Starting phenix.real_space_refine on Sat Aug 3 10:39:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/08_2024/8ien_35387_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/08_2024/8ien_35387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/08_2024/8ien_35387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/08_2024/8ien_35387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/08_2024/8ien_35387_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ien_35387/08_2024/8ien_35387_trim.cif" } resolution = 3.25 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= 0.003 sd= 0.075 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 53 5.16 5 C 4959 2.51 5 N 1320 2.21 5 O 1340 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 235": "OE1" <-> "OE2" Residue "P GLU 303": "OE1" <-> "OE2" Residue "P GLU 348": "OE1" <-> "OE2" Residue "P GLU 367": "OE1" <-> "OE2" Residue "P GLU 520": "OE1" <-> "OE2" Residue "P GLU 616": "OE1" <-> "OE2" Residue "P GLU 782": "OE1" <-> "OE2" Residue "P GLU 861": "OE1" <-> "OE2" Residue "P GLU 1135": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7678 Number of models: 1 Model: "" Number of chains: 2 Chain: "P" Number of atoms: 7644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7644 Classifications: {'peptide': 991} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 65, 'TRANS': 922} Chain breaks: 6 Chain: "P" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, 'ALF': 1, 'SPM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.75, per 1000 atoms: 0.62 Number of scatterers: 7678 At special positions: 0 Unit cell: (86.505, 112.785, 124.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 53 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1340 8.00 N 1320 7.00 C 4959 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1846 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 48.2% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'P' and resid 50 through 59 Processing helix chain 'P' and resid 61 through 66 Processing helix chain 'P' and resid 69 through 77 removed outlier: 3.828A pdb=" N ARG P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 201 Processing helix chain 'P' and resid 208 through 217 removed outlier: 3.652A pdb=" N ARG P 212 " --> pdb=" O ASP P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 236 Processing helix chain 'P' and resid 238 through 254 Processing helix chain 'P' and resid 256 through 290 Processing helix chain 'P' and resid 310 through 312 No H-bonds generated for 'chain 'P' and resid 310 through 312' Processing helix chain 'P' and resid 403 through 413 removed outlier: 4.003A pdb=" N VAL P 408 " --> pdb=" O LYS P 404 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS P 413 " --> pdb=" O SER P 409 " (cutoff:3.500A) Processing helix chain 'P' and resid 427 through 451 removed outlier: 3.719A pdb=" N ILE P 444 " --> pdb=" O THR P 440 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG P 449 " --> pdb=" O PHE P 445 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG P 451 " --> pdb=" O LEU P 447 " (cutoff:3.500A) Processing helix chain 'P' and resid 456 through 469 removed outlier: 3.582A pdb=" N ARG P 460 " --> pdb=" O GLU P 456 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU P 462 " --> pdb=" O VAL P 458 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL P 469 " --> pdb=" O VAL P 465 " (cutoff:3.500A) Processing helix chain 'P' and resid 472 through 492 removed outlier: 4.347A pdb=" N CYS P 480 " --> pdb=" O ALA P 476 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR P 481 " --> pdb=" O MET P 477 " (cutoff:3.500A) Processing helix chain 'P' and resid 498 through 504 removed outlier: 4.416A pdb=" N ASN P 502 " --> pdb=" O PRO P 498 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU P 503 " --> pdb=" O LEU P 499 " (cutoff:3.500A) Processing helix chain 'P' and resid 549 through 558 Processing helix chain 'P' and resid 571 through 581 Processing helix chain 'P' and resid 656 