Starting phenix.real_space_refine on Sat Apr 6 13:05:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/04_2024/8hij_34818_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/04_2024/8hij_34818.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/04_2024/8hij_34818_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/04_2024/8hij_34818_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/04_2024/8hij_34818_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/04_2024/8hij_34818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/04_2024/8hij_34818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/04_2024/8hij_34818_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hij_34818/04_2024/8hij_34818_neut_updated.pdb" } resolution = 3.54 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= 0.018 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 5304 2.51 5 N 1379 2.21 5 O 1536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "N ARG 27": "NH1" <-> "NH2" Residue "N ARG 53": "NH1" <-> "NH2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 25": "NH1" <-> "NH2" Residue "L ARG 213": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8245 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3969 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 17, 'TRANS': 480} Chain breaks: 1 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'THH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.74, per 1000 atoms: 0.57 Number of scatterers: 8245 At special positions: 0 Unit cell: (66.34, 101.65, 151.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1536 8.00 N 1379 7.00 C 5304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.02 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: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB THH A 601 " Number of C-beta restraints generated: 1972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 35.4% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid -79 through -65 Processing helix chain 'A' and resid -56 through -44 Processing helix chain 'A' and resid -37 through -34 No H-bonds generated for 'chain 'A' and resid -37 through -34' Processing helix chain 'A' and resid -24 through -4 removed outlier: 3.799A pdb=" N LEU A -5 " --> pdb=" O ASP A -9 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.747A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 Processing helix chain 'A' and resid 93 through 111 Processing helix chain 'A' and resid 116 through 131 removed outlier: 4.289A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 149 through 175 Processing helix chain 'A' and resid 182 through 201 Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 265 through 295 removed outlier: 4.723A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 336 through 354 Processing helix chain 'A' and resid 359 through 388 removed outlier: 3.780A pdb=" N ILE A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TRP A 363 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN A 377 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 378 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 380 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 3.747A pdb=" N ILE A 387 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 388 " --> pdb=" O PHE A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 418 Processing helix chain 'A' and resid 428 through 450 Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 108 through 111 No H-bonds generated for 'chain 'H' and resid 108 through 111' Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.689A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL H 8 " --> pdb=" O ALA H 26 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 20 through 22 Processing sheet with id= C, first strand: chain 'H' and resid 