Starting phenix.real_space_refine on Wed Jan 17 19:42:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/01_2024/7to2_26027_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/01_2024/7to2_26027.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/01_2024/7to2_26027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/01_2024/7to2_26027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/01_2024/7to2_26027_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to2_26027/01_2024/7to2_26027_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= 0.004 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 Zn 1 6.06 5 P 32 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3733 2.51 5 N 1039 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 372": "OD1" <-> "OD2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 481": "OD1" <-> "OD2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A GLU 556": "OE1" <-> "OE2" Residue "A ASP 569": "OD1" <-> "OD2" Residue "A PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A ASP 705": "OD1" <-> "OD2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A ARG 811": "NH1" <-> "NH2" Residue "A ASP 822": "OD1" <-> "OD2" Residue "A GLU 827": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6052 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5384 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 25, 'TRANS': 644} Chain breaks: 1 Chain: "B" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 639 Classifications: {'RNA': 30} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 15} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4570 SG CYS A 810 40.487 21.767 28.769 1.00 38.49 S ATOM 4596 SG CYS A 813 39.020 18.506 27.949 1.00 48.41 S ATOM 4908 SG CYS A 864 40.109 19.526 24.622 1.00 65.65 S ATOM 4947 SG CYS A 869 37.263 21.217 26.585 1.00 66.55 S Time building chain proxies: 4.08, per 1000 atoms: 0.67 Number of scatterers: 6052 At special positions: 0 Unit cell: (87.15, 97.65, 72.45, 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) Zn 1 29.99 S 33 16.00 P 32 15.00 Mg 1 11.99 O 1213 8.00 N 1039 7.00 C 3733 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: 2.64 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 813 " Number of angles added : 6 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 5 sheets defined 43.4% alpha, 8.4% beta 15 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 2.74 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 270 through 282 Processing helix chain 'A' and resid 300 through 314 Processing helix chain 'A' and resid 334 through 340 removed outlier: 4.419A pdb=" N VAL A 338 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N GLU A 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 446 through 449 No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 470 through 490 Processing helix chain 'A' and resid 493 through 495 No H-bonds generated for 'chain 'A' and resid 493 through 495' Processing helix chain 'A' and resid 507 through 520 Processing helix chain 'A' and resid 528 through 555 Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 581 through 592 Processing helix chain 'A' and resid 594 through 601 Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 648 Processing helix chain 'A' and resid 675 through 682 Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 747 through 770 removed outlier: 3.873A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 793 removed outlier: 3.883A pdb=" N SER A 793 " --> pdb=" O PHE A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 841 removed outlier: 3.711A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 836 through 841' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id= A, first strand: chain 'A' and resid 404 through 408 Processing sheet with id= B, first strand: chain 'A' and resid 457 through 462 Processing sheet with id= C, first strand: chain 'A' and resid 658 through 661 removed outlier: 6.771A pdb=" N ILE A 693 " --> pdb=" O GLY A 659 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU A 661 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE A 695 " --> pdb=" O LEU A 661 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 892 through 896 removed outlier: 3.692A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 842 through 844 removed outlier: 