through 664 removed outlier: 3.583A pdb=" N VAL P 660 " --> pdb=" O SER P 656 " (cutoff:3.500A) Processing helix chain 'P' and resid 673 through 683 removed outlier: 3.614A pdb=" N LEU P 677 " --> pdb=" O PHE P 673 " (cutoff:3.500A) Processing helix chain 'P' and resid 731 through 742 removed outlier: 3.754A pdb=" N VAL P 735 " --> pdb=" O GLN P 731 " (cutoff:3.500A) Processing helix chain 'P' and resid 753 through 765 removed outlier: 3.520A pdb=" N ALA P 757 " --> pdb=" O ASN P 753 " (cutoff:3.500A) Processing helix chain 'P' and resid 826 through 835 Processing helix chain 'P' and resid 840 through 847 Processing helix chain 'P' and resid 855 through 868 Processing helix chain 'P' and resid 882 through 889 Processing helix chain 'P' and resid 914 through 955 removed outlier: 4.249A pdb=" N MET P 918 " --> pdb=" O GLU P 914 " (cutoff:3.500A) Processing helix chain 'P' and resid 959 through 970 Processing helix chain 'P' and resid 970 through 978 Processing helix chain 'P' and resid 998 through 1026 removed outlier: 3.750A pdb=" N LEU P1017 " --> pdb=" O THR P1013 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY P1018 " --> pdb=" O GLY P1014 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY P1019 " --> pdb=" O VAL P1015 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR P1020 " --> pdb=" O GLN P1016 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA P1025 " --> pdb=" O PHE P1021 " (cutoff:3.500A) Processing helix chain 'P' and resid 1037 through 1041 removed outlier: 3.651A pdb=" N ASN P1041 " --> pdb=" O ALA P1038 " (cutoff:3.500A) Processing helix chain 'P' and resid 1044 through 1065 removed outlier: 3.776A pdb=" N THR P1048 " --> pdb=" O ASN P1044 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU P1059 " --> pdb=" O SER P1055 " (cutoff:3.500A) Processing helix chain 'P' and resid 1078 through 1098 Processing helix chain 'P' and resid 1113 through 1139 Processing helix chain 'P' and resid 1141 through 1146 Processing helix chain 'P' and resid 1156 through 1169 Processing sheet with id=AA1, first strand: chain 'P' and resid 40 through 41 removed outlier: 4.136A pdb=" N CYS P 41 " --> pdb=" O ILE P 90 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE P 90 " --> pdb=" O CYS P 41 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE P 103 " --> pdb=" O LEU P 167 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU P 167 " --> pdb=" O PHE P 103 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR P 166 " --> pdb=" O TYR P 173 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE P 174 " --> pdb=" O TYR P 183 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR P 183 " --> pdb=" O ILE P 174 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE P 176 " --> pdb=" O ALA P 181 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA P 181 " --> pdb=" O ILE P 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 303 through 308 removed outlier: 3.843A pdb=" N GLU P 303 " --> pdb=" O ARG P 299 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS P 296 " --> pdb=" O VAL P 319 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N CYS P 317 " --> pdb=" O CYS P 298 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU P 392 " --> pdb=" O VAL P 334 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR P 396 " --> pdb=" O ASP P 330 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASP P 330 " --> pdb=" O THR P 396 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA P 331 " --> pdb=" O LEU P 374 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU P 374 " --> pdb=" O ALA P 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 351 through 354 removed outlier: 3.770A pdb=" N VAL P 340 " --> pdb=" O VAL P 352 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS P 354 " --> pdb=" O CYS P 338 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASN P 341 " --> pdb=" O ILE P 380 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE P 380 " --> pdb=" O ASN P 