101 through 103 removed outlier: 3.580A pdb=" N LEU H 37 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 40 through 43 Processing sheet with id= E, first strand: chain 'H' and resid 74 through 76 removed outlier: 3.654A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 134 through 138 removed outlier: 3.680A pdb=" N LYS H 157 " --> pdb=" O SER H 134 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 164 through 168 Processing sheet with id= H, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.671A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.923A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL N 12 " --> pdb=" O THR N 118 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.598A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 20 through 25 removed outlier: 3.785A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR L 75 " --> pdb=" O SER L 64 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 34 through 36 Processing sheet with id= M, first strand: chain 'L' and resid 118 through 120 removed outlier: 3.894A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL L 134 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 147 through 151 removed outlier: 3.634A pdb=" N LYS L 147 " --> pdb=" O THR L 199 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA L 195 " --> pdb=" O LYS L 151 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR L 194 " --> pdb=" O PHE L 211 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS L 196 " --> pdb=" O LYS L 209 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS L 209 " --> pdb=" O CYS L 196 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 915 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: 2.13 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1289 1.31 - 1.44: 2457 1.44 - 1.56: 4662 1.56 - 1.69: 2 1.69 - 1.81: 38 Bond restraints: 8448 Sorted by residual: bond pdb=" C4 THH A 601 " pdb=" O4 THH A 601 " ideal model delta sigma weight residual 1.401 1.191 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" N THH A 601 " pdb=" C THH A 601 " ideal model delta sigma weight residual 1.452 1.523 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C6 THH A 601 " pdb=" C9 THH A 601 " ideal model delta sigma weight residual 1.585 1.645 -0.060 2.00e-02 2.50e+03 9.15e+00 bond pdb=" CD THH A 601 " pdb=" OE1 THH A 601 " ideal model delta sigma weight residual 1.259 1.315 -0.056 2.00e-02 2.50e+03 7.76e+00 bond pdb=" C9 THH A 601 " pdb=" N10 THH A 601 " ideal model delta sigma weight residual 1.458 1.510 -0.052 2.00e-02 2.50e+03 6.77e+00 ... (remaining 8443 not shown) Histogram of bond angle deviations from ideal: 99.48 - 106.43: 221 106.43 - 113.37: 4545 113.37 - 120.32: 3120 120.32 - 127.26: 3513 127.26 - 134.21: 94 Bond angle restraints: 11493 Sorted by residual: angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.81 117.88 -8.07 2.21e+00 2.05e-01 1.33e+01 angle pdb=" C ASN L 212 " pdb=" N ARG L 213 " pdb=" CA ARG L 213 " ideal model delta sigma weight residual 121.70 128.02 -6.32 1.80e+00 3.09e-01 1.23e+01 angle pdb=" C PHE N 103 " pdb=" N TYR N 104 " pdb=" CA TYR N 104 " ideal model delta sigma weight residual 122.36 127.05 -4.69 1.42e+00 4.96e-01 1.09e+01 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.64 -6.10 1.91e+00 2.74e-01 1.02e+01 angle pdb=" CA THR A 69 " pdb=" C THR A 69 " pdb=" N PRO A 70 " ideal model delta sigma weight residual 118.44 122.82 -4.38 1.59e+00 3.96e-01 7.59e+00 ... (remaining 11488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.62: 4853 20.62 - 41.23: 95 41.23 - 61.85: 6 61.85 - 82.46: 15 82.46 - 103.08: 1 Dihedral angle restraints: 4970 sinusoidal: 1893 harmonic: 3077 Sorted by residual: dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 172.05 -79.05 