Starting phenix.real_space_refine on Fri Dec 8 08:57:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/12_2023/7sp8_25368.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/12_2023/7sp8_25368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/12_2023/7sp8_25368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/12_2023/7sp8_25368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/12_2023/7sp8_25368.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp8_25368/12_2023/7sp8_25368.pdb" } resolution = 2.7 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= -0.001 sd= 0.791 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1820 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 S 35 5.16 5 C 3935 2.51 5 N 999 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 140": "OD1" <-> "OD2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6090 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4088 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 500, 4077 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 13, 'TRANS': 486} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 500, 4077 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 13, 'TRANS': 486} Chain breaks: 1 bond proxies already assigned to first conformer: 4176 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "C" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 925 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain breaks: 1 Chain: "A" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 127 Unusual residues: {' MN': 2, '3PE': 1, 'UD1': 1, 'Y01': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 303 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 303 " occ=0.50 Time building chain proxies: 6.12, per 1000 atoms: 1.00 Number of scatterers: 6090 At special positions: 0 Unit cell: (73.44, 72.36, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 35 16.00 P 3 15.00 O 1116 8.00 N 999 7.00 C 3935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 2.59 Conformation dependent library (CDL) restraints added in 2.1 seconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 47.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.648A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.655A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.509A pdb=" N SER A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.560A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 4.051A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 289 removed outlier: 5.221A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 331 through 357 removed outlier: 4.281A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 361 Processing helix chain 'A' and resid 364 through 392 Processing helix chain 'A' and resid 393 through 420 removed outlier: 3.507A pdb=" N GLN A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.707A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 4.031A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 468 through 497 removed outlier: 4.083A pdb=" N GLN A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 476 " --> pdb=" O TRP A 472 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 478 " --> pdb=" O LYS A 474 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR A 479 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 535 Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.750A pdb=" N LYS A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.522A pdb=" N THR B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143 removed outlier: 3.656A pdb=" N ILE A 168 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.639A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.789A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.554A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.630A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 18 " --> pdb=" O MET B 82 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 20 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.292A pdb=" N VAL B 12 " --> pdb=" O SER B 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.877A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.877A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.592A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.050A pdb=" N PHE C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG C 38 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR C 93 " --> pdb=" O GLY C 119 