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 493 through 495 removed outlier: 5.895A pdb=" N GLY P 892 " --> pdb=" O PHE P 906 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER P 908 " --> pdb=" O GLY P 892 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER P 894 " --> pdb=" O SER P 908 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL P 873 " --> pdb=" O VAL P 891 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ILE P 893 " --> pdb=" O VAL P 873 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N MET P 875 " --> pdb=" O ILE P 893 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU P 509 " --> pdb=" O GLY P 874 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N CYS P 876 " --> pdb=" O LEU P 509 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS P 511 " --> pdb=" O CYS P 876 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR P 849 " --> pdb=" O ALA P 746 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU P 823 " --> pdb=" O GLY P 848 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N HIS P 772 " --> pdb=" O ALA P 824 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER P 788 " --> pdb=" O LEU P 773 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 624 through 627 removed outlier: 4.350A pdb=" N HIS P 626 " --> pdb=" O VAL P 640 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL P 640 " --> pdb=" O HIS P 626 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL P 641 " --> pdb=" O GLU P 650 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU P 650 " --> pdb=" O VAL P 641 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY P 655 " --> pdb=" O ALA P 689 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA P 689 " --> pdb=" O GLY P 655 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY P 720 " --> pdb=" O LEU P 690 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N SER P 692 " --> pdb=" O LEU P 718 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU P 718 " --> pdb=" O SER P 692 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2449 1.35 - 1.46: 1687 1.46 - 1.58: 3623 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 7842 Sorted by residual: bond pdb=" C11 SPM P1204 " pdb=" C12 SPM P1204 " ideal model delta sigma weight residual 1.527 1.395 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C12 SPM P1204 " pdb=" C13 SPM P1204 " ideal model delta sigma weight residual 1.527 1.407 0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" F3 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 7837 not shown) Histogram of bond angle deviations from ideal: 89.99 - 107.99: 391 107.99 - 125.99: 10137 125.99 - 143.99: 139 143.99 - 162.00: 0 162.00 - 180.00: 2 Bond angle restraints: 10669 Sorted by residual: angle pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " pdb=" F2 ALF P1202 " ideal model delta sigma weight residual 108.68 179.98 -71.30 3.00e+00 1.11e-01 5.65e+02 angle pdb=" F3 ALF P1202 " pdb="AL ALF P1202 " pdb=" F4 ALF P1202 " ideal model delta sigma weight residual 109.63 180.00 -70.37 3.00e+00 1.11e-01 5.50e+02 angle pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " pdb=" F4 ALF P1202 " ideal model delta sigma weight residual 110.21 89.99 20.22 3.00e+00 1.11e-01 4.54e+01 angle pdb=" F1 ALF P1202 " pdb="AL ALF P1202 " pdb=" F3 ALF P1202 " ideal model delta sigma weight residual 109.69 90.01 19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" F2 ALF P1202 " pdb="AL ALF P1202 " pdb=" F3 ALF P1202 " ideal model delta sigma weight residual 109.59 90.01 19.58 3.00e+00 1.11e-01 4.26e+01 ... (remaining 10664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4247 17.68 - 35.35: 401 35.35 - 53.03: 71 53.03 - 70.70: 16 70.70 - 88.38: 5 Dihedral angle restraints: 4740 sinusoidal: 1880 harmonic: 2860 Sorted by residual: dihedral pdb=" CA ASP P 189 " pdb=" CB ASP P 189 " pdb=" CG ASP P 189 " pdb=" OD1 ASP P 189 " ideal model delta sinusoidal sigma weight residual -30.00 -86.84 56.84 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU P 650 " pdb=" CG GLU P 650 " pdb=" CD GLU P 650 " pdb=" OE1 GLU P 650 " ideal model delta sinusoidal sigma weight residual 0.00 88.38 -88.38 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA LEU P 968 " pdb=" C LEU P 968 " pdb=" N VAL P 969 " pdb=" CA VAL P 969 " ideal model delta harmonic sigma weight residual 180.00 -164.60 -15.40 0 5.00e+00 4.00e-02 9.49e+00 ... (remaining 4737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 996 0.044 - 0.088: 197 0.088 - 0.132: 69 0.132 - 0.176: 2 0.176 - 0.220: 2 Chirality restraints: 1266 Sorted by residual: chirality pdb=" CA SER P 425 " pdb=" N SER P 425 " pdb=" C SER P 425 " pdb=" CB SER P 425 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA HIS P 424 " pdb=" N HIS P 424 " pdb=" C HIS P 424 " pdb=" CB HIS P 424 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA PRO P 618 " pdb=" N PRO P 618 " pdb=" C PRO P 618 " pdb=" CB PRO P 618 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 1263 not shown) Planarity restraints: 1339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO P 618 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO P 619 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO P 619 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO P 619 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET P 426 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C MET P 426 " -0.030 2.00e-02 2.50e+03 pdb=" O MET P 426 " 0.011 2.00e-02 2.50e+03 pdb=" N LYS P 427 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU P1042 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO P1043 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO P1043 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO P1043 " -0.019 5.00e-02 4.00e+02 ... (remaining 1336 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 215 2.71 - 3.26: 7394 3.26 - 3.81: 11972 3.81 - 4.35: 14110 4.35 - 4.90: 24051 Nonbonded interactions: 57742 Sorted by model distance: nonbonded pdb="MG MG P1201 " pdb=" F1 ALF P1202 " model vdw 2.168 2.120 nonbonded pdb=" CG2 VAL P 467 " pdb=" C12 SPM P1204 " model vdw 2.241 3.860 nonbonded pdb=" OD2 ASP P 513 " pdb="MG MG P1201 " model vdw 2.252 2.170 nonbonded pdb=" O THR P 515 " pdb="MG MG P1201 " model vdw 2.280 2.170 nonbonded pdb=" CZ3 TRP P 251 " pdb=" C9 SPM P1204 " model vdw 2.282 3.740 ... (remaining 57737 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.180 Find NCS groups from input model: 0.080 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0170 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 : 0.004 0.132 7842 Z= 0.243 Angle : 1.211 71.295 10669 Z= 0.486 Chirality : 0.040 0.220 1266 Planarity : 0.004 0.050 1339 Dihedral : 14.043 88.379 2894 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 0.24 % Allowed : 2.49 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.25), residues: 977 helix: -0.46 (0.23), residues: 450 sheet: -1.34 (0.62), residues: 61 loop : -2.50 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 67 HIS 0.002 0.000 HIS P 190 PHE 0.015 0.001 PHE P1128 TYR 0.015 0.001 TYR P 256 ARG 0.002 0.000 ARG P1148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2877 (mt) cc_final: 0.2586 (pt) REVERT: P 326 LEU cc_start: 0.3219 (tp) cc_final: 0.2997 (pp) REVERT: P 526 MET cc_start: -0.0095 (pmm) cc_final: -0.1444 (tpp) REVERT: P 577 MET cc_start: 0.1892 (mtp) cc_final: 0.0826 (tmm) REVERT: P 637 MET cc_start: 0.1190 (tmm) cc_final: 0.0942 (mtp) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.1854 time to fit residues: 22.3825 Evaluate side-chains 55 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 77 optimal weight: 0.2980 chunk 30 optimal weight: 0.0570 chunk 47 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 101 GLN P 198 HIS ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 219 ASN P 281 GLN P 559 HIS ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 944 GLN P1127 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0689 