Starting phenix.real_space_refine on Fri Mar 15 03:40:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny2_8996/03_2024/6ny2_8996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny2_8996/03_2024/6ny2_8996.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/6ny2_8996/03_2024/6ny2_8996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny2_8996/03_2024/6ny2_8996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny2_8996/03_2024/6ny2_8996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ny2_8996/03_2024/6ny2_8996.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= 0.002 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 180 5.49 5 S 21 5.16 5 C 6035 2.51 5 N 1921 2.21 5 O 2381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y GLU 51": "OE1" <-> "OE2" Residue "Y GLU 77": "OE1" <-> "OE2" Residue "Y PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 194": "OD1" <-> "OD2" Residue "Y PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 288": "OE1" <-> "OE2" Residue "Y PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 415": "OE1" <-> "OE2" Residue "Y GLU 447": "OE1" <-> "OE2" Residue "Y GLU 448": "OE1" <-> "OE2" Residue "Y ARG 475": "NH1" <-> "NH2" Residue "Y PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 763": "OD1" <-> "OD2" Residue "Y GLU 786": "OE1" <-> "OE2" Residue "Y PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10538 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 715 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "D" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 708 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "Y" Number of atoms: 6771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 915, 6771 Classifications: {'peptide': 915} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 193} Link IDs: {'PTRANS': 29, 'TRANS': 885} Chain breaks: 8 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 691 Unresolved non-hydrogen dihedrals: 332 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 4, 'TYR:plan': 1, 'UNK:plan-1': 121, 'ASP:plan': 16, 'GLU:plan': 26, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 316 Chain: "B" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 2344 Classifications: {'RNA': 110} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 45} Link IDs: {'rna2p': 10, 'rna3p': 99} Chain breaks: 2 Time building chain proxies: 6.63, per 1000 atoms: 0.63 Number of scatterers: 10538 At special positions: 0 Unit cell: (98.1, 140.4, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 180 15.00 O 2381 8.00 N 1921 7.00 C 6035 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Y 826 " - pdb=" SG CYS Y 928 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.25 Conformation dependent library (CDL) restraints added in 1.5 seconds 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 47.4% alpha, 5.9% beta 64 base pairs and 114 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'Y' and resid 4 through 13 removed outlier: 3.833A pdb=" N ILE Y 8 " --> pdb=" O ARG Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 42 Processing helix chain 'Y' and resid 60 through 88 Processing helix chain 'Y' and resid 90 through 98 Processing helix chain 'Y' and resid 194 through 198 Processing helix chain 'Y' and resid 209 through 214 Processing helix chain 'Y' and resid 222 through 259 removed outlier: 4.249A pdb=" N ASP Y 245 " --> pdb=" O SER Y 241 " (cutoff:3.500A) Processing helix chain 'Y' and resid 262 through 271 Processing helix chain 'Y' and resid 287 through 308 Processing helix chain 'Y' and resid 342 through 357 removed outlier: 3.590A pdb=" N THR Y 346 " --> pdb=" O ASP Y 342 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS Y 357 " --> pdb=" O LEU Y 353 " (cutoff:3.500A) Processing helix