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ALA A 17 " pdb=" C ALA A 17 " pdb=" N TYR A 18 " pdb=" CA TYR A 18 " ideal model delta harmonic sigma weight residual -180.00 -156.52 -23.48 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 4967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 996 0.050 - 0.101: 235 0.101 - 0.151: 61 0.151 - 0.201: 4 0.201 - 0.252: 2 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA TRP A 107 " pdb=" N TRP A 107 " pdb=" C TRP A 107 " pdb=" CB TRP A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 ... (remaining 1295 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 102 " -0.014 2.00e-02 2.50e+03 1.39e-02 4.81e+00 pdb=" CG TRP H 102 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP H 102 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 102 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 102 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 102 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 102 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 102 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 102 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP H 102 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 103 " 0.014 2.00e-02 2.50e+03 1.53e-02 4.09e+00 pdb=" CG PHE A 103 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 103 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 103 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 103 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 103 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 103 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.033 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO H 109 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.027 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2587 2.83 - 3.35: 7107 3.35 - 3.87: 13432 3.87 - 4.38: 14459 4.38 - 4.90: 25702 Nonbonded interactions: 63287 Sorted by model distance: nonbonded pdb=" OG1 THR A 49 " pdb=" O4 THH A 601 " model vdw 2.315 2.440 nonbonded pdb=" O ARG A 61 " pdb=" OG1 THR A 65 " model vdw 2.330 2.440 nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.337 2.440 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.341 2.440 nonbonded pdb=" OD2 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.350 2.440 ... (remaining 63282 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 group one per residue 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: 1.390 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: 6.850 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.820 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.210 8448 Z= 0.244 Angle : 0.724 8.532 11493 Z= 0.382 Chirality : 0.047 0.252 1298 Planarity : 0.006 0.048 1440 Dihedral : 9.922 103.078 2983 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -3.81 (0.21), residues: 1045 helix: -1.71 (0.19), residues: 384 sheet: -3.00 (0.29), residues: 231 loop : -2.88 (0.24), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 102 HIS 0.004 0.001 HIS H 38 PHE 0.033 0.002 PHE A 103 TYR 0.026 0.002 TYR A 435 ARG 0.004 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -55 ASP cc_start: 0.6609 (t0) cc_final: 0.6405 (t0) REVERT: A -51 LYS cc_start: 0.8509 (mttt) cc_final: 0.8247 (mttt) REVERT: A -50 MET cc_start: 0.6978 (mmm) cc_final: 0.6731 (mmm) REVERT: A -16 ILE cc_start: 0.8500 (tp) cc_final: 0.8173 (mt) REVERT: A 1 VAL cc_start: 0.8584 (m) cc_final: 0.8263 (p) REVERT: A 46 SER cc_start: 0.7456 (m) cc_final: 0.6633 (t) REVERT: A 81 VAL cc_start: 0.7706 (t) cc_final: 0.7475 (m) REVERT: A 127 SER cc_start: 0.8834 (p) cc_final: 0.8229 (t) REVERT: A 139 TYR cc_start: 0.7092 (t80) cc_final: 0.6886 (t80) REVERT: A 149 TYR cc_start: 0.6915 (t80) cc_final: 0.6580 (t80) REVERT: A 155 TYR cc_start: 0.6982 (m-80) cc_final: 