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7842 Z= 0.194 Angle : 0.921 31.632 10669 Z= 0.381 Chirality : 0.043 0.169 1266 Planarity : 0.005 0.046 1339 Dihedral : 5.826 57.124 1095 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.59 % Allowed : 9.23 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -1.14 (0.27), residues: 977 helix: 0.51 (0.24), residues: 446 sheet: -0.51 (0.60), residues: 76 loop : -2.17 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 251 HIS 0.004 0.001 HIS P 822 PHE 0.012 0.002 PHE P1128 TYR 0.024 0.002 TYR P 483 ARG 0.007 0.000 ARG P 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2967 (mt) cc_final: 0.2635 (pt) REVERT: P 288 MET cc_start: -0.1237 (ptt) cc_final: -0.1547 (tpt) REVERT: P 326 LEU cc_start: 0.4112 (tp) cc_final: 0.3217 (pp) REVERT: P 477 MET cc_start: 0.1809 (tpp) cc_final: 0.1470 (mmm) REVERT: P 526 MET cc_start: -0.0967 (pmm) cc_final: -0.2070 (tmm) REVERT: P 573 MET cc_start: 0.2113 (ptt) cc_final: 0.1785 (mmm) REVERT: P 577 MET cc_start: 0.2223 (mtp) cc_final: 0.0683 (tmm) REVERT: P 637 MET cc_start: 0.0721 (tmm) cc_final: 0.0050 (mtp) REVERT: P 978 MET cc_start: 0.2033 (mtt) cc_final: 0.1285 (mmm) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1659 time to fit residues: 16.2145 Evaluate side-chains 53 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 219 ASN Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 659 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.4980 chunk 27 optimal weight: 0.0170 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 90 optimal weight: 0.2980 chunk 97 optimal weight: 0.7980 chunk 80 optimal weight: 0.0970 chunk 89 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 180 GLN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 944 GLN P 962 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0755 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7842 Z= 0.156 Angle : 0.867 29.778 10669 Z= 0.346 Chirality : 0.040 0.160 1266 Planarity : 0.004 0.044 1339 Dihedral : 5.322 59.586 1095 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.47 % Allowed : 12.07 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.66 (0.27), residues: 977 helix: 0.95 (0.25), residues: 449 sheet: -0.33 (0.57), residues: 76 loop : -1.96 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 643 HIS 0.002 0.001 HIS P 497 PHE 0.009 0.001 PHE P1128 TYR 0.026 0.001 TYR P 483 ARG 0.003 0.000 ARG P 725 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 63 LEU cc_start: 0.2917 (mt) cc_final: 0.2602 (pt) REVERT: P 288 MET cc_start: -0.1359 (ptt) cc_final: -0.1676 (tpp) REVERT: P 326 LEU cc_start: 0.4434 (tp) cc_final: 0.3200 (pp) REVERT: P 526 MET cc_start: -0.0439 (pmm) cc_final: -0.2471 (tmm) REVERT: P 577 MET cc_start: 0.2268 (mtp) cc_final: 0.0484 (tmm) REVERT: P 637 MET cc_start: 0.0207 (tmm) cc_final: -0.0133 (mtp) REVERT: P 978 MET cc_start: 0.1918 (mtt) cc_final: 0.1491 (mmm) outliers start: 4 outliers final: 1 residues processed: 61 average time/residue: 0.1530 time to fit residues: 14.7009 Evaluate side-chains 54 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 279 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 219 ASN ** P 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1436 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7842 Z= 0.239 Angle : 0.964 31.034 10669 Z= 0.412 Chirality : 0.044 0.155 1266 Planarity : 0.006 0.054 1339 Dihedral : 5.998 56.369 1095 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.78 % Allowed : 14.56 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.98 (0.27), residues: 977 helix: 0.50 (0.24), residues: 446 sheet: 0.47 (0.57), residues: 76 loop : -2.08 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P1028 HIS 0.004 0.001 HIS P 390 PHE 0.022 0.002 PHE P 906 TYR 0.028 0.002 TYR P 173 ARG 0.006 0.001 ARG P 279 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 483 TYR cc_start: 0.2160 (m-80) cc_final: 0.1907 (m-10) REVERT: P 526 MET cc_start: 0.1065 (pmm) cc_final: 