP B 201 " pdb=" C2' AMP B 201 " ideal model delta sigma weight residual 1.526 1.363 0.163 1.50e-02 4.44e+03 1.18e+02 bond pdb=" C4' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 1.454 1.292 0.162 1.50e-02 4.44e+03 1.17e+02 bond pdb=" C6 AMP B 201 " pdb=" N6 AMP B 201 " ideal model delta sigma weight residual 1.355 1.496 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C4 AMP B 201 " pdb=" C5 AMP B 201 " ideal model delta sigma weight residual 1.490 1.373 0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 9846 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.93: 203 103.93 - 111.66: 4666 111.66 - 119.39: 3630 119.39 - 127.12: 4754 127.12 - 134.85: 166 Bond angle restraints: 13419 Sorted by residual: angle pdb=" C2' AMP B 201 " pdb=" C1' AMP B 201 " pdb=" N9 AMP B 201 " ideal model delta sigma weight residual 114.00 127.40 -13.40 1.50e+00 4.44e-01 7.99e+01 angle pdb=" N9 AMP B 201 " pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 108.20 96.21 11.99 1.50e+00 4.44e-01 6.39e+01 angle pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " pdb=" C4' AMP B 201 " ideal model delta sigma weight residual 109.70 101.81 7.89 1.00e+00 1.00e+00 6.22e+01 angle pdb=" O2P AMP B 201 " pdb=" P AMP B 201 " pdb=" O3P AMP B 201 " ideal model delta sigma weight residual 119.90 105.09 14.81 3.00e+00 1.11e-01 2.44e+01 angle pdb=" C3' AMP B 201 " pdb=" C4' AMP B 201 " pdb=" C5' AMP B 201 " ideal model delta sigma weight residual 115.20 109.40 5.80 1.50e+00 4.44e-01 1.50e+01 ... (remaining 13414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 5800 29.88 - 59.77: 128 59.77 - 89.65: 10 89.65 - 119.54: 0 119.54 - 149.42: 1 Dihedral angle restraints: 5939 sinusoidal: 2399 harmonic: 3540 Sorted by residual: dihedral pdb=" C5' AMP B 201 " pdb=" O5' AMP B 201 " pdb=" P AMP B 201 " pdb=" O3P AMP B 201 " ideal model delta sinusoidal sigma weight residual 300.00 150.58 149.42 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" C1' AMP B 201 " pdb=" C4' AMP B 201 " pdb=" O4' AMP B 201 " pdb=" C5' AMP B 201 " ideal model delta sinusoidal sigma weight residual -123.00 -156.55 33.55 1 8.00e+00 1.56e-02 2.50e+01 dihedral pdb=" CA GLN A 923 " pdb=" C GLN A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 5936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 855 0.025 - 0.050: 407 0.050 - 0.074: 123 0.074 - 0.099: 77 0.099 - 0.124: 34 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA ILE C 85 " pdb=" N ILE C 85 " pdb=" C ILE C 85 " pdb=" CB ILE C 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" C2' AMP B 201 " pdb=" C1' AMP B 201 " pdb=" C3' AMP B 201 " pdb=" O2' AMP B 201 " both_signs ideal model delta sigma weight residual False -2.52 -2.40 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 214 " pdb=" N ILE A 214 " pdb=" C ILE A 214 " pdb=" CB ILE A 214 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1493 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 645 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 646 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 646 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 646 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 517 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 518 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 692 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 693 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 693 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 693 " -0.017 5.00e-02 4.00e+02 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1095 2.75 - 3.29: 9826 3.29 - 3.83: 16019 3.83 - 4.36: 18622 4.36 - 4.90: 32187 Nonbonded interactions: 77749 Sorted by model distance: nonbonded pdb=" OG1 THR A 927 " pdb=" O LEU A 967 " model vdw 2.213 2.440 nonbonded pdb=" OD1 ASP A 517 " pdb=" OG1 