0.6754 (m-80) REVERT: A 162 LEU cc_start: 0.7897 (tp) cc_final: 0.7613 (tp) REVERT: A 254 MET cc_start: 0.7477 (mtt) cc_final: 0.7163 (mtt) REVERT: A 314 THR cc_start: 0.8067 (m) cc_final: 0.7829 (p) REVERT: A 405 PHE cc_start: 0.8105 (t80) cc_final: 0.7820 (t80) REVERT: A 406 PHE cc_start: 0.7492 (m-80) cc_final: 0.6995 (m-80) REVERT: A 411 LYS cc_start: 0.8025 (ttpt) cc_final: 0.7746 (ttpt) REVERT: H 37 LEU cc_start: 0.7269 (mt) cc_final: 0.6950 (mm) REVERT: H 46 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7788 (mmtt) REVERT: H 152 LEU cc_start: 0.7479 (tp) cc_final: 0.7115 (tp) REVERT: N 34 MET cc_start: 0.6920 (mtp) cc_final: 0.6480 (mtp) REVERT: L 4 GLN cc_start: 0.7196 (mm-40) cc_final: 0.6633 (mm-40) REVERT: L 38 GLN cc_start: 0.8298 (tt0) cc_final: 0.8093 (tt0) REVERT: L 73 THR cc_start: 0.8035 (m) cc_final: 0.7832 (t) REVERT: L 83 ASP cc_start: 0.6949 (m-30) cc_final: 0.6615 (m-30) REVERT: L 93 LEU cc_start: 0.7949 (tp) cc_final: 0.7464 (tp) REVERT: L 97 LEU cc_start: 0.8607 (mp) cc_final: 0.8387 (mt) REVERT: L 104 THR cc_start: 0.8497 (p) cc_final: 0.8194 (t) REVERT: L 142 TYR cc_start: 0.7731 (t80) cc_final: 0.7496 (t80) REVERT: L 147 LYS cc_start: 0.7312 (ttmm) cc_final: 0.7103 (ttmm) REVERT: L 211 PHE cc_start: 0.8091 (p90) cc_final: 0.7847 (p90) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2133 time to fit residues: 80.2598 Evaluate side-chains 223 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 60 optimal weight: 0.1980 chunk 94 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -61 ASN A -3 ASN A 63 GLN ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN A 172 GLN ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 GLN L 191 HIS L 200 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8448 Z= 0.236 Angle : 0.618 10.381 11493 Z= 0.313 Chirality : 0.042 0.272 1298 Planarity : 0.004 0.046 1440 Dihedral : 6.521 91.071 1166 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.13 % Allowed : 8.73 % Favored : 89.14 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -2.20 (0.24), residues: 1045 helix: 0.31 (0.25), residues: 377 sheet: -2.49 (0.31), residues: 233 loop : -2.42 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 102 HIS 0.004 0.001 HIS L 200 PHE 0.018 0.002 PHE A 211 TYR 0.023 0.001 TYR A 438 ARG 0.007 0.000 ARG A -21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 226 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -70 ASN cc_start: 0.7418 (m110) cc_final: 0.7203 (m110) REVERT: A -55 ASP cc_start: 0.6851 (t0) cc_final: 0.6627 (t0) REVERT: A -51 LYS cc_start: 0.8723 (mttt) cc_final: 0.8437 (mttt) REVERT: A -16 ILE cc_start: 0.8425 (tp) cc_final: 0.8210 (mt) REVERT: A 11 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7084 (tm) REVERT: A 46 SER cc_start: 0.7375 (m) cc_final: 0.6984 (t) REVERT: A 127 SER cc_start: 0.8767 (p) cc_final: 0.8344 (t) REVERT: A 139 TYR cc_start: 0.7302 (t80) cc_final: 0.7042 (t80) REVERT: A 162 LEU cc_start: 0.8057 (tp) cc_final: 0.7776 (tp) REVERT: A 190 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8264 (tp) REVERT: A 254 MET cc_start: 0.7591 (mtt) cc_final: 0.7166 (mtt) REVERT: A 286 TYR cc_start: 0.7670 (m-10) cc_final: 0.7056 (m-80) REVERT: A 314 THR cc_start: 0.8251 (m) cc_final: 0.7980 (p) REVERT: A 394 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 405 PHE cc_start: 0.8198 (t80) cc_final: 0.7887 (t80) REVERT: A 406 PHE cc_start: 0.7615 (m-80) cc_final: 0.7155 (m-10) REVERT: A 415 THR cc_start: 0.8373 (m) cc_final: 0.8008 (p) REVERT: A 445 ILE cc_start: 0.6794 (mt) cc_final: 0.6537 (mt) REVERT: H 70 ARG cc_start: 0.8378 (ttp80) cc_final: 0.8037 (ttp80) REVERT: H 80 ASN cc_start: 0.8277 (t0) cc_final: 0.8013 (t0) REVERT: H 152 LEU cc_start: 0.7726 (tp) cc_final: 0.7510 (tp) REVERT: N 34 MET