Starting phenix.real_space_refine on Mon Mar 11 13:59:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/03_2024/7ozv_13138_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/03_2024/7ozv_13138.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/03_2024/7ozv_13138_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/03_2024/7ozv_13138_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/03_2024/7ozv_13138_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/03_2024/7ozv_13138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/03_2024/7ozv_13138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/03_2024/7ozv_13138_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ozv_13138/03_2024/7ozv_13138_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 22 5.49 5 S 57 5.16 5 C 5284 2.51 5 N 1405 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 284": "OD1" <-> "OD2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 684": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8409 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6565 Classifications: {'peptide': 814} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 786} Chain breaks: 3 Chain: "B" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Chain: "C" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 478 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 213 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p': 1, 'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1692 SG CYS A 301 47.732 66.352 36.395 1.00 55.92 S ATOM 1733 SG CYS A 306 47.334 65.879 32.523 1.00 52.97 S ATOM 1765 SG CYS A 310 50.364 65.588 34.819 1.00 49.18 S ATOM 3132 SG CYS A 487 30.327 62.531 45.778 1.00 62.63 S ATOM 4385 SG CYS A 645 28.837 62.401 41.815 1.00 65.93 S ATOM 4391 SG CYS A 646 31.679 64.363 43.369 1.00 60.57 S Time building chain proxies: 4.83, per 1000 atoms: 0.57 Number of scatterers: 8409 At special positions: 0 Unit cell: (91.74, 93.408, 99.246, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 57 16.00 P 22 15.00 O 1639 8.00 N 1405 7.00 C 5284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " Number of angles added : 6 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 7 sheets defined 46.2% alpha, 10.1% beta 5 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 4.07 Creating SS restraints... Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 169 through 199 removed outlier: 4.015A pdb=" N TYR A 175 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 247 Proline residue: A 243 - end of helix removed outlier: 4.032A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 276 through 286 Processing helix chain 'A' and resid 304 through 319 removed outlier: 3.581A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.784A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 3.718A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 581 removed outlier: 5.758A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.637A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 687 through 708 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 854 through 863 Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 875 through 895 removed outlier: 3.870A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 915 No H-bonds generated for 'chain 'A' and resid 913 through 915' Processing helix chain 'A' and resid 918 through 922 Processing helix chain 'B' and resid 78 through 96 Processing helix chain 'B' and resid 101 through 109 removed outlier: 4.132A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 4 through 19 Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 45 through 60 Processing sheet with id= A, first strand: chain 'A' and resid 32 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= C, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= D, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.497A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.260A pdb=" N TRP A 617 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA A 762 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 815 through 822 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.065A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1332 1.31 - 1.43: 2522 1.43 - 1.56: 4657 1.56 - 1.69: 46 1.69 - 1.81: 86 Bond restraints: 8643 Sorted by residual: bond pdb=" O4' 16B T 9 " pdb=" C1' 16B T 9 " ideal model delta sigma weight residual 1.412 1.625 -0.213 1.50e-02 4.44e+03 2.01e+02 bond pdb=" C2' 16B T 9 " pdb=" C1' 16B T 9 " ideal model delta sigma weight residual 1.529 1.345 0.184 1.50e-02 4.44e+03 1.51e+02 bond pdb=" C4' 16B T 9 " pdb=" O4' 16B T 9 " ideal model delta sigma weight residual 1.451 1.299 0.152 1.50e-02 4.44e+03 1.03e+02 bond pdb=" C2 16B T 9 " pdb=" N3 16B T 9 " ideal model delta sigma weight residual 1.520 1.327 0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" P 16B T 9 " pdb=" OP2 16B T 9 " ideal model delta sigma weight residual 1.490 1.653 -0.163 2.00e-02 2.50e+03 6.60e+01 ... (remaining 8638 not shown) Histogram of bond angle deviations from ideal: 92.06 - 100.45: 13 100.45 - 108.84: 636 108.84 - 117.23: 5508 117.23 - 125.62: 5493 125.62 - 134.01: 183 Bond angle restraints: 11833 Sorted by residual: angle pdb=" O3' 16B T 9 " pdb=" P A T 10 " pdb=" O5' A T 10 " ideal model delta sigma weight residual 104.00 92.06 11.94 1.50e+00 4.44e-01 6.33e+01 angle pdb=" C2' 16B T 9 " pdb=" C1' 16B T 9 " pdb=" N1 16B T 9 " ideal model delta sigma weight residual 112.00 121.73 -9.73 1.50e+00 4.44e-01 4.21e+01 angle pdb=" O4' 16B T 9 " pdb=" C1' 16B T 9 " pdb=" N1 16B T 9 " ideal model delta sigma weight residual 108.50 100.62 7.88 1.50e+00 4.44e-01 2.76e+01 angle pdb=" O3' 16B T 9 " pdb=" P A T 10 " pdb=" OP1 A T 10 " ideal model delta sigma weight residual 108.00 122.71 -14.71 3.00e+00 1.11e-01 2.40e+01 angle pdb=" C4' 16B T 9 " pdb=" O4' 16B T 9 " pdb=" C1' 16B T 9 " ideal model delta sigma weight residual 109.90 105.90 4.00 1.00e+00 1.00e+00 1.60e+01 ... (remaining 11828 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 4616 16.85 - 33.70: 392 33.70 - 50.55: 91 50.55 - 67.39: 47 67.39 - 84.24: 13 Dihedral angle restraints: 5159 sinusoidal: 2219 harmonic: 2940 Sorted by residual: dihedral pdb=" CA LEU A 758 " pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ILE A 757 " pdb=" C ILE A 757 " pdb=" N LEU A 758 " pdb=" CA LEU A 758 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ASP A 608 " pdb=" CB ASP A 608 " pdb=" CG ASP A 608 " pdb=" OD1 ASP A 608 " ideal model delta sinusoidal sigma weight residual -30.00 -89.96 59.96 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 5156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1249 0.078 - 0.156: 93 0.156 - 0.235: 0 0.235 - 0.313: 0 0.313 - 0.391: 1 Chirality restraints: 1343 Sorted by residual: chirality pdb=" C2' 16B T 9 " pdb=" C3' 16B T 9 " pdb=" O2' 16B T 9 " pdb=" C1' 16B T 9 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA VAL B 160 " pdb=" N VAL B 160 " pdb=" C VAL B 160 " pdb=" CB VAL B 160 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE A 757 " pdb=" N ILE A 757 " pdb=" C ILE A 757 " pdb=" CB ILE A 757 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 1340 not shown) Planarity restraints: 1425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 16B T 9 " -0.096 2.00e-02 2.50e+03 1.37e-01 4.70e+02 pdb=" N1 16B T 9 " -0.010 2.00e-02 2.50e+03 pdb=" C2 16B T 9 " -0.017 2.00e-02 2.50e+03 pdb=" O2 16B T 9 " -0.078 2.00e-02 2.50e+03 pdb=" N3 16B T 9 " 0.047 2.00e-02 2.50e+03 pdb=" C4 16B T 9 " 0.117 2.00e-02 2.50e+03 pdb=" N4 16B T 9 " 0.184 2.00e-02 2.50e+03 pdb=" C5 16B T 9 " 0.120 2.00e-02 2.50e+03 pdb=" C6 16B T 9 " 0.057 2.00e-02 2.50e+03 pdb=" OAC 16B T 9 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 758 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C LEU A 758 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU A 758 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 759 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 120 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO B 121 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 121 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 121 " -0.024 5.00e-02 4.00e+02 ... (remaining 1422 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 800 2.74 - 3.28: 8422 3.28 - 3.82: 14203 3.82 - 4.36: 17753 4.36 - 4.90: 29639 Nonbonded interactions: 70817 Sorted by model distance: nonbonded pdb=" O TYR A 915 " pdb=" OH