0.0434 (mpp) REVERT: P 573 MET cc_start: 0.2433 (ptt) cc_final: 0.2180 (mmm) REVERT: P 577 MET cc_start: 0.2600 (mtp) cc_final: 0.0777 (tmm) REVERT: P 964 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.6609 (tp) REVERT: P 1091 VAL cc_start: 0.2425 (p) cc_final: 0.1988 (t) outliers start: 15 outliers final: 6 residues processed: 82 average time/residue: 0.1823 time to fit residues: 21.8020 Evaluate side-chains 70 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 312 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 964 LEU Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 71 optimal weight: 0.0870 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 0.0670 chunk 24 optimal weight: 0.8980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 847 GLN P1047 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1422 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7842 Z= 0.161 Angle : 0.881 29.830 10669 Z= 0.355 Chirality : 0.041 0.147 1266 Planarity : 0.005 0.042 1339 Dihedral : 5.394 58.924 1095 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.42 % Allowed : 16.80 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.57 (0.27), residues: 977 helix: 0.94 (0.25), residues: 452 sheet: 0.46 (0.57), residues: 76 loop : -2.01 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P1028 HIS 0.003 0.001 HIS P 198 PHE 0.010 0.001 PHE P1051 TYR 0.017 0.001 TYR P 256 ARG 0.004 0.000 ARG P 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: P 459 ILE cc_start: 0.0702 (OUTLIER) cc_final: 0.0351 (mm) REVERT: P 526 MET cc_start: 0.0918 (pmm) cc_final: -0.2659 (tmm) REVERT: P 577 MET cc_start: 0.2670 (mtp) cc_final: 0.0744 (tmm) REVERT: P 637 MET cc_start: 0.0088 (ttt) cc_final: -0.0389 (mtp) REVERT: P 964 LEU cc_start: 0.7927 (tt) cc_final: 0.6812 (tp) REVERT: P 1091 VAL cc_start: 0.1920 (p) cc_final: 0.1599 (t) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.1303 time to fit residues: 16.1109 Evaluate side-chains 71 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 459 ILE Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 1028 TRP Chi-restraints excluded: chain P residue 1032 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 44 optimal weight: 0.0270 chunk 7 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 944 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1588 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7842 Z= 0.167 Angle : 0.886 30.344 10669 Z= 0.360 Chirality : 0.041 0.150 1266 Planarity : 0.005 0.043 1339 Dihedral : 5.020 57.235 1095 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.54 % Allowed : 17.51 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.49 (0.27), residues: 977 helix: 1.00 (0.25), residues: 452 sheet: 0.49 (0.58), residues: 82 loop : -1.98 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 583 HIS 0.002 0.001 HIS P 772 PHE 0.011 0.001 PHE P1051 TYR 0.018 0.001 TYR P 871 ARG 0.005 0.000 ARG P 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: P 210 MET cc_start: 0.5071 (tmm) cc_final: 0.4610 (tmm) REVERT: P 526 MET cc_start: 0.0708 (pmm) cc_final: -0.2397 (tmm) REVERT: P 637 MET cc_start: -0.0053 (ttt) cc_final: -0.0298 (mtp) REVERT: P 837 PHE cc_start: 0.4949 (t80) cc_final: 0.4636 (m-80) REVERT: P 964 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7422 (tp) REVERT: P 1032 LEU cc_start: 0.4043 (OUTLIER) cc_final: 0.3837 (pp) REVERT: P 1091 VAL cc_start: 0.2997 (p) cc_final: 0.2636 (t) outliers start: 13 outliers final: 7 residues processed: 77 average time/residue: 0.1446 time to fit residues: 17.4403 Evaluate side-chains 72 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 964 LEU Chi-restraints excluded: chain P residue 1032 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 0.0470 chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1961 moved from start: 0.7308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7842 Z= 0.224 Angle : 0.952 31.836 10669 Z= 0.401 Chirality : 0.043 0.151 1266 