cc_start: 0.6928 (mtp) cc_final: 0.6426 (mtp) REVERT: N 90 ASP cc_start: 0.7911 (t0) cc_final: 0.7709 (t70) REVERT: L 4 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6759 (mm-40) REVERT: L 73 THR cc_start: 0.8086 (m) cc_final: 0.7545 (p) REVERT: L 83 ASP cc_start: 0.7190 (m-30) cc_final: 0.6941 (m-30) REVERT: L 93 LEU cc_start: 0.8284 (tp) cc_final: 0.8015 (tp) REVERT: L 120 PHE cc_start: 0.7822 (m-80) cc_final: 0.7567 (m-80) REVERT: L 172 ASP cc_start: 0.8474 (p0) cc_final: 0.8244 (p0) REVERT: L 211 PHE cc_start: 0.8243 (p90) cc_final: 0.7936 (p90) outliers start: 19 outliers final: 11 residues processed: 236 average time/residue: 0.2280 time to fit residues: 72.0349 Evaluate side-chains 234 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 125 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 78 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A -3 ASN A 99 GLN A 186 ASN H 178 HIS ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8448 Z= 0.255 Angle : 0.594 8.028 11493 Z= 0.302 Chirality : 0.043 0.257 1298 Planarity : 0.004 0.036 1440 Dihedral : 6.594 92.777 1166 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.14 % Allowed : 10.64 % Favored : 86.23 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -1.59 (0.25), residues: 1045 helix: 0.76 (0.25), residues: 378 sheet: -2.22 (0.31), residues: 234 loop : -1.98 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 102 HIS 0.004 0.001 HIS L 191 PHE 0.012 0.001 PHE A -18 TYR 0.019 0.002 TYR L 50 ARG 0.003 0.000 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -76 TRP cc_start: 0.7446 (t-100) cc_final: 0.7199 (t-100) REVERT: A -51 LYS cc_start: 0.8603 (mttt) cc_final: 0.8320 (mttt) REVERT: A -6 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7999 (ttpt) REVERT: A 2 LYS cc_start: 0.8105 (ptpt) cc_final: 0.7887 (ptpt) REVERT: A 11 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7080 (tm) REVERT: A 127 SER cc_start: 0.8850 (p) cc_final: 0.8534 (t) REVERT: A 139 TYR cc_start: 0.7498 (t80) cc_final: 0.7102 (t80) REVERT: A 162 LEU cc_start: 0.8091 (tp) cc_final: 0.7813 (tp) REVERT: A 190 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8262 (tp) REVERT: A 254 MET cc_start: 0.7623 (mtt) cc_final: 0.7192 (mtt) REVERT: A 314 THR cc_start: 0.8254 (m) cc_final: 0.8002 (p) REVERT: A 326 PHE cc_start: 0.6685 (m-10) cc_final: 0.6406 (m-10) REVERT: A 382 ILE cc_start: 0.8174 (mt) cc_final: 0.7915 (pt) REVERT: A 394 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7723 (mm-30) REVERT: A 405 PHE cc_start: 0.8230 (t80) cc_final: 0.7943 (t80) REVERT: A 406 PHE cc_start: 0.7586 (m-80) cc_final: 0.7141 (m-10) REVERT: A 445 ILE cc_start: 0.6927 (mt) cc_final: 0.6666 (mt) REVERT: H 70 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8171 (ttp80) REVERT: H 74 SER cc_start: 0.7866 (t) cc_final: 0.7272 (p) REVERT: H 80 ASN cc_start: 0.8290 (t0) cc_final: 0.7959 (t0) REVERT: H 131 LYS cc_start: 0.7614 (ptmm) cc_final: 0.7337 (ptpp) REVERT: N 34 MET cc_start: 0.6940 (mtp) cc_final: 0.6429 (mtp) REVERT: N 89 GLU cc_start: 0.7564 (mp0) cc_final: 0.7123 (mp0) REVERT: N 90 ASP cc_start: 0.7709 (t0) cc_final: 0.7458 (t0) REVERT: L 4 GLN cc_start: 0.7327 (mm-40) cc_final: 0.6804 (mm-40) REVERT: L 68 SER cc_start: 0.7790 (m) cc_final: 0.7291 (p) REVERT: L 83 ASP cc_start: 0.7246 (m-30) cc_final: 0.6974 (m-30) REVERT: L 172 ASP cc_start: 0.8483 (p0) cc_final: 0.8234 (p0) outliers start: 28 outliers final: 18 residues processed: 240 average time/residue: 0.2597 time to fit residues: 81.6154 Evaluate side-chains 242 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 222 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -3 ASN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 125 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 10 