3.968A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1473 1.33 - 1.45: 1254 1.45 - 1.57: 3397 1.57 - 1.70: 61 1.70 - 1.82: 46 Bond restraints: 6231 Sorted by residual: bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.394 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.25e+01 bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.19e-02 7.06e+03 9.61e+00 bond pdb=" N VAL A 800 " pdb=" CA VAL A 800 " ideal model delta sigma weight residual 1.457 1.485 -0.028 9.00e-03 1.23e+04 9.47e+00 bond pdb=" N VAL A 699 " pdb=" CA VAL A 699 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.18e-02 7.18e+03 9.11e+00 ... (remaining 6226 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.74: 316 106.74 - 113.60: 3493 113.60 - 120.46: 2586 120.46 - 127.32: 2061 127.32 - 134.18: 94 Bond angle restraints: 8550 Sorted by residual: angle pdb=" C PRO A 658 " pdb=" N GLY A 659 " pdb=" CA GLY A 659 " ideal model delta sigma weight residual 121.65 124.64 -2.99 6.80e-01 2.16e+00 1.93e+01 angle pdb=" C2' U B 8 " pdb=" C1' U B 8 " pdb=" N1 U B 8 " ideal model delta sigma weight residual 112.00 116.55 -4.55 1.50e+00 4.44e-01 9.20e+00 angle pdb=" N1 ADP A1003 " pdb=" C2 ADP A1003 " pdb=" N3 ADP A1003 " ideal model delta sigma weight residual 120.00 129.09 -9.09 3.00e+00 1.11e-01 9.19e+00 angle pdb=" N ILE A 467 " pdb=" CA ILE A 467 " pdb=" C ILE A 467 " ideal model delta sigma weight residual 111.90 109.57 2.33 8.10e-01 1.52e+00 8.27e+00 angle pdb=" CA LYS A 528 " pdb=" C LYS A 528 " pdb=" O LYS A 528 " ideal model delta sigma weight residual 120.70 117.78 2.92 1.03e+00 9.43e-01 8.03e+00 ... (remaining 8545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3411 16.18 - 32.37: 271 32.37 - 48.55: 73 48.55 - 64.73: 45 64.73 - 80.91: 19 Dihedral angle restraints: 3819 sinusoidal: 1854 harmonic: 1965 Sorted by residual: dihedral pdb=" O2A ADP A1003 " pdb=" O3A ADP A1003 " pdb=" PA ADP A1003 " pdb=" PB ADP A1003 " ideal model delta sinusoidal sigma weight residual -60.00 -7.40 -52.60 1 2.00e+01 2.50e-03 9.42e+00 dihedral pdb=" CA LEU A 430 " pdb=" CB LEU A 430 " pdb=" CG LEU A 430 " pdb=" CD1 LEU A 430 " ideal model delta sinusoidal sigma weight residual 180.00 124.30 55.70 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CA ASP A 562 " pdb=" CB ASP A 562 " pdb=" CG ASP A 562 " pdb=" OD1 ASP A 562 " ideal model delta sinusoidal sigma weight residual -30.00 -81.64 51.64 1 2.00e+01 2.50e-03 9.11e+00 ... (remaining 3816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 427 0.043 - 0.085: 294 0.085 - 0.128: 224 0.128 - 0.171: 32 0.171 - 0.213: 2 Chirality restraints: 979 Sorted by residual: chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB ILE A 631 " pdb=" CA ILE A 631 " pdb=" CG1 ILE A 631 " pdb=" CG2 ILE A 631 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" P G B 45 " pdb=" OP1 G B 45 " pdb=" OP2 G B 45 " pdb=" O5' G B 45 " both_signs ideal model delta sigma weight residual True 2.41 -2.25 0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 976 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 10 " -0.026 2.00e-02 2.50e+03 9.93e-03 2.96e+00 pdb=" N9 G B 10 " 0.015 2.00e-02 2.50e+03 pdb=" C8 G B 10 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G B 10 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 10 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 10 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G B 10 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 10 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 490 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C CYS A 490 " -0.028 2.00e-02 2.50e+03 pdb=" O CYS A 490 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A 491 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1003 " 0.011 2.00e-02 2.50e+03 9.35e-03 2.40e+00 pdb=" C2 ADP A1003 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ADP A1003 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP A1003 " -0.008 2.00e-02 2.50e+03 pdb=" C6 ADP A1003 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ADP A1003 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ADP A1003 " 0.003 2.00e-02 2.50e+03 pdb=" N3 ADP A1003 " -0.013 2.00e-02 2.50e+03 pdb=" N6 ADP A1003 " 0.006 2.00e-02 2.50e+03 pdb=" N7 ADP A1003 " -0.008 2.00e-02 2.50e+03 pdb=" N9 ADP A1003 " -0.013 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1192 