Planarity : 0.005 0.042 1339 Dihedral : 5.232 59.090 1095 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.78 % Allowed : 18.82 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.73 (0.27), residues: 977 helix: 0.73 (0.24), residues: 459 sheet: 0.53 (0.65), residues: 64 loop : -1.99 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 175 HIS 0.004 0.001 HIS P 626 PHE 0.013 0.001 PHE P1051 TYR 0.030 0.002 TYR P 871 ARG 0.004 0.001 ARG P 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.781 Fit side-chains REVERT: P 210 MET cc_start: 0.4795 (tmm) cc_final: 0.4580 (tmm) REVERT: P 235 GLU cc_start: 0.2094 (OUTLIER) cc_final: 0.0545 (pt0) REVERT: P 837 PHE cc_start: 0.5638 (t80) cc_final: 0.4935 (m-10) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.1456 time to fit residues: 19.1914 Evaluate side-chains 71 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 235 GLU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 626 HIS Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.9990 chunk 28 optimal weight: 0.0050 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 0.0370 chunk 91 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 overall best weight: 0.3872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 881 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1936 moved from start: 0.7683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7842 Z= 0.173 Angle : 0.909 31.756 10669 Z= 0.372 Chirality : 0.041 0.147 1266 Planarity : 0.005 0.042 1339 Dihedral : 4.888 58.252 1095 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.13 % Allowed : 19.41 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.49 (0.27), residues: 977 helix: 1.03 (0.24), residues: 457 sheet: 0.57 (0.71), residues: 55 loop : -1.91 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 643 HIS 0.003 0.001 HIS P 772 PHE 0.008 0.001 PHE P 906 TYR 0.019 0.002 TYR P 871 ARG 0.005 0.000 ARG P 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.696 Fit side-chains REVERT: P 339 MET cc_start: 0.1811 (ptp) cc_final: 0.1476 (ptt) REVERT: P 637 MET cc_start: -0.0655 (ttt) cc_final: -0.1081 (mtp) outliers start: 18 outliers final: 13 residues processed: 78 average time/residue: 0.1297 time to fit residues: 16.2794 Evaluate side-chains 78 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 526 MET Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 84 optimal weight: 0.0970 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2050 moved from start: 0.8276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7842 Z= 0.177 Angle : 0.934 31.438 10669 Z= 0.381 Chirality : 0.041 0.154 1266 Planarity : 0.005 0.042 1339 Dihedral : 4.656 54.791 1095 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.66 % Allowed : 20.36 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % 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: -0.37 (0.27), residues: 977 helix: 1.12 (0.24), residues: 458 sheet: 0.56 (0.72), residues: 55 loop : -1.85 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 175 HIS 0.002 0.001 HIS P 772 PHE 0.009 0.001 PHE P 906 TYR 0.022 0.002 TYR P 952 ARG 0.007 0.001 ARG P 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 339 MET cc_start: 0.2134 (ptp) cc_final: 0.1795 (ptt) REVERT: P 573 MET cc_start: 0.3925 (pmm) cc_final: 0.1999 (mmm) REVERT: P 676 MET cc_start: -0.0117 (ttm) cc_final: -0.0358 (tpp) REVERT: P 1009 MET cc_start: 0.5111 (mmt) cc_final: 0.4871 (mmt) outliers start: 14 outliers final: 14 residues processed: 77 average time/residue: 0.1360 time to fit residues: 16.7731 Evaluate side-chains 79 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 526 MET Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 948 VAL Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0000 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 847 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2138 moved from start: 0.8732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7842 Z= 0.178 Angle : 