chain 'Y' and resid 357 through 366 removed outlier: 3.616A pdb=" N GLY Y 361 " --> pdb=" O LYS Y 357 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL Y 363 " --> pdb=" O ASP Y 359 " (cutoff:3.500A) Processing helix chain 'Y' and resid 370 through 380 Processing helix chain 'Y' and resid 405 through 418 Processing helix chain 'Y' and resid 424 through 449 removed outlier: 3.545A pdb=" N GLU Y 428 " --> pdb=" O LYS Y 424 " (cutoff:3.500A) Processing helix chain 'Y' and resid 456 through 473 Processing helix chain 'Y' and resid 474 through 476 No H-bonds generated for 'chain 'Y' and resid 474 through 476' Processing helix chain 'Y' and resid 483 through 501 Processing helix chain 'Y' and resid 602 through 610 Processing helix chain 'Y' and resid 711 through 728 removed outlier: 4.368A pdb=" N ARG Y 728 " --> pdb=" O VAL Y 724 " (cutoff:3.500A) Processing helix chain 'Y' and resid 738 through 762 removed outlier: 3.757A pdb=" N HIS Y 762 " --> pdb=" O HIS Y 758 " (cutoff:3.500A) Processing helix chain 'Y' and resid 788 through 802 removed outlier: 3.663A pdb=" N MET Y 792 " --> pdb=" O GLN Y 788 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU Y 793 " --> pdb=" O TYR Y 789 " (cutoff:3.500A) Processing helix chain 'Y' and resid 886 through 893 Processing helix chain 'Y' and resid 897 through 903 Processing helix chain 'Y' and resid 906 through 914 removed outlier: 3.996A pdb=" N UNK Y 910 " --> pdb=" O UNK Y 906 " (cutoff:3.500A) Processing helix chain 'Y' and resid 935 through 950 removed outlier: 3.715A pdb=" N LEU Y 947 " --> pdb=" O ALA Y 943 " (cutoff:3.500A) Processing helix chain 'Y' and resid 965 through 981 removed outlier: 3.595A pdb=" N ALA Y 969 " --> pdb=" O PRO Y 965 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG Y 976 " --> pdb=" O ALA Y 972 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS Y 979 " --> pdb=" O LYS Y 975 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 18 through 20 Processing sheet with id=AA2, first strand: chain 'Y' and resid 27 through 29 removed outlier: 6.826A pdb=" N THR Y 651 " --> pdb=" O ALA Y 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 33 through 34 Processing sheet with id=AA4, first strand: chain 'Y' and resid 557 through 558 removed outlier: 3.596A pdb=" N ARG Y 557 " --> pdb=" O THR Y 586 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 633 through 634 removed outlier: 3.878A pdb=" N GLU Y 643 " --> pdb=" O ILE Y 634 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Y' and resid 669 through 670 removed outlier: 6.351A pdb=" N ILE Y 669 " --> pdb=" O VAL Y 767 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ALA Y 769 " --> pdb=" O ILE Y 669 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Y' and resid 923 through 924 removed outlier: 3.587A pdb=" N VAL Y 932 " --> pdb=" O PHE Y 923 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 837 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 156 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 114 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 5.62 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: 1893 1.33 - 1.45: 3611 1.45 - 1.57: 5213 1.57 - 1.69: 355 1.69 - 1.82: 34 Bond restraints: 11106 Sorted by residual: bond pdb=" C ASN Y 501 " pdb=" N PRO Y 502 " ideal model delta sigma weight residual 1.334 1.355 -0.021 8.40e-03 1.42e+04 6.32e+00 bond pdb=" CA LEU Y 615 " pdb=" CB LEU Y 615 " ideal model delta sigma weight residual 1.531 1.457 0.073 3.28e-02 9.30e+02 5.00e+00 bond pdb=" CA THR Y 782 " pdb=" CB THR Y 782 " ideal model delta sigma weight residual 1.526 1.497 0.030 1.53e-02 4.27e+03 3.75e+00 bond pdb=" CG1 ILE Y 79 " pdb=" CD1 ILE Y 79 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.86e+00 bond pdb=" C THR