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY C 119 " --> pdb=" O TYR C 93 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N CYS C 95 " --> pdb=" O GLY C 117 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 942 1.31 - 1.43: 1856 1.43 - 1.56: 3363 1.56 - 1.69: 28 1.69 - 1.81: 53 Bond restraints: 6242 Sorted by residual: bond pdb=" C2B UD1 A 601 " pdb=" C3B UD1 A 601 " ideal model delta sigma weight residual 1.533 1.303 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C5 UD1 A 601 " pdb=" C6 UD1 A 601 " ideal model delta sigma weight residual 1.342 1.484 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C2 UD1 A 601 " pdb=" N3 UD1 A 601 " ideal model delta sigma weight residual 1.371 1.501 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" CBD Y01 A 603 " pdb=" CBG Y01 A 603 " ideal model delta sigma weight residual 1.520 1.644 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" C7' UD1 A 601 " pdb=" N2' UD1 A 601 " ideal model delta sigma weight residual 1.347 1.465 -0.118 2.00e-02 2.50e+03 3.49e+01 ... (remaining 6237 not shown) Histogram of bond angle deviations from ideal: 98.99 - 105.98: 97 105.98 - 112.98: 3298 112.98 - 119.98: 2147 119.98 - 126.97: 2853 126.97 - 133.97: 74 Bond angle restraints: 8469 Sorted by residual: angle pdb=" O1' UD1 A 601 " pdb=" PB UD1 A 601 " pdb=" O3A UD1 A 601 " ideal model delta sigma weight residual 92.88 109.25 -16.37 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O3A UD1 A 601 " pdb=" PA UD1 A 601 " pdb=" O5B UD1 A 601 " ideal model delta sigma weight residual 94.40 109.61 -15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O12 3PE A 602 " pdb=" P 3PE A 602 " pdb=" O14 3PE A 602 " ideal model delta sigma weight residual 123.79 109.19 14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" CAM Y01 A 603 " pdb=" CAY Y01 A 603 " pdb=" OAW Y01 A 603 " ideal model delta sigma weight residual 111.19 124.36 -13.17 3.00e+00 1.11e-01 1.93e+01 angle pdb=" CAI Y01 A 603 " pdb=" CAZ Y01 A 603 " pdb=" CAV Y01 A 603 " ideal model delta sigma weight residual 120.03 131.68 -11.65 3.00e+00 1.11e-01 1.51e+01 ... (remaining 8464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.02: 3558 28.02 - 56.04: 147 56.04 - 84.06: 19 84.06 - 112.08: 1 112.08 - 140.10: 1 Dihedral angle restraints: 3726 sinusoidal: 1560 harmonic: 2166 Sorted by residual: dihedral pdb=" O21 3PE A 602 " pdb=" C2 3PE A 602 " pdb=" C3 3PE A 602 " pdb=" O31 3PE A 602 " ideal model delta sinusoidal sigma weight residual 60.47 -159.43 -140.10 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" CA GLU A 548 " pdb=" C GLU A 548 " pdb=" N ARG A 549 " pdb=" CA ARG A 549 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP C 59 " pdb=" CB ASP C 59 " pdb=" CG ASP C 59 " pdb=" OD1 ASP C 59 " ideal model delta sinusoidal sigma weight residual -30.00 -84.64 54.64 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 3723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 844 0.079 - 0.158: 62 0.158 - 0.237: 8 0.237 - 0.316: 2 0.316 - 0.395: 3 Chirality restraints: 919 Sorted by residual: chirality pdb=" CBG Y01 A 603 " pdb=" CAQ Y01 A 603 " pdb=" CBD Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CBE Y01 A 603 " pdb=" CAP Y01 A 603 " pdb=" CBB Y01 A 603 " pdb=" CBI Y01 A 603 " both_signs ideal model delta sigma weight residual False 2.57 2.93 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CBI Y01 A 603 " pdb=" CAU Y01 A 603 " pdb=" CBE Y01 A 603 " pdb=" CBG Y01 A 603 " both_signs ideal model delta sigma weight residual False 2.94 2.61 0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 916 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 544 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C GLU A 544 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU A 544 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 545 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 86 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 87 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 545 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C LEU A 545 " 0.020 2.00e-02 2.50e+03 pdb=" O LEU A 545 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 546 " -0.007 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 454 2.74 - 3.28: 5804 3.28 - 3.82: 10316 3.82 - 4.36: 11542 4.36 - 4.90: 20548 Nonbonded interactions: 48664 Sorted by model distance: nonbonded pdb=" OD2 ASP A 203 " pdb="MN MN A 605 " model vdw 