0.938 32.545 10669 Z= 0.383 Chirality : 0.042 0.147 1266 Planarity : 0.005 0.042 1339 Dihedral : 4.505 51.248 1095 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.54 % Allowed : 21.30 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.28), residues: 977 helix: 1.23 (0.24), residues: 459 sheet: 0.48 (0.72), residues: 55 loop : -1.82 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 643 HIS 0.002 0.001 HIS P 780 PHE 0.009 0.001 PHE P 906 TYR 0.020 0.002 TYR P 256 ARG 0.010 0.000 ARG P 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 339 MET cc_start: 0.2183 (ptp) cc_final: 0.1856 (ptt) REVERT: P 573 MET cc_start: 0.3974 (pmm) cc_final: 0.2260 (mmm) REVERT: P 1009 MET cc_start: 0.5100 (mmt) cc_final: 0.4882 (mmt) REVERT: P 1045 TYR cc_start: 0.1581 (m-80) cc_final: 0.0840 (m-80) outliers start: 13 outliers final: 13 residues processed: 80 average time/residue: 0.1446 time to fit residues: 18.1423 Evaluate side-chains 76 residues out of total 845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 197 VAL Chi-restraints excluded: chain P residue 198 HIS Chi-restraints excluded: chain P residue 231 LEU Chi-restraints excluded: chain P residue 256 TYR Chi-restraints excluded: chain P residue 373 THR Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 441 ILE Chi-restraints excluded: chain P residue 526 MET Chi-restraints excluded: chain P residue 854 MET Chi-restraints excluded: chain P residue 894 SER Chi-restraints excluded: chain P residue 902 VAL Chi-restraints excluded: chain P residue 940 TYR Chi-restraints excluded: chain P residue 1028 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 63.1466 > 50: distance: 73 - 79: 27.429 distance: 79 - 80: 23.544 distance: 80 - 81: 42.411 distance: 80 - 83: 50.379 distance: 81 - 82: 54.291 distance: 81 - 88: 60.516 distance: 83 - 84: 41.123 distance: 84 - 85: 13.242 distance: 85 - 86: 48.507 distance: 85 - 87: 43.202 distance: 88 - 89: 39.266 distance: 89 - 90: 29.511 distance: 89 - 92: 58.505 distance: 90 - 91: 40.552 distance: 90 - 93: 37.104 distance: 93 - 94: 32.850 distance: 94 - 95: 22.052 distance: 94 - 97: 24.587 distance: 95 - 96: 49.564 distance: 95 - 104: 14.054 distance: 97 - 98: 34.511 distance: 98 - 99: 43.366 distance: 98 - 100: 21.872 distance: 99 - 101: 25.811 distance: 100 - 102: 7.415 distance: 101 - 103: 28.480 distance: 102 - 103: 31.665 distance: 104 - 105: 41.191 distance: 105 - 106: 7.462 distance: 105 - 108: 47.324 distance: 106 - 107: 27.956 distance: 106 - 116: 44.624 distance: 108 - 109: 45.216 distance: 109 - 110: 42.090 distance: 109 - 111: 5.935 distance: 110 - 112: 39.656 distance: 111 - 113: 10.096 distance: 112 - 114: 42.880 distance: 113 - 114: 38.052 distance: 114 - 115: 28.964 distance: 116 - 117: 29.829 distance: 117 - 120: 35.737 distance: 118 - 119: 44.319 distance: 118 - 125: 23.733 distance: 120 - 121: 27.410 distance: 121 - 122: 40.299 distance: 122 - 123: 37.842 distance: 122 - 124: 24.640 distance: 125 - 126: 4.295 distance: 126 - 127: 40.410 distance: 126 - 129: 56.326 distance: 127 - 128: 5.570 distance: 127 - 132: 53.886 distance: 129 - 130: 57.166 distance: 129 - 131: 45.651 distance: 132 - 133: 10.642 distance: 133 - 134: 19.221 distance: 133 - 136: 38.814 distance: 134 - 135: 32.783 distance: 134 - 138: 35.719 distance: 136 - 137: 41.924 distance: 138 - 139: 38.710 distance: 139 - 140: 14.267 distance: 139 - 142: 45.138 distance: 140 - 141: 56.775 distance: 140 - 146: 7.475 distance: 142 - 143: 3.619 distance: 143 - 144: 5.557 distance: 143 - 145: 9.032 distance: 146 - 147: 32.966 distance: 147 - 148: 4.851 distance: 147 - 150: 34.805 distance: 148 - 149: 9.414 distance: 148 - 154: 37.866 distance: 150 - 151: 23.811 distance: 151 - 152: 27.265 distance: 151 - 153: 30.002 distance: 154 - 155: 8.994 distance: 155 - 156: 26.350 distance: 155 - 158: 35.153 distance: 156 - 157: 19.347 distance: 156 - 162: 20.109 distance: 158 - 159: 25.508 distance: 159 - 160: 26.791 distance: 159 - 161: 34.592