Y 279 " pdb=" N LEU Y 280 " ideal model delta sigma weight residual 1.331 1.296 0.035 2.07e-02 2.33e+03 2.82e+00 ... (remaining 11101 not shown) Histogram of bond angle deviations from ideal: 97.12 - 104.50: 818 104.50 - 111.88: 5550 111.88 - 119.26: 3787 119.26 - 126.64: 5115 126.64 - 134.02: 584 Bond angle restraints: 15854 Sorted by residual: angle pdb=" N SER Y 197 " pdb=" CA SER Y 197 " pdb=" C SER Y 197 " ideal model delta sigma weight residual 114.64 104.07 10.57 1.52e+00 4.33e-01 4.84e+01 angle pdb=" N GLY Y 572 " pdb=" CA GLY Y 572 " pdb=" C GLY Y 572 " ideal model delta sigma weight residual 113.18 127.78 -14.60 2.37e+00 1.78e-01 3.79e+01 angle pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta sigma weight residual 121.54 133.12 -11.58 1.91e+00 2.74e-01 3.68e+01 angle pdb=" CA TRP Y 534 " pdb=" CB TRP Y 534 " pdb=" CG TRP Y 534 " ideal model delta sigma weight residual 113.60 124.37 -10.77 1.90e+00 2.77e-01 3.21e+01 angle pdb=" C SER Y 772 " pdb=" N ARG Y 773 " pdb=" CA ARG Y 773 " ideal model delta sigma weight residual 121.31 129.16 -7.85 1.49e+00 4.50e-01 2.77e+01 ... (remaining 15849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 5926 34.26 - 68.51: 596 68.51 - 102.77: 53 102.77 - 137.03: 1 137.03 - 171.29: 4 Dihedral angle restraints: 6580 sinusoidal: 3923 harmonic: 2657 Sorted by residual: dihedral pdb=" O4' U B 17 " pdb=" C1' U B 17 " pdb=" N1 U B 17 " pdb=" C2 U B 17 " ideal model delta sinusoidal sigma weight residual 232.00 60.71 171.29 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" CA ILE Y 198 " pdb=" C ILE Y 198 " pdb=" N HIS Y 199 " pdb=" CA HIS Y 199 " ideal model delta harmonic sigma weight residual -180.00 -142.36 -37.64 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA GLY Y 367 " pdb=" C GLY Y 367 " pdb=" N VAL Y 368 " pdb=" CA VAL Y 368 " ideal model delta harmonic sigma weight residual 180.00 -144.29 -35.71 0 5.00e+00 4.00e-02 5.10e+01 ... (remaining 6577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1566 0.066 - 0.133: 259 0.133 - 0.199: 44 0.199 - 0.265: 6 0.265 - 0.331: 5 Chirality restraints: 1880 Sorted by residual: chirality pdb=" C3' C B 40 " pdb=" C4' C B 40 " pdb=" O3' C B 40 " pdb=" C2' C B 40 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C3' G B 44 " pdb=" C4' G B 44 " pdb=" O3' G B 44 " pdb=" C2' G B 44 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C3' G B 60 " pdb=" C4' G B 60 " pdb=" O3' G B 60 " pdb=" C2' G B 60 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1877 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN Y 501 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO Y 502 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO Y 502 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO Y 502 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE Y 609 " -0.021 2.00e-02 2.50e+03 1.95e-02 6.64e+00 pdb=" CG PHE Y 609 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE Y 609 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE Y 609 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE Y 609 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE Y 609 " -0.017 2.00e-02 2.50e+03 pdb=" CZ PHE Y 609 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 56 " 0.033 2.00e-02 2.50e+03 1.53e-02 6.40e+00 pdb=" N9 A B 56 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A B 56 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 56 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A B 56 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A B 56 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A B 56 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A B 56 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A B 56 " -0.010 2.00e-02 2.50e+03 pdb=" N3 A B 56 