TYR A 921 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR A 710 " pdb=" O GLY A 774 " model vdw 2.210 2.440 nonbonded pdb=" OE2 GLU A 254 " pdb=" OH TYR A 286 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR A 206 " pdb=" OD1 ASN A 209 " model vdw 2.219 2.440 nonbonded pdb=" OG SER A 318 " pdb=" O ARG A 349 " model vdw 2.236 2.440 ... (remaining 70812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 3.350 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 29.760 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.213 8643 Z= 0.455 Angle : 0.583 14.712 11833 Z= 0.318 Chirality : 0.042 0.391 1343 Planarity : 0.005 0.137 1425 Dihedral : 15.017 84.243 3261 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.22 (0.26), residues: 979 helix: 0.20 (0.23), residues: 471 sheet: -0.05 (0.53), residues: 102 loop : -0.40 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.019 0.002 PHE A 920 TYR 0.018 0.002 TYR A 530 ARG 0.006 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.837 Fit side-chains REVERT: A 729 GLU cc_start: 0.6875 (tp30) cc_final: 0.6637 (mt-10) REVERT: A 825 ASP cc_start: 0.6068 (m-30) cc_final: 0.5741 (m-30) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1913 time to fit residues: 32.4399 Evaluate side-chains 87 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.0701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8643 Z= 0.262 Angle : 0.524 6.699 11833 Z= 0.273 Chirality : 0.041 0.138 1343 Planarity : 0.004 0.038 1425 Dihedral : 12.789 74.006 1423 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.91 % Allowed : 6.85 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.26), residues: 979 helix: 0.23 (0.23), residues: 472 sheet: -0.25 (0.54), residues: 100 loop : -0.34 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.016 0.002 PHE A 920 TYR 0.013 0.001 TYR A 877 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.002 Fit side-chains REVERT: A 729 GLU cc_start: 0.6947 (tp30) cc_final: 0.6689 (mt-10) REVERT: A 825 ASP cc_start: 0.5998 (m-30) cc_final: 0.5659 (m-30) outliers start: 8 outliers final: 6 residues processed: 93 average time/residue: 0.1708 time to fit residues: 23.5279 Evaluate side-chains 90 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 817 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 61 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- 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: 0.7592 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8643 Z= 0.354 Angle : 0.568 6.809 11833 Z= 0.298 Chirality : 0.043 0.137 1343 Planarity : 0.004 0.038 1425 Dihedral : 12.834 74.156 1423 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.94 % Allowed : 9.93 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.48 (0.26), residues: 979 helix: 0.03 (0.23), residues: 470 sheet: -0.31 (0.57), residues: 90 loop : -0.57 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 916 HIS 0.007 0.001 HIS C 36 PHE 0.018 0.002 PHE A 652 TYR 0.014 0.002 TYR A 877 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.831 Fit side-chains REVERT: A 280 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7269 (mp) REVERT: A 729 GLU cc_start: 0.6953 (tp30) cc_final: 0.6698 (mt-10) REVERT: A 825 ASP cc_start: 0.6083 (m-30) cc_final: 0.5717 (m-30) outliers start: 17 outliers final: 13 residues processed: 96 average time/residue: 0.1885 time to fit residues: 26.3550 Evaluate side-chains 93 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.7566 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8643 Z= 0.267 Angle : 0.512 6.443 11833 Z= 0.269 Chirality : 0.040 0.135 1343 Planarity : 0.003 0.036 1425 Dihedral : 12.742 73.824 1423 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.40 % Allowed : 11.87 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -0.38 (0.26), residues: 979 helix: 0.10 (0.23), residues: 472 sheet: -0.38 (0.56), residues: 90 loop : -0.46 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS A 309 PHE 0.014 0.002 PHE A 652 TYR 0.011 0.001 TYR A 149 ARG 0.004 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 1.666 Fit side-chains REVERT: A 280 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7250 (mp) REVERT: A 729 GLU cc_start: 