THR A 519 " model vdw 2.231 2.440 nonbonded pdb=" O THR A 553 " pdb=" NH2 ARG A 916 " model vdw 2.264 2.520 nonbonded pdb=" O GLU A 621 " pdb=" OG SER A 626 " model vdw 2.268 2.440 nonbonded pdb=" OG1 THR C 99 " pdb=" OE1 GLN C 103 " model vdw 2.277 2.440 ... (remaining 77744 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: 3.050 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: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.330 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 0.206 9851 Z= 0.320 Angle : 0.583 14.813 13419 Z= 0.305 Chirality : 0.037 0.124 1496 Planarity : 0.004 0.053 1762 Dihedral : 12.083 149.425 3644 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 1.74 % Allowed : 8.02 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.67 (0.25), residues: 1217 helix: 1.62 (0.25), residues: 448 sheet: 0.19 (0.39), residues: 182 loop : -0.34 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.002 0.000 HIS A 817 PHE 0.008 0.001 PHE A 146 TYR 0.007 0.001 TYR A 388 ARG 0.002 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7078 (mm-30) REVERT: A 177 LEU cc_start: 0.6400 (mm) cc_final: 0.5709 (mt) REVERT: A 224 ASP cc_start: 0.8906 (m-30) cc_final: 0.8695 (p0) REVERT: A 229 HIS cc_start: 0.6930 (t-90) cc_final: 0.6423 (t-90) REVERT: A 256 VAL cc_start: 0.8355 (t) cc_final: 0.7773 (m) REVERT: A 258 ARG cc_start: 0.7278 (ptp-110) cc_final: 0.6752 (mtt-85) REVERT: A 410 LEU cc_start: 0.8792 (mp) cc_final: 0.8499 (mt) REVERT: A 473 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 476 ASN cc_start: 0.7845 (m110) cc_final: 0.7611 (m-40) REVERT: A 490 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8209 (mtm110) REVERT: A 565 SER cc_start: 0.8111 (t) cc_final: 0.7471 (p) REVERT: A 738 MET cc_start: -0.0859 (mtp) cc_final: -0.1281 (mpp) REVERT: A 867 GLU cc_start: 0.7224 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 988 ARG cc_start: 0.7076 (mmp-170) cc_final: 0.6728 (mmp80) REVERT: B 87 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7732 (tpp80) REVERT: C 26 SER cc_start: 0.7760 (p) cc_final: 0.7399 (t) REVERT: C 67 MET cc_start: 0.7287 (mpp) cc_final: 0.7021 (mpp) REVERT: C 136 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5768 (m-80) outliers start: 18 outliers final: 6 residues processed: 177 average time/residue: 0.2432 time to fit residues: 58.3446 Evaluate side-chains 104 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 30.0000 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 132 GLN ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 HIS A 433 GLN A 508 GLN A 831 ASN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9851 Z= 0.305 Angle : 0.611 7.347 13419 Z= 0.298 Chirality : 0.041 0.179 1496 Planarity : 0.004 0.057 1762 Dihedral : 6.422 121.875 1337 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer: Outliers : 2.90 % Allowed : 11.50 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.47 (0.25), residues: 1217 helix: 1.46 (0.24), residues: 457 sheet: -0.04 (0.38), residues: 186 loop : -0.45 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 666 HIS 0.010 0.001 HIS A 142 PHE 0.013 0.001 PHE A 146 TYR 0.013 0.001 TYR C 21 ARG 0.009 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7854 (mmm) cc_final: 0.7347 (mmm) REVERT: A 84 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7045 (mm-30) REVERT: A 224 ASP cc_start: 0.9004 (m-30) cc_final: 0.8800 (p0) REVERT: A 229 HIS cc_start: 0.6742 (t-90) cc_final: 0.6318 (t-90) REVERT: A 256 VAL cc_start: 0.8538 (t) cc_final: 0.8063 (m) REVERT: A 258 ARG cc_start: 0.7229 (ptp-110) cc_final: 0.6706 (mtt-85) REVERT: A 410 LEU cc_start: 0.8742 (mp) cc_final: 0.8539 (mt) REVERT: A 477 LEU cc_start: 0.7792 (pt) cc_final: 0.7543 (pt) REVERT: A 480 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7703 (mp10) REVERT: A 643 MET cc_start: -0.0420 (tpt) cc_final: -0.0948 (mpp) REVERT: A 738 MET cc_start: -0.0916 (mtp) cc_final: -0.1343 (mpp) REVERT: A 988 ARG cc_start: 0.7272 (mmp-170) cc_final: 0.6927 (mmp80) REVERT: B 87 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7515 (tpp80) REVERT: C 26 SER cc_start: 0.8078 (p) cc_final: 0.7666 (t) REVERT: C 54 ARG cc_start: 0.6538 (ttm170) cc_final: 0.5979 (ptm160) REVERT: C 105 LEU cc_start: 0.9044 (mt) cc_final: 0.8716 (pp) REVERT: C 106 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8369 (mt-10) REVERT: C 136 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.5830 (m-80) outliers start: 30 outliers final: 20 residues processed: 129 average time/residue: 0.2325 time to fit residues: 41.4341 Evaluate side-chains 113 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 110 optimal weight: 0.0980 chunk 118 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9851 Z= 0.184 Angle : 0.550 6.801 13419 Z= 0.264 Chirality : 0.039 0.157 1496 Planarity : 0.004 0.058 1762 Dihedral : 5.983 90.121 1335 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 3.48 % Allowed : 11.98 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.60 (0.25), residues: 1217 helix: 1.58 (0.24), residues: 460 sheet: -0.10 (0.37), residues: 185 loop : -0.36 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 666 HIS 0.005 0.001 HIS A 142 PHE 0.009 0.001 PHE C 63 TYR 0.011 0.001 TYR A1010 ARG 0.011 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6379 (tt) REVERT: A 54 MET cc_start: 0.7817 (mmm) cc_final: 0.7361 (mmm) REVERT: A 84 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7128 (mm-30) REVERT: A 224 ASP cc_start: 0.9019 (m-30) cc_final: 0.8810 (p0) REVERT: A 229 HIS cc_start: 0.6727 (t-90) cc_final: 0.6323 (t-90) REVERT: A 256 VAL cc_start: 0.8592 (t) cc_final: 0.8173 (m) REVERT: A 258 ARG cc_start: 0.7245 (ptp-110) cc_final: 0.6711 (mtt-85) REVERT: A 477 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7545 (pt) REVERT: A 565 SER cc_start: 0.7934 (t) cc_final: 0.7327 (p) REVERT: A 738 MET cc_start: -0.1033 (mtp) cc_final: -0.1438 (mpp) REVERT: A 988 ARG cc_start: 0.7206 (mmp-170) cc_final: 0.6874 (mmp80) REVERT: B 87 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7473 (tpp80) REVERT: C 26 SER cc_start: 0.8070 (p) cc_final: 0.7646 (t) REVERT: C 54 ARG cc_start: 0.6407 (ttm170) cc_final: 0.6018 (ptm160) REVERT: C 57 PHE cc_start: 0.7740 (m-80) cc_final: 0.7463 (m-80) REVERT: C 105 LEU cc_start: 0.9093 (mt) cc_final: 0.8740 (pp) REVERT: C 106 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8285 (mt-10) REVERT: C 136 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.5752 (m-80) outliers start: 36 outliers final: 20 residues processed: 128 average time/residue: 0.2383 time to fit residues: 42.0350 Evaluate side-chains 115 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 chunk 31 optimal weight: 0.0010 chunk 97 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9851 Z= 0.235 Angle : 0.566 9.093 13419 Z= 0.272 Chirality : 0.040 0.243 1496 Planarity : 0.004 0.058 1762 Dihedral : 5.603 64.614 1335 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.60 % Favored : 95.32 % Rotamer: Outliers : 3.67 % Allowed : 13.33 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.53 (0.25), residues: 1217 helix: 1.52 (0.24), residues: 461 sheet: -0.22 (0.37), residues: 186 loop : -0.36 (0.28), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 666 HIS 0.004 0.001 HIS A 142 PHE 0.011 0.001 PHE A 881 TYR 0.010 0.001 TYR A1010 ARG 0.007 0.000 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 98 time to evaluate : 1.042 Fit side-chains REVERT: A 40 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6420 (tt) REVERT: A 54 MET cc_start: 0.7802 (mmm) cc_final: 0.7353 (mmm) REVERT: A 84 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7148 (mm-30) REVERT: A 256 VAL cc_start: 0.8663 (t) cc_final: 0.8261 (m) REVERT: A 258 ARG cc_start: 0.7275 (ptp-110) cc_final: 0.6728 (mtt-85) REVERT: A 503 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7162 (tt) REVERT: A 565 SER cc_start: 0.7950 (t) cc_final: 0.7343 (p) REVERT: A 643 MET cc_start: -0.0619 (tpt) cc_final: -0.1114 (mpp) REVERT: A 738 MET cc_start: -0.1009 (mtp) cc_final: -0.1414 (mpp) REVERT: A 867 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7037 (mm-30) REVERT: A 988 ARG cc_start: 0.7218 (mmp-170) cc_final: 0.6886 (mmp80) REVERT: B 87 ARG cc_start: 0.7920 (tpp80) cc_final: 0.7526 (tpp80) REVERT: C 54 ARG cc_start: 0.6354 (ttm170) cc_final: 0.5969 (ptt90) REVERT: C 57 PHE cc_start: 0.7818 (m-80) cc_final: 0.7492 (m-80) REVERT: C 105 LEU cc_start: 0.9112 (mt) cc_final: 0.8789 (pp) REVERT: C 106 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8259 (mt-10) REVERT: C 136 PHE cc_start: 0.6281 (OUTLIER) cc_final: 0.5730 (m-80) outliers start: 38 outliers final: 22 residues processed: 124 average time/residue: 0.2235 time to fit residues: 39.0723 Evaluate side-chains 115 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 133 ASP Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2972 > 50: distance: 104 - 106: 8.633 distance: 106 - 107: 27.073 distance: 107 - 108: 26.960 distance: 107 - 110: 11.337 distance: 108 - 109: 30.942 distance: 108 - 112: 39.685 distance: 110 - 111: 11.459 distance: 112 - 113: 13.057 distance: 113 - 114: 44.071 distance: 113 - 116: 48.804 distance: 114 - 115: 51.454 distance: 114 - 123: 39.170 distance: 116 - 117: 35.037 distance: 117 - 118: 18.957 distance: 118 - 119: 28.944 distance: 119 - 120: 8.413 distance: 120 - 121: 27.344 distance: 120 - 122: 14.506 distance: 123 - 124: 31.696 distance: 124 - 125: 9.833 distance: 124 - 127: 31.296 distance: 125 - 126: 20.349 distance: 125 - 135: 6.926 distance: 126 - 156: 25.922 distance: 127 - 128: 7.457 distance: 128 - 129: 40.957 distance: 128 - 130: 13.252 distance: 129 - 131: 13.217 distance: 130 - 132: 15.194 distance: 131 - 133: 23.081 distance: 132 - 133: 26.792 distance: 133 - 134: 16.988 distance: 135 - 136: 8.416 distance: 136 - 137: 22.214 distance: 136 - 139: 12.184 distance: 137 - 138: 29.971 distance: 137 - 143: 23.758 distance: 138 - 164: 22.068 distance: 139 - 140: 3.778 distance: 140 - 141: 17.327 distance: 140 - 142: 21.683 distance: 143 - 144: 24.436 distance: 144 - 145: 42.880 distance: 145 - 146: 40.246 distance: 145 - 147: 49.479 distance: 146 - 169: 40.726 distance: 147 - 148: 15.205 distance: 148 - 149: 11.482 distance: 148 - 151: 8.051 distance: 149 - 150: 26.076 distance: 149 - 156: 8.522 distance: 150 - 176: 21.264 distance: 151 - 152: 11.259 distance: 152 - 153: 19.171 distance: 153 - 154: 10.931 distance: 153 - 155: 18.412 distance: 156 - 157: 23.788 distance: 157 - 158: 47.202 distance: 157 - 160: 16.582 distance: 158 - 159: 31.420 distance: 158 - 164: 39.698 distance: 159 - 187: 12.106 distance: 160 - 161: 23.000 distance: 160 - 162: 19.123 distance: 161 - 163: 20.445 distance: 164 - 165: 18.196 distance: 165 - 166: 25.189 distance: 165 - 168: 3.868 distance: 166 - 167: 20.082 distance: 166 - 169: 25.885 distance: 169 - 170: 26.792 distance: 170 - 171: 20.991 distance: 170 - 173: 24.158 distance: 171 - 172: 10.380 distance: 171 - 176: 12.656 distance: 173 - 174: 20.171 distance: 173 - 175: 30.162 distance: 176 - 177: 24.858 distance: 177 - 178: 26.280 distance: 177 - 180: 31.563 distance: 178 - 179: 13.661 distance: 178 - 187: 24.790 distance: 180 - 181: 5.191 distance: 181 - 182: 27.858 distance: 181 - 183: 6.069 distance: 182 - 184: 26.040 distance: 183 - 185: 4.704 distance: 184 - 186: 23.926 distance: 185 - 186: 28.222