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A B 56 " -0.002 2.00e-02 2.50e+03 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2526 2.79 - 3.32: 8775 3.32 - 3.85: 19254 3.85 - 4.37: 21458 4.37 - 4.90: 32711 Nonbonded interactions: 84724 Sorted by model distance: nonbonded pdb=" OH TYR Y 196 " pdb=" O SER Y 221 " model vdw 2.266 2.440 nonbonded pdb=" OG1 THR Y 684 " pdb=" O ASP Y 685 " model vdw 2.268 2.440 nonbonded pdb=" O SER Y 738 " pdb=" OG SER Y 738 " model vdw 2.297 2.440 nonbonded pdb=" OG1 THR Y 603 " pdb=" OP2 A B 18 " model vdw 2.306 2.440 nonbonded pdb=" ND2 ASN Y 549 " pdb=" O GLY Y 554 " model vdw 2.308 2.520 ... (remaining 84719 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.890 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 36.170 Find NCS groups from input model: 0.250 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 0.073 11106 Z= 0.429 Angle : 1.015 14.600 15854 Z= 0.557 Chirality : 0.055 0.331 1880 Planarity : 0.007 0.079 1380 Dihedral : 22.803 171.287 4853 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.60 % Favored : 83.63 % Rotamer: Outliers : 0.66 % Allowed : 8.39 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.26 % 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: -4.66 (0.23), residues: 782 helix: -2.21 (0.20), residues: 344 sheet: -2.52 (0.53), residues: 97 loop : -4.25 (0.24), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP Y 534 HIS 0.015 0.002 HIS Y 250 PHE 0.042 0.003 PHE Y 609 TYR 0.018 0.003 TYR Y 818 ARG 0.009 0.001 ARG Y 673 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 302 MET cc_start: 0.7905 (ttp) cc_final: 0.7688 (ttm) REVERT: Y 778 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8164 (tm-30) outliers start: 4 outliers final: 2 residues processed: 86 average time/residue: 0.3665 time to fit residues: 41.2610 Evaluate side-chains 60 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 583 ILE Chi-restraints excluded: chain Y residue 684 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 283 GLN Y 285 HIS Y 501 ASN Y 715 GLN Y 742 ASN Y 788 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11106 Z= 0.179 Angle : 0.682 10.057 15854 Z= 0.362 Chirality : 0.038 0.230 1880 Planarity : 0.005 0.037 1380 Dihedral : 24.260 177.426 3416 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.96 % Favored : 84.91 % Rotamer: Outliers : 3.12 % Allowed : 12.83 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.00 (0.28), residues: 782 helix: -0.23 (0.26), residues: 354 sheet: -2.37 (0.55), residues: 92 loop : -3.95 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Y 534 HIS 0.005 0.001 HIS Y 250 PHE 0.026 0.002 PHE Y 609 TYR 0.012 0.001 TYR Y 818 ARG 0.005 0.000 ARG Y 777 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 707 ILE cc_start: 0.8302 (mt) cc_final: 0.8098 (mt) REVERT: Y 778 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8057 (tm-30) REVERT: Y 970 TRP cc_start: 0.8006 (t60) cc_final: 0.7757 (t60) outliers start: 19 outliers final: 10 residues processed: 90 average time/residue: 0.2451 time to fit residues: 30.8371 Evaluate side-chains 73 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 197 SER Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 245 ASP Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 807 SER Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 30.0000 chunk 97 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 91 HIS ** Y 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11106 Z= 0.270 Angle : 0.693 9.181 15854 Z= 0.371 Chirality : 0.039 0.200 1880 Planarity : 0.005 0.037 1380 Dihedral : 24.253 169.497 3414 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.60 % Favored : 84.14 % Rotamer: Outliers : 4.44 % Allowed : 14.64 