Starting phenix.real_space_refine on Thu Sep 26 12:12:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/09_2024/6rb9_4789.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/09_2024/6rb9_4789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/09_2024/6rb9_4789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/09_2024/6rb9_4789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/09_2024/6rb9_4789.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rb9_4789/09_2024/6rb9_4789.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 35 5.16 5 C 8414 2.51 5 N 2212 2.21 5 O 2730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13391 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1913 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 238} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.58, per 1000 atoms: 0.34 Number of scatterers: 13391 At special positions: 0 Unit cell: (129.47, 129.47, 114.49, 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 35 16.00 O 2730 8.00 N 2212 7.00 C 8414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.8 seconds 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3262 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 0 sheets defined 22.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS B 26 " --> pdb=" O THR B 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS D 26 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS F 26 " --> pdb=" O THR F 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 38 removed outlier: 3.768A pdb=" N LYS G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 5.863A pdb=" N ALA A 48 " --> pdb=" O ASN A 45 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A 50 " --> pdb=" O MET A 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'A' and resid 226 through 230 removed outlier: 5.470A pdb=" N LEU A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS B 26 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 5.863A pdb=" N ALA B 48 " --> pdb=" O ASN B 45 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE B 50 " --> pdb=" O MET B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 50' Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 226 through 230 removed outlier: 5.470A pdb=" N LEU B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU C 23 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 50 removed outlier: 5.863A pdb=" N ALA C 48 " --> pdb=" O ASN C 45 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE C 50 " --> pdb=" O MET C 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 50' Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 226 through 230 removed outlier: 5.471A pdb=" N LEU C 230 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 40 removed outlier: 4.443A pdb=" N LEU D 23 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 26 " --> pdb=" O THR D 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 removed outlier: 5.863A pdb=" N ALA D 48 " --> pdb=" O ASN D 45 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE D 50 " --> pdb=" O MET D 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 50' Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 226 through 230 removed outlier: 5.470A pdb=" N LEU D 230 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 50 removed outlier: 5.862A pdb=" N ALA E 48 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE E 50 " --> pdb=" O MET E 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 50' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 226 through 230 removed outlier: 5.471A pdb=" N LEU E 230 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU F 23 " --> pdb=" O ASN F 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS F 26 " --> pdb=" O THR F 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET F 39 " --> pdb=" O TYR F 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 50 removed outlier: 5.862A pdb=" N ALA F 48 " --> pdb=" O ASN F 45 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE F 50 " --> pdb=" O MET F 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 45 through 50' Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 226 through 230 removed outlier: 5.470A pdb=" N LEU F 230 " --> pdb=" O LYS F 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 40 removed outlier: 4.444A pdb=" N LEU G 23 " --> pdb=" O ASN G 19 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET G 39 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 50 removed outlier: 5.863A pdb=" N ALA G 48 " --> pdb=" O ASN G 45 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE G 50 " --> pdb=" O MET G 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 50' Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 226 through 230 removed outlier: 5.470A pdb=" N LEU G 230 " --> pdb=" O LYS G 227 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 588 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: 2.40 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4251 1.33 - 1.45: 1713 1.45 - 1.56: 7609 1.56 - 1.68: 0 1.68 - 1.80: 63 Bond restraints: 13636 Sorted by residual: bond pdb=" CB VAL F 192 " pdb=" CG1 VAL F 192 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB VAL C 192 " pdb=" CG1 VAL C 192 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.16e+00 bond pdb=" CB VAL E 192 " pdb=" CG1 VAL E 192 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CB VAL D 192 " pdb=" CG1 VAL D 192 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.14e+00 bond pdb=" CB VAL B 192 " pdb=" CG1 VAL B 192 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.13e+00 ... (remaining 13631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 17368 