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -70 ASN A -61 ASN ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 HIS ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8448 Z= 0.181 Angle : 0.559 7.799 11493 Z= 0.281 Chirality : 0.042 0.240 1298 Planarity : 0.004 0.039 1440 Dihedral : 6.217 82.925 1166 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.91 % Allowed : 13.33 % Favored : 83.76 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -1.25 (0.25), residues: 1045 helix: 0.99 (0.25), residues: 379 sheet: -1.86 (0.33), residues: 217 loop : -1.86 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 270 HIS 0.005 0.001 HIS A -20 PHE 0.012 0.001 PHE L 100 TYR 0.026 0.001 TYR A 286 ARG 0.004 0.000 ARG A -21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 221 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -51 LYS cc_start: 0.8609 (mttt) cc_final: 0.8329 (mttt) REVERT: A 2 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7815 (ptpt) REVERT: A 11 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7059 (tm) REVERT: A 127 SER cc_start: 0.8847 (p) cc_final: 0.8579 (t) REVERT: A 139 TYR cc_start: 0.7486 (t80) cc_final: 0.7111 (t80) REVERT: A 162 LEU cc_start: 0.8102 (tp) cc_final: 0.7833 (tp) REVERT: A 186 ASN cc_start: 0.7203 (m-40) cc_final: 0.6877 (t0) REVERT: A 204 LYS cc_start: 0.7974 (tttt) cc_final: 0.7618 (tttt) REVERT: A 254 MET cc_start: 0.7628 (mtt) cc_final: 0.7180 (mtt) REVERT: A 273 TRP cc_start: 0.5312 (t60) cc_final: 0.5058 (t60) REVERT: A 326 PHE cc_start: 0.6659 (m-10) cc_final: 0.6402 (m-10) REVERT: A 394 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 405 PHE cc_start: 0.8260 (t80) cc_final: 0.7943 (t80) REVERT: A 406 PHE cc_start: 0.7588 (m-80) cc_final: 0.7148 (m-10) REVERT: A 445 ILE cc_start: 0.6913 (mt) cc_final: 0.6657 (mt) REVERT: H 70 ARG cc_start: 0.8481 (ttp80) cc_final: 0.8181 (ttp80) REVERT: H 74 SER cc_start: 0.7908 (t) cc_final: 0.7292 (p) REVERT: H 80 ASN cc_start: 0.8249 (t0) cc_final: 0.7914 (t0) REVERT: H 131 LYS cc_start: 0.7600 (ptmm) cc_final: 0.7317 (ptpp) REVERT: N 34 MET cc_start: 0.6931 (mtp) cc_final: 0.6416 (mtp) REVERT: N 89 GLU cc_start: 0.7571 (mp0) cc_final: 0.7118 (mp0) REVERT: L 4 GLN cc_start: 0.7286 (mm-40) cc_final: 0.6773 (mm-40) REVERT: L 68 SER cc_start: 0.7933 (m) cc_final: 0.7439 (p) REVERT: L 83 ASP cc_start: 0.7241 (m-30) cc_final: 0.6930 (m-30) REVERT: L 145 GLU cc_start: 0.7697 (mp0) cc_final: 0.7267 (mp0) REVERT: L 175 TYR cc_start: 0.7879 (m-10) cc_final: 0.7368 (m-10) outliers start: 26 outliers final: 16 residues processed: 232 average time/residue: 0.2772 time to fit residues: 84.5257 Evaluate side-chains 233 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 216 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 125 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -70 ASN A -3 ASN ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8448 Z= 0.240 Angle : 0.593 6.607 11493 Z= 0.299 Chirality : 0.042 0.202 1298 Planarity : 0.004 0.048 1440 Dihedral : 5.825 78.686 1166 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.81 % Allowed : 13.89 % Favored : 82.31 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % 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: -1.08 (0.26), residues: 1045 helix: 1.12 (0.26), residues: 378 sheet: -1.69 (0.33), residues: 220 loop : -1.79 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 292 HIS 0.007 0.001 HIS A 355 PHE 0.017 0.001 PHE L 100 TYR 0.032 0.002 TYR A 286 ARG 0.010 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 222 time to evaluate : 0.890 Fit side-chains REVERT: A -51 LYS cc_start: 0.8541 (mttt) cc_final: 0.8286 (mttt) REVERT: A 2 LYS cc_start: 0.8119 (ptpt) cc_final: 0.7854 (ptpt) REVERT: A 11 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7102 (tm) REVERT: A 127 SER cc_start: 0.8885 (p) cc_final: 0.8430 (t) REVERT: A 139 TYR cc_start: 0.7627 (t80) cc_final: 0.7160 (t80) REVERT: A 145 ARG cc_start: 0.5654 (mtm110) cc_final: 0.5333 (mtm110) REVERT: A 162 LEU cc_start: 0.8121 (tp) cc_final: 0.7871 (tp) REVERT: A 204 LYS cc_start: 0.7991 (tttt) cc_final: 0.7608 (tttt) REVERT: A 211 PHE cc_start: 0.7936 (m-80) cc_final: 0.7420 (m-80) REVERT: A 254 MET cc_start: 0.7656 (mtt) cc_final: 0.7194 (mtt) REVERT: A 326 PHE cc_start: 0.6704 (m-10) cc_final: 0.6439 (m-10) REVERT: A 373 ARG cc_start: 0.7600 (mtp-110) cc_final: 0.7011 (mtp-110) REVERT: A 394 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7788 (mm-30) REVERT: A 405 PHE cc_start: 0.8270 (t80) cc_final: 0.7944 (t80) REVERT: A 446 TYR cc_start: 0.7433 (m-80) cc_final: 0.7182 (m-10) REVERT: H 35 PHE cc_start: 0.6991 (m-80) cc_final: 0.6450 (m-80) REVERT: H 70 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8252 (ttp80) REVERT: H 74 SER cc_start: 0.7968 (t) cc_final: 0.7366 (p) REVERT: H 80 ASN cc_start: 0.8273 (t0) cc_final: 0.7932 (t0) REVERT: H 131 LYS cc_start: 0.7571 (ptmm) cc_final: 0.7268 (ptpp) REVERT: H 138 LEU cc_start: 0.8327 (mt) cc_final: 0.8119 (mt) REVERT: H 195 VAL cc_start: 0.8417 (p) cc_final: 0.8138 (m) REVERT: N 34 MET cc_start: 0.6947 (mtp) cc_final: 0.6372 (mtp) REVERT: N 89 GLU cc_start: 0.7626 (mp0) cc_final: 0.7179 (mp0) REVERT: N 90 ASP cc_start: 0.7842 (t0) cc_final: 0.7596 (t70) REVERT: L 4 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6877 (mm-40) REVERT: L 68 SER cc_start: 0.8014 (m) cc_final: 0.7491 (p) REVERT: L 90 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7092 (tt0) REVERT: L 145 GLU cc_start: 0.7696 (mp0) cc_final: 0.7217 (mp0) REVERT: L 168 GLN cc_start: 0.7758 (tt0) cc_final: 0.7434 (mm-40) outliers start: 34 outliers final: 23 residues processed: 234 average time/residue: 0.2417 time to fit residues: 74.9139 Evaluate side-chains 235 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -3 ASN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 186 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 125 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 97 optimal weight: 0.1980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -61 ASN ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8448 Z= 0.218 Angle : 0.595 6.718 11493 Z= 0.298 Chirality : 0.043 0.212 1298 Planarity : 0.004 0.037 1440 Dihedral : 5.535 77.763 1166 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.47 % Allowed : 15.12 % Favored : 81.41 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.26), residues: 1045 helix: 1.18 (0.26), residues: 378 sheet: -1.55 (0.34), residues: 219 loop : -1.64 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 292 HIS 0.007 0.001 HIS A 355 PHE 0.024 0.001 PHE A 37 TYR 0.029 0.002 TYR A 286 ARG 0.010 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -51 LYS cc_start: 0.8444 (mttt) cc_final: 0.8204 (mttt) REVERT: A 2 LYS cc_start: 0.8118 (ptpt) cc_final: 0.7851 (ptpt) REVERT: A 11 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7112 (tm) REVERT: A 81 VAL cc_start: 0.8683 (t) cc_final: 0.8469 (t) REVERT: A 123 GLU cc_start: 0.6452 (tm-30) cc_final: 0.6132 (tm-30) REVERT: A 127 SER cc_start: 0.8827 (p) cc_final: 0.8426 (t) REVERT: A 162 LEU cc_start: 0.8118 (tp) cc_final: 0.7874 (tp) REVERT: A 182 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.6931 (m-10) REVERT: A 186 ASN cc_start: 0.7107 (m-40) cc_final: 0.6756 (t0) REVERT: A 204 LYS cc_start: 0.8004 (tttt) cc_final: 0.7738 (tttt) REVERT: A 211 PHE cc_start: 0.7910 (m-80) cc_final: 0.7247 (m-80) REVERT: A 254 MET cc_start: 0.7646 (mtt) cc_final: 0.7176 (mtt) REVERT: A 326 PHE cc_start: 0.6684 (m-10) cc_final: 0.6431 (m-10) REVERT: A 373 ARG cc_start: 0.7681 (mtp-110) cc_final: 0.7403 (mtp85) REVERT: A 394 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 405 PHE cc_start: 0.8272 (t80) cc_final: 0.7968 (t80) REVERT: A 428 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7653 (m) REVERT: H 35 PHE cc_start: 0.7040 (m-80) cc_final: 0.6517 (m-80) REVERT: H 74 SER cc_start: 0.7990 (t) cc_final: 0.7399 (p) REVERT: H 80 ASN cc_start: 0.8264 (t0) cc_final: 0.7912 (t0) REVERT: H 131 LYS cc_start: 0.7555 (ptmm) cc_final: 0.7250 (ptpp) REVERT: H 138 LEU cc_start: 0.8341 (mt) cc_final: 0.8118 (mt) REVERT: H 195 VAL cc_start: 0.8426 (p) cc_final: 0.8137 (m) REVERT: N 34 MET cc_start: 0.6956 (mtp) cc_final: 0.6361 (mtp) REVERT: N 89 GLU cc_start: 0.7640 (mp0) cc_final: 0.7211 (mp0) REVERT: N 90 ASP cc_start: 0.7842 (t0) cc_final: 0.7629 (t0) REVERT: L 4 GLN cc_start: 0.7328 (mm-40) cc_final: 0.6857 (mm-40) REVERT: L 68 SER cc_start: 0.8037 (m) cc_final: 0.7517 (p) REVERT: L 90 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7130 (tt0) REVERT: L 145 GLU cc_start: 0.7696 (mp0) cc_final: 0.7183 (mp0) REVERT: L 168 GLN cc_start: 0.7785 (tt0) cc_final: 0.7547 (mm-40) outliers start: 31 outliers final: 23 residues processed: 232 average time/residue: 0.2408 time to fit residues: 73.2704 Evaluate side-chains 236 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 210 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 182 PHE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 165 THR Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain N residue 104 TYR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 125 SER Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 165 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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: 68.6105 > 50: distance: 4 - 6: 28.110 distance: 6 - 7: 30.148 distance: 6 - 12: 44.798 distance: 7 - 8: 26.993 distance: 7 - 10: 17.987 distance: 8 - 9: 15.908 distance: 8 - 13: 37.004 distance: 10 - 11: 30.205 distance: 11 - 12: 12.448 distance: 13 - 14: 33.175 distance: 13 - 124: 19.664 distance: 14 - 15: 18.852 distance: 14 - 17: 39.438 distance: 15 - 16: 21.903 distance: 15 - 19: 27.585 distance: 17 - 18: 28.233 distance: 19 - 20: 30.825 distance: 20 - 21: 41.880 distance: 20 - 23: 44.181 distance: 21 - 22: 46.441 distance: 21 - 26: 52.170 distance: 23 - 24: 20.414 distance: 23 - 25: 20.873 distance: 26 - 27: 45.581 distance: 26 - 113: 24.537 distance: 27 - 28: 3.563 distance: 27 - 30: 27.038 distance: 28 - 29: 46.181 distance: 28 - 37: 40.019 distance: 29 - 110: 28.892 distance: 30 - 31: 13.863 distance: 31 - 32: 14.105 distance: 31 - 33: 41.717 distance: 32 - 34: 50.049 distance: 33 - 35: 44.579 distance: 34 - 36: 41.476 distance: 35 - 36: 8.456 distance: 37 - 38: 40.638 distance: 37 - 43: 44.245 distance: 38 - 39: 23.037 distance: 38 - 41: 25.589 distance: 39 - 40: 50.098 distance: 39 - 44: 50.155 distance: 41 - 42: 34.262 distance: 42 - 43: 14.684 distance: 44 - 45: 41.236 distance: 44 - 103: 36.365 distance: 45 - 46: 53.875 distance: 45 - 48: 42.902 distance: 46 - 47: 7.164 distance: 46 - 52: 54.788 distance: 48 - 49: 9.635 distance: 49 - 50: 16.622 distance: 49 - 51: 5.536 distance: 52 - 53: 56.993 distance: 53 - 54: 39.381 distance: 53 - 56: 44.581 distance: 54 - 55: 43.713 distance: 57 - 58: 31.862 distance: 57 - 63: 20.390 distance: 58 - 59: 19.658 distance: 58 - 61: 28.697 distance: 59 - 60: 43.852 distance: 59 - 64: 18.331 distance: 61 - 62: 24.124 distance: 62 - 63: 15.139 distance: 64 - 65: 23.560 distance: 65 - 66: 18.096 distance: 65 - 68: 50.399 distance: 66 - 67: 40.283 distance: 66 - 70: 42.549 distance: 68 - 69: 29.949 distance: 70 - 71: 11.684 distance: 71 - 72: 7.334 distance: 71 - 74: 16.842 distance: 72 - 73: 16.561 distance: 72 - 76: 20.568 distance: 74 - 75: 37.446