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.29), residues: 782 helix: 0.54 (0.28), residues: 354 sheet: -2.30 (0.56), residues: 92 loop : -3.87 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Y 534 HIS 0.005 0.001 HIS Y 250 PHE 0.025 0.002 PHE Y 609 TYR 0.013 0.002 TYR Y 575 ARG 0.004 0.000 ARG Y 734 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 60 time to evaluate : 0.918 Fit side-chains REVERT: Y 313 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7631 (mtpt) REVERT: Y 707 ILE cc_start: 0.8591 (mt) cc_final: 0.8335 (mt) REVERT: Y 778 GLN cc_start: 0.8462 (tm-30) cc_final: 0.8088 (tm-30) REVERT: Y 784 MET cc_start: 0.8621 (mmm) cc_final: 0.7928 (tmm) REVERT: Y 970 TRP cc_start: 0.8047 (t60) cc_final: 0.7486 (t60) outliers start: 27 outliers final: 18 residues processed: 80 average time/residue: 0.2095 time to fit residues: 24.7022 Evaluate side-chains 71 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 38 ASP Chi-restraints excluded: chain Y residue 91 HIS Chi-restraints excluded: chain Y residue 197 SER Chi-restraints excluded: chain Y residue 245 ASP Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 425 VAL Chi-restraints excluded: chain Y residue 531 LEU Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 807 SER Chi-restraints excluded: chain Y residue 812 SER Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 91 HIS ** Y 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11106 Z= 0.263 Angle : 0.678 9.563 15854 Z= 0.364 Chirality : 0.039 0.201 1880 Planarity : 0.004 0.035 1380 Dihedral : 24.220 171.503 3414 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 15.73 % Favored : 84.02 % Rotamer: Outliers : 3.95 % Allowed : 17.11 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.30), residues: 782 helix: 0.83 (0.29), residues: 354 sheet: -2.27 (0.56), residues: 92 loop : -3.74 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP Y 534 HIS 0.017 0.002 HIS Y 91 PHE 0.020 0.002 PHE Y 609 TYR 0.013 0.002 TYR Y 818 ARG 0.002 0.000 ARG Y 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 57 time to evaluate : 0.918 Fit side-chains REVERT: Y 707 ILE cc_start: 0.8636 (mt) cc_final: 0.8375 (mt) REVERT: Y 736 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7367 (p90) REVERT: Y 778 GLN cc_start: 0.8417 (tm-30) cc_final: 0.8012 (tm-30) REVERT: Y 784 MET cc_start: 0.8618 (mmm) cc_final: 0.8372 (mmm) REVERT: Y 970 TRP cc_start: 0.8056 (t60) cc_final: 0.7594 (t60) outliers start: 24 outliers final: 18 residues processed: 76 average time/residue: 0.2144 time to fit residues: 24.4372 Evaluate side-chains 73 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 67 MET Chi-restraints excluded: chain Y residue 197 SER Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 245 ASP Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 302 MET Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 531 LEU Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 807 SER Chi-restraints excluded: chain Y residue 812 SER Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 967 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 40.0000 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11106 Z= 0.219 Angle : 0.658 9.113 15854 Z= 0.352 Chirality : 0.038 0.205 1880 Planarity : 0.004 0.052 1380 Dihedral : 24.158 172.591 3414 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.47 % Favored : 84.40 % Rotamer: Outliers : 3.78 % Allowed : 17.43 % Favored : 78.78 % 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: -1.83 (0.31), residues: 782 helix: 1.07 (0.29), residues: 355 sheet: -2.26 (0.57), residues: 92 loop : -3.62 (0.28), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Y 534 HIS 0.003 0.001 HIS Y 250 PHE 0.016 0.002 PHE Y 503 TYR 0.012 0.001 TYR Y 818 ARG 0.004 0.000 ARG Y 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1564 Ramachandran restraints generated. 