0.6933 (tp30) cc_final: 0.6731 (mt-10) outliers start: 21 outliers final: 15 residues processed: 106 average time/residue: 0.1886 time to fit residues: 28.7010 Evaluate side-chains 102 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 8643 Z= 0.557 Angle : 0.691 7.803 11833 Z= 0.364 Chirality : 0.048 0.145 1343 Planarity : 0.005 0.048 1425 Dihedral : 12.860 74.705 1423 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.77 % Allowed : 12.67 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.25), residues: 979 helix: -0.48 (0.22), residues: 468 sheet: -0.82 (0.51), residues: 103 loop : -0.87 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 916 HIS 0.009 0.002 HIS C 36 PHE 0.023 0.003 PHE A 571 TYR 0.013 0.002 TYR A 149 ARG 0.004 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 93 time to evaluate : 0.932 Fit side-chains REVERT: A 280 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7403 (mp) REVERT: A 729 GLU cc_start: 0.7022 (tp30) cc_final: 0.6732 (mt-10) REVERT: B 177 SER cc_start: 0.7644 (OUTLIER) cc_final: 0.7363 (m) outliers start: 33 outliers final: 21 residues processed: 119 average time/residue: 0.1679 time to fit residues: 29.6201 Evaluate side-chains 110 residues out of total 876 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 87 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 33 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9535 > 50: distance: 89 - 98: 14.991 distance: 98 - 99: 6.936 distance: 99 - 100: 7.530 distance: 99 - 102: 5.610 distance: 100 - 101: 5.618 distance: 100 - 110: 4.699 distance: 102 - 103: 32.172 distance: 103 - 104: 17.696 distance: 103 - 105: 30.230 distance: 106 - 108: 16.963 distance: 107 - 108: 23.001 distance: 108 - 109: 11.705 distance: 110 - 111: 18.498 distance: 111 - 112: 16.984 distance: 111 - 114: 23.870 distance: 112 - 113: 28.348 distance: 112 - 124: 43.561 distance: 114 - 115: 15.994 distance: 115 - 116: 6.190 distance: 115 - 117: 11.367 distance: 116 - 118: 11.034 distance: 117 - 119: 6.051 distance: 117 - 120: 14.065 distance: 118 - 119: 11.346 distance: 119 - 121: 8.632 distance: 120 - 122: 7.236 distance: 121 - 123: 14.793 distance: 122 - 123: 8.032 distance: 124 - 125: 31.182 distance: 125 - 126: 11.439 distance: 125 - 128: 32.211 distance: 126 - 127: 18.432 distance: 126 - 133: 10.923 distance: 128 - 129: 23.949 distance: 129 - 130: 20.819 distance: 130 - 131: 4.010 distance: 130 - 132: 11.023 distance: 133 - 134: 20.357 distance: 133 - 139: 13.515 distance: 134 - 135: 13.646 distance: 134 - 137: 16.877 distance: 135 - 136: 13.292 distance: 135 - 140: 13.776 distance: 136 - 172: 36.014 distance: 137 - 138: 4.022 distance: 138 - 139: 27.034 distance: 140 - 141: 7.579 distance: 141 - 142: 14.003 distance: 141 - 144: 14.696 distance: 142 - 143: 31.405 distance: 142 - 149: 27.243 distance: 144 - 145: 14.630 distance: 145 - 146: 11.741 distance: 146 - 147: 10.790 distance: 146 - 148: 5.697 distance: 149 - 150: 9.308 distance: 150 - 151: 15.361 distance: 150 - 153: 11.544 distance: 151 - 152: 21.670 distance: 151 - 160: 13.565 distance: 153 - 154: 7.667 distance: 154 - 155: 6.071 distance: 154 - 156: 10.630 distance: 155 - 157: 16.862 distance: 156 - 158: 9.365 distance: 157 - 159: 8.660 distance: 158 - 159: 4.050 distance: 160 - 161: 13.946 distance: 161 - 162: 5.709 distance: 161 - 164: 3.067 distance: 162 - 163: 26.777 distance: 162 - 172: 14.366 distance: 164 - 165: 6.193 distance: 165 - 166: 9.640 distance: 165 - 167: 10.567 distance: 166 - 168: 15.997 distance: 167 - 169: 18.889 distance: 168 - 170: 13.745 distance: 169 - 170: 11.046 distance: 170 - 171: 25.564 distance: 173 - 174: 14.608 distance: 173 - 176: 19.069 distance: 174 - 175: 9.846 distance: 174 - 181: 9.245 distance: 176 - 177: 20.006 distance: 177 - 178: 16.882 distance: 178 - 179: 32.236 distance: 178 - 180: 24.306 distance: 181 - 182: 10.311 distance: 182 - 183: 9.960 distance: 182 - 185: 17.530 distance: 183 - 184: 19.177 distance: 183 - 186: 14.324 distance: 186 - 187: 14.347 distance: 187 - 188: 22.605 distance: 187 - 190: 15.691 distance: 188 - 189: 24.104 distance: 188 - 194: 18.132 distance: 190 - 191: 21.854 distance: 191 - 192: 20.725 distance: 192 - 193: 19.160