2.81 - 3.33: 5969 3.33 - 3.85: 10248 3.85 - 4.38: 11747 4.38 - 4.90: 19777 Nonbonded interactions: 48933 Sorted by model distance: nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.284 2.520 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.296 2.440 nonbonded pdb=" O THR A 662 " pdb=" NE2 GLN A 678 " model vdw 2.334 2.520 nonbonded pdb=" O ASP A 690 " pdb=" ND1 HIS A 691 " model vdw 2.348 2.520 nonbonded pdb=" O SER A 698 " pdb=" OG SER A 698 " model vdw 2.353 2.440 ... (remaining 48928 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: 0.310 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: 1.880 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.730 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.011 0.096 6231 Z= 0.690 Angle : 1.131 9.092 8550 Z= 0.827 Chirality : 0.069 0.213 979 Planarity : 0.004 0.016 979 Dihedral : 15.192 80.913 2543 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.84 % Allowed : 6.86 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.30), residues: 666 helix: 0.75 (0.28), residues: 298 sheet: -3.26 (0.49), residues: 75 loop : -3.04 (0.29), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 771 HIS 0.005 0.001 HIS A 782 PHE 0.011 0.003 PHE A 460 TYR 0.012 0.003 TYR A 548 ARG 0.008 0.001 ARG A 461 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.679 Fit side-chains REVERT: A 457 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7624 (tp-100) outliers start: 5 outliers final: 3 residues processed: 94 average time/residue: 0.2046 time to fit residues: 24.8871 Evaluate side-chains 60 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 775 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 375 HIS ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 GLN A 500 GLN A 769 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6231 Z= 0.172 Angle : 0.474 6.618 8550 Z= 0.230 Chirality : 0.038 0.136 979 Planarity : 0.002 0.023 979 Dihedral : 14.273 80.981 1179 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.84 % Allowed : 13.04 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.32), residues: 666 helix: 1.95 (0.30), residues: 299 sheet: -3.03 (0.50), residues: 76 loop : -2.57 (0.31), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 512 HIS 0.002 0.000 HIS A 876 PHE 0.006 0.001 PHE A 295 TYR 0.006 0.001 TYR A 246 ARG 0.003 0.000 ARG A 728 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 0.682 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.1603 time to fit residues: 16.4581 Evaluate side-chains 58 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 56 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6231 Z= 0.195 Angle : 0.484 5.761 8550 Z= 0.234 Chirality : 0.038 0.132 979 Planarity : 0.002 0.024 979 Dihedral : 14.223 83.160 1175 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.01 % Allowed : 13.88 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.33), residues: 666 helix: 2.31 (0.30), residues: 299 sheet: -2.65 (0.57), residues: 64 loop : -2.25 (0.31), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.002 0.000 HIS A 876 PHE 0.005 0.001 PHE A 295 TYR 0.007 0.001 TYR A 566 ARG 0.005 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.688 Fit side-chains REVERT: A 457 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7600 (mm-40) outliers start: 18 outliers final: 7 residues processed: 76 average time/residue: 0.1335 time to fit residues: 14.9268 Evaluate side-chains 65 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 18 optimal weight: 0.0870 chunk 56 optimal weight: 0.0040 chunk 38 optimal weight: 0.8980 overall best weight: 0.9572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6231 Z= 0.186 Angle : 0.475 5.655 8550 Z= 0.231 Chirality : 0.038 0.139 979 Planarity : 0.003 0.027 979 Dihedral : 14.203 84.202 1173 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.51 % Allowed : 15.05 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.33), residues: 666 helix: 2.45 (0.30), residues: 300 sheet: -2.52 (0.59), residues: 64 loop : -2.11 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.002 0.000 HIS A 280 PHE 0.005 0.001 PHE A 295 TYR 0.010 0.001 TYR A 473 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.649 Fit side-chains REVERT: A 457 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7593 (mm-40) REVERT: A 878 LYS cc_start: 0.8321 (tmtt) cc_final: 0.7585 (tmtt) outliers start: 15 outliers final: 6 residues processed: 71 average time/residue: 0.1339 time to fit residues: 14.1304 Evaluate side-chains 64 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6231 Z= 0.206 Angle : 0.496 5.849 8550 Z= 0.242 Chirality : 0.038 0.136 979 Planarity : 0.003 0.028 979 Dihedral : 14.219 84.711 1173 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.17 % Allowed : 16.22 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.33), residues: 666 helix: 2.50 (0.30), residues: 301 sheet: -2.41 (0.60), residues: 64 loop : -2.05 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.002 0.000 HIS A 280 PHE 0.006 0.001 PHE A 295 TYR 0.013 0.001 TYR A 473 ARG 0.003 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.750 Fit side-chains REVERT: A 457 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7583 (mm-40) REVERT: A 878 LYS cc_start: 0.8375 (tmtt) cc_final: 0.7613 (tmtt) outliers start: 13 outliers final: 8 residues processed: 69 average time/residue: 0.1396 time to fit residues: 14.0570 Evaluate side-chains 66 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6231 Z= 0.145 Angle : 0.470 5.647 8550 Z= 0.229 Chirality : 0.037 0.138 979 Planarity : 0.003 0.029 979 Dihedral : 14.226 85.543 1173 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.01 % Allowed : 17.06 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.34), residues: 666 helix: 2.64 (0.30), residues: 301 sheet: -2.31 (0.61), residues: 64 loop : -1.93 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 512 HIS 0.001 0.000 HIS A 280 PHE 0.005 0.001 PHE A 371 TYR 0.013 0.001 TYR A 473 ARG 0.002 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.652 Fit side-chains REVERT: A 339 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8143 (tm-30) REVERT: A 457 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7596 (mm-40) REVERT: A 878 LYS cc_start: 0.8322 (tmtt) cc_final: 0.7593 (tmtt) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.1440 time to fit residues: 14.6952 Evaluate side-chains 67 residues out of total 598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.8192 > 50: distance: 57 - 62: 13.986 distance: 62 - 63: 7.394 distance: 63 - 64: 9.163 distance: 63 - 66: 10.811 distance: 64 - 65: 5.420 distance: 64 - 70: 21.370 distance: 66 - 67: 7.730 distance: 66 - 68: 20.926 distance: 67 - 69: 7.878 distance: 70 - 71: 8.919 distance: 71 - 74: 11.374 distance: 72 - 73: 11.361 distance: 72 - 75: 15.123 distance: 75 - 76: 5.307 distance: 76 - 77: 6.631 distance: 76 - 79: 7.243 distance: 77 - 78: 11.833 distance: 77 - 82: 7.705 distance: 79 - 80: 11.123 distance: 79 - 81: 13.475 distance: 82 - 83: 18.921 distance: 83 - 84: 20.471 distance: 83 - 86: 19.542 distance: 84 - 85: 37.136 distance: 84 - 89: 21.986 distance: 86 - 87: 5.868 distance: 86 - 88: 7.158 distance: 89 - 90: 25.132 distance: 90 - 91: 13.699 distance: 90 - 93: 40.969 distance: 91 - 92: 19.233 distance: 91 - 98: 14.149 distance: 93 - 94: 36.510 distance: 94 - 95: 5.857 distance: 95 - 96: 13.386 distance: 96 - 97: 16.172 distance: 98 - 99: 6.401 distance: 99 - 100: 4.843 distance: 99 - 102: 8.362 distance: 100 - 101: 16.197 distance: 100 - 108: 14.173 distance: 102 - 103: 6.666 distance: 103 - 104: 9.747 distance: 103 - 105: 15.856 distance: 104 - 106: 3.106 distance: 105 - 107: 8.436 distance: 106 - 107: 6.694 distance: 108 - 109: 9.905 distance: 109 - 110: 10.133 distance: 110 - 111: 15.030 distance: 110 - 116: 13.470 distance: 112 - 113: 8.613 distance: 113 - 114: 13.882 distance: 113 - 115: 10.937 distance: 116 - 117: 10.627 distance: 117 - 118: 15.535 distance: 117 - 120: 10.457 distance: 118 - 119: 16.326 distance: 118 - 124: 12.799 distance: 120 - 121: 4.838 distance: 121 - 122: 17.430 distance: 121 - 123: 31.691 distance: 124 - 125: 10.794 distance: 125 - 126: 4.397 distance: 125 - 128: 13.468 distance: 126 - 127: 8.487 distance: 126 - 133: 16.234 distance: 128 - 129: 12.255 distance: 129 - 130: 14.491 distance: 130 - 131: 13.042 distance: 130 - 132: 13.071 distance: 133 - 134: 7.782 distance: 134 - 135: 6.184 distance: 134 - 137: 4.914 distance: 135 - 136: 10.923 distance: 135 - 142: 13.525 distance: 137 - 138: 8.311 distance: 138 - 139: 6.259 distance: 139 - 140: 5.565 distance: 139 - 141: 14.350