782 Oldfield, 0 Emsley, 782 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 1.042 Fit side-chains REVERT: Y 707 ILE cc_start: 0.8514 (mt) cc_final: 0.8246 (mt) REVERT: Y 736 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7367 (p90) REVERT: Y 778 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8031 (tm-30) REVERT: Y 784 MET cc_start: 0.8630 (mmm) cc_final: 0.8309 (mmm) REVERT: Y 970 TRP cc_start: 0.8046 (t60) cc_final: 0.7645 (t60) outliers start: 23 outliers final: 19 residues processed: 78 average time/residue: 0.1831 time to fit residues: 22.0156 Evaluate side-chains 76 residues out of total 681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 56 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 38 ASP Chi-restraints excluded: chain Y residue 91 HIS Chi-restraints excluded: chain Y residue 199 HIS Chi-restraints excluded: chain Y residue 245 ASP Chi-restraints excluded: chain Y residue 246 ILE Chi-restraints excluded: chain Y residue 261 LEU Chi-restraints excluded: chain Y residue 302 MET Chi-restraints excluded: chain Y residue 343 TRP Chi-restraints excluded: chain Y residue 368 VAL Chi-restraints excluded: chain Y residue 425 VAL Chi-restraints excluded: chain Y residue 512 VAL Chi-restraints excluded: chain Y residue 639 ILE Chi-restraints excluded: chain Y residue 651 THR Chi-restraints excluded: chain Y residue 677 ILE Chi-restraints excluded: chain Y residue 684 THR Chi-restraints excluded: chain Y residue 736 PHE Chi-restraints excluded: chain Y residue 807 SER Chi-restraints excluded: chain Y residue 812 SER Chi-restraints excluded: chain Y residue 932 VAL Chi-restraints excluded: chain Y residue 967 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: 69.5463 > 50: distance: 34 - 39: 28.517 distance: 39 - 40: 25.330 distance: 40 - 41: 26.747 distance: 40 - 43: 36.006 distance: 41 - 46: 56.065 distance: 43 - 44: 40.841 distance: 43 - 45: 41.042 distance: 46 - 47: 56.907 distance: 47 - 48: 55.099 distance: 47 - 50: 69.546 distance: 48 - 49: 3.253 distance: 48 - 52: 40.357 distance: 50 - 51: 57.127 distance: 52 - 53: 40.323 distance: 53 - 54: 20.133 distance: 53 - 56: 32.388 distance: 54 - 55: 45.826 distance: 54 - 63: 21.500 distance: 56 - 57: 41.579 distance: 57 - 58: 29.381 distance: 58 - 59: 26.503 distance: 59 - 60: 13.213 distance: 60 - 61: 4.073 distance: 60 - 62: 14.755 distance: 64 - 67: 32.530 distance: 65 - 66: 40.067 distance: 65 - 69: 39.406 distance: 67 - 68: 9.489 distance: 69 - 70: 38.794 distance: 70 - 71: 23.366 distance: 71 - 72: 43.238 distance: 71 - 73: 44.362 distance: 73 - 74: 52.880 distance: 73 - 79: 15.653 distance: 74 - 75: 65.010 distance: 74 - 77: 47.653 distance: 75 - 76: 22.229 distance: 75 - 80: 16.222 distance: 77 - 78: 42.662 distance: 78 - 79: 40.741 distance: 80 - 81: 41.065 distance: 81 - 82: 44.142 distance: 81 - 84: 32.728 distance: 82 - 83: 42.812 distance: 82 - 88: 44.598 distance: 84 - 85: 44.065 distance: 85 - 86: 12.111 distance: 86 - 87: 28.543 distance: 88 - 89: 12.455 distance: 88 - 162: 28.487 distance: 89 - 90: 41.016 distance: 89 - 92: 38.685 distance: 90 - 91: 20.620 distance: 90 - 97: 39.960 distance: 91 - 159: 19.819 distance: 92 - 93: 35.419 distance: 93 - 94: 37.539 distance: 95 - 96: 45.651 distance: 97 - 98: 69.348 distance: 98 - 99: 61.315 distance: 98 - 101: 56.105 distance: 99 - 100: 48.975 distance: 99 - 104: 48.097 distance: 101 - 102: 40.813 distance: 101 - 103: 43.250 distance: 104 - 105: 38.949 distance: 105 - 106: 63.184 distance: 105 - 108: 39.809 distance: 106 - 107: 42.055 distance: 106 - 112: 28.547 distance: 108 - 109: 24.099 distance: 109 - 110: 45.043 distance: 109 - 111: 32.392