2.204 2.320 nonbonded pdb=" OE2 GLU A 93 " pdb="MN MN A 604 " model vdw 2.247 2.320 nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLN A 506 " pdb=" OG1 THR B 56 " model vdw 2.296 2.440 nonbonded pdb=" OD2 ASP B 104 " pdb=" OG1 THR B 107 " model vdw 2.321 2.440 ... (remaining 48659 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 4.080 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 25.410 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.008 0.230 6242 Z= 0.499 Angle : 0.770 16.370 8469 Z= 0.303 Chirality : 0.049 0.395 919 Planarity : 0.003 0.031 1040 Dihedral : 14.940 140.099 2342 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.16 % Allowed : 0.47 % Favored : 99.37 % 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: 2.53 (0.32), residues: 735 helix: 2.59 (0.30), residues: 316 sheet: 2.50 (0.42), residues: 161 loop : -0.08 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP A 346 HIS 0.001 0.000 HIS A 552 PHE 0.014 0.001 PHE A 49 TYR 0.008 0.001 TYR A 414 ARG 0.001 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.648 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.9252 time to fit residues: 138.6269 Evaluate side-chains 109 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 338 GLN A 537 ASN B 39 GLN B 73 ASN C 76 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6242 Z= 0.124 Angle : 0.478 7.153 8469 Z= 0.244 Chirality : 0.040 0.139 919 Planarity : 0.003 0.024 1040 Dihedral : 9.535 109.256 1008 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 3.16 % Allowed : 9.95 % Favored : 86.89 % 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: 2.51 (0.31), residues: 735 helix: 2.77 (0.30), residues: 317 sheet: 2.08 (0.40), residues: 160 loop : -0.06 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.001 0.000 HIS A 360 PHE 0.013 0.001 PHE A 49 TYR 0.013 0.001 TYR A 46 ARG 0.002 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.709 Fit side-chains outliers start: 19 outliers final: 4 residues processed: 130 average time/residue: 0.8997 time to fit residues: 124.4870 Evaluate side-chains 121 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 0.760 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.0599 time to fit residues: 1.2179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.0000 chunk 55 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 0.0050 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6242 Z= 0.159 Angle : 0.503 8.224 8469 Z= 0.262 Chirality : 0.040 0.132 919 Planarity : 0.003 0.032 1040 Dihedral : 9.019 89.158 1008 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.16 % Allowed : 12.32 % Favored : 84.52 % 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: 2.34 (0.31), residues: 735 helix: 2.59 (0.29), residues: 318 sheet: 2.13 (0.41), residues: 153 loop : -0.12 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.002 0.001 HIS A 360 PHE 0.014 0.001 PHE A 49 TYR 0.018 0.001 TYR A 414 ARG 0.002 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.668 Fit side-chains outliers start: 19 outliers final: 10 residues processed: 128 average time/residue: 0.9351 time to fit residues: 126.9922 Evaluate side-chains 121 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.703 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 4 residues processed: 6 average time/residue: 0.5554 time to fit residues: 4.5314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6242 Z= 0.206 Angle : 0.530 8.736 8469 Z= 0.278 Chirality : 0.042 0.148 919 Planarity : 0.003 0.036 1040 Dihedral : 8.957 72.906 1008 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.58 % Allowed : 13.59 % Favored : 81.83 % 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: 2.08 (0.31), residues: 735 helix: 2.33 (0.29), residues: 322 sheet: 1.99 (0.39), residues: 151 loop : -0.21 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 472 HIS 0.004 0.001 HIS A 360 PHE 0.017 0.001 PHE A 49 TYR 0.018 0.002 TYR A 414 ARG 0.008 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 0.775 Fit side-chains outliers start: 28 outliers final: 11 residues processed: 122 average time/residue: 1.0180 time to fit residues: 131.2216 Evaluate side-chains 112 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.682 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.0771 time to fit residues: 1.4707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6242 Z= 0.205 Angle : 0.524 7.402 8469 Z= 0.274 Chirality : 0.042 0.152 919 Planarity : 0.003 0.039 1040 Dihedral : 9.087 65.972 1008 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 5.06 % Allowed : 14.53 % Favored : 80.41 % 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: 2.02 (0.30), residues: 735 helix: 2.29 (0.29), residues: 320 sheet: 2.00 (0.39), residues: 149 loop : -0.26 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 472 HIS 0.004 0.001 HIS A 360 PHE 0.016 0.001 PHE A 49 TYR 0.018 0.001 TYR A 414 ARG 0.003 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 0.730 Fit side-chains outliers start: 31 outliers final: 12 residues processed: 121 average time/residue: 1.0294 time to fit residues: 131.5766 Evaluate side-chains 110 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.752 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.0855 time to fit residues: 1.8043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6242 Z= 0.167 Angle : 0.521 8.850 8469 Z= 0.265 Chirality : 0.042 0.133 919 Planarity : 0.003 0.039 1040 Dihedral : 8.916 64.107 1008 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.37 % Allowed : 17.54 % Favored : 80.09 % 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: 2.08 (0.30), residues: 735 helix: 2.39 (0.29), residues: 319 sheet: 2.02 (0.39), residues: 149 loop : -0.28 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 472 HIS 0.003 0.001 HIS A 360 PHE 0.015 0.001 PHE A 49 TYR 0.018 0.001 TYR C 106 ARG 0.002 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.758 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 112 average time/residue: 1.0770 time to fit residues: 127.6824 Evaluate side-chains 108 residues out of total 631 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 0.0871 time to fit residues: 1.4073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/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-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.8158 > 50: distance: 36 - 244: 24.441 distance: 39 - 241: 28.874 distance: 95 - 228: 31.280 distance: 98 - 237: 17.187 distance: 110 - 240: 29.794 distance: 113 - 255: 22.564 distance: 176 - 181: 6.707 distance: 181 - 182: 19.806 distance: 182 - 183: 22.802 distance: 182 - 185: 18.156 distance: 183 - 184: 11.045 distance: 183 - 188: 40.117 distance: 185 - 186: 22.060 distance: 185 - 187: 8.459 distance: 188 - 189: 23.084 distance: 189 - 190: 14.147 distance: 189 - 192: 23.960 distance: 190 - 191: 15.862 distance: 190 - 200: 9.286 distance: 192 - 193: 11.563 distance: 193 - 194: 18.808 distance: 193 - 195: 12.245 distance: 194 - 196: 6.273 distance: 195 - 197: 9.517 distance: 196 - 198: 22.137 distance: 197 - 198: 12.431 distance: 198 - 199: 9.068 distance: 200 - 201: 31.973 distance: 201 - 202: 3.632 distance: 201 - 204: 15.658 distance: 202 - 203: 30.765 distance: 202 - 207: 31.531 distance: 204 - 205: 7.993 distance: 204 - 206: 20.283 distance: 207 - 208: 22.698 distance: 207 - 213: 15.075 distance: 208 - 209: 23.968 distance: 208 - 211: 42.068 distance: 209 - 210: 9.308 distance: 209 - 214: 38.905 distance: 211 - 212: 36.095 distance: 212 - 213: 55.834 distance: 214 - 215: 11.995 distance: 215 - 216: 9.410 distance: 215 - 218: 18.590 distance: 216 - 217: 3.353 distance: 216 - 225: 6.186 distance: 218 - 219: 11.397 distance: 219 - 220: 16.019 distance: 219 - 221: 27.844 distance: 220 - 222: 19.038 distance: 221 - 223: 12.817 distance: 222 - 224: 25.459 distance: 223 - 224: 10.952 distance: 225 - 226: 3.340 distance: 226 - 227: 10.764 distance: 226 - 229: 11.745 distance: 227 - 228: 13.315 distance: 227 - 230: 8.058 distance: 230 - 231: 8.485 distance: 231 - 232: 11.824 distance: 231 - 234: 4.361 distance: 232 - 233: 10.105 distance: 232 - 237: 9.192 distance: 234 - 235: 18.234 distance: 234 - 236: 12.471 distance: 237 - 238: 15.272 distance: 238 - 239: 28.246 distance: 239 - 240: 28.857 distance: 239 - 241: 18.930 distance: 241 - 242: 17.980 distance: 242 - 243: 8.559 distance: 242 - 245: 4.824 distance: 243 - 244: 4.912 distance: 243 - 255: 19.931 distance: 245 - 246: 4.866 distance: 246 - 247: 10.848 distance: 246 - 248: 4.605 distance: 248 - 250: 4.368 distance: 248 - 251: 8.038 distance: 249 - 250: 6.889 distance: 250 - 252: 6.817 distance: 251 - 253: 7.500 distance: 252 - 254: 10.622 distance: 253 - 254: 9.424 distance: 255 - 256: 8.153 distance: 256 - 259: 20.135 distance: 257 - 258: 15.518 distance: 257 - 261: 28.207 distance: 259 - 260: 37.634