1.54 - 3.08: 1075 3.08 - 4.62: 88 4.62 - 6.16: 26 6.16 - 7.70: 14 Bond angle restraints: 18571 Sorted by residual: angle pdb=" N LYS E 41 " pdb=" CA LYS E 41 " pdb=" C LYS E 41 " ideal model delta sigma weight residual 112.72 108.61 4.11 1.28e+00 6.10e-01 1.03e+01 angle pdb=" N LYS A 41 " pdb=" CA LYS A 41 " pdb=" C LYS A 41 " ideal model delta sigma weight residual 112.72 108.62 4.10 1.28e+00 6.10e-01 1.02e+01 angle pdb=" N LYS F 41 " pdb=" CA LYS F 41 " pdb=" C LYS F 41 " ideal model delta sigma weight residual 112.72 108.63 4.09 1.28e+00 6.10e-01 1.02e+01 angle pdb=" N LYS C 41 " pdb=" CA LYS C 41 " pdb=" C LYS C 41 " ideal model delta sigma weight residual 112.72 108.64 4.08 1.28e+00 6.10e-01 1.02e+01 angle pdb=" N LYS D 41 " pdb=" CA LYS D 41 " pdb=" C LYS D 41 " ideal model delta sigma weight residual 112.72 108.64 4.08 1.28e+00 6.10e-01 1.02e+01 ... (remaining 18566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.25: 6566 11.25 - 22.50: 1051 22.50 - 33.75: 419 33.75 - 44.99: 91 44.99 - 56.24: 42 Dihedral angle restraints: 8169 sinusoidal: 3073 harmonic: 5096 Sorted by residual: dihedral pdb=" CA ASN G 19 " pdb=" C ASN G 19 " pdb=" N VAL G 20 " pdb=" CA VAL G 20 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASN C 19 " pdb=" C ASN C 19 " pdb=" N VAL C 20 " pdb=" CA VAL C 20 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ASN B 19 " pdb=" C ASN B 19 " pdb=" N VAL B 20 " pdb=" CA VAL B 20 " ideal model delta harmonic sigma weight residual 180.00 159.26 20.74 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 8166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 927 0.029 - 0.058: 708 0.058 - 0.086: 285 0.086 - 0.115: 185 0.115 - 0.144: 51 Chirality restraints: 2156 Sorted by residual: chirality pdb=" CA VAL E 164 " pdb=" N VAL E 164 " pdb=" C VAL E 164 " pdb=" CB VAL E 164 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA VAL F 164 " pdb=" N VAL F 164 " pdb=" C VAL F 164 " pdb=" CB VAL F 164 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2153 not shown) Planarity restraints: 2415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 171 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO C 172 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 172 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 172 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 171 " -0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 172 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 172 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 172 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 171 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO D 172 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " 0.025 5.00e-02 4.00e+02 ... (remaining 2412 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 196 2.62 - 3.19: 12496 3.19 - 3.76: 20246 3.76 - 4.33: 29230 4.33 - 4.90: 49372 Nonbonded interactions: 111540 Sorted by model distance: nonbonded pdb=" CE LYS F 130 " pdb=" OE1 GLU G 137 " model vdw 2.049 3.440 nonbonded pdb=" CE LYS D 130 " pdb=" OE1 GLU E 137 " model vdw 2.049 3.440 nonbonded pdb=" CE LYS B 130 " pdb=" OE1 GLU C 137 " model vdw 2.050 3.440 nonbonded pdb=" OE1 GLU A 137 " pdb=" CE LYS G 130 " model vdw 2.050 3.440 nonbonded pdb=" CE LYS C 130 " pdb=" OE1 GLU D 137 " model vdw 2.050 3.440 ... (remaining 111535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 25.750 Find NCS groups from input model: 0.430 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.010 0.059 13636 Z= 0.651 Angle : 0.824 7.702 18571 Z= 0.463 Chirality : 0.051 0.144 2156 Planarity : 0.005 0.045 2415 Dihedral : 13.721 56.242 4907 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.85 % Favored : 84.15 % Rotamer: Outliers : 1.42 % Allowed : 12.46 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.55 (0.15), residues: 1722 helix: -1.81 (0.32), residues: 140 sheet: -3.54 (0.18), residues: 595 loop : -4.22 (0.14), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP E 203 HIS 0.004 0.002 HIS G 162 PHE 0.028 0.003 PHE G 135 TYR 0.018 0.003 TYR G 84 ARG 0.003 0.001 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 276 time to evaluate : 1.644 Fit side-chains REVERT: A 68 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8309 (mttp) REVERT: A 205 GLU cc_start: 0.8130 (pp20) cc_final: 0.7344 (pt0) REVERT: B 68 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8344 (mttp) REVERT: B 77 MET cc_start: 0.8922 (mmt) cc_final: 0.8193 (mmt) REVERT: B 82 ASP cc_start: 0.8086 (m-30) cc_final: 0.7873 (m-30) REVERT: B 205 GLU cc_start: 0.8088 (pp20) cc_final: 0.7523 (pp20) REVERT: C 68 LYS cc_start: 0.8839 (mtpt) cc_final: 0.8376 (mttp) REVERT: C 77 MET cc_start: 0.8948 (mmt) cc_final: 0.8382 (mmt) REVERT: C 81 GLU cc_start: 0.7578 (pm20) cc_final: 0.7227 (pm20) REVERT: C 205 GLU cc_start: 0.8196 (pp20) cc_final: 0.7911 (pp20) REVERT: D 21 ASP cc_start: 0.7753 (m-30) cc_final: 0.7470 (m-30) REVERT: D 68 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8483 (mttp) REVERT: D 205 GLU cc_start: 0.8197 (pp20) cc_final: 0.7516 (pt0) REVERT: E 68 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8327 (mttp) REVERT: E 81 GLU cc_start: 0.7707 (pm20) cc_final: 0.7469 (pm20) REVERT: E 205 GLU cc_start: 0.8090 (pp20) cc_final: 0.7495 (pt0) REVERT: F 25 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: F 68 LYS cc_start: 0.8640 (mtpt) cc_final: 0.8278 (mttp) REVERT: F 205 GLU cc_start: 0.8085 (pp20) cc_final: 0.7742 (pp20) REVERT: G 39 MET cc_start: 0.4813 (mmm) cc_final: 0.4607 (mmp) REVERT: G 68 LYS cc_start: 0.8767 (mtpt) cc_final: 0.8356 (mttp) REVERT: G 205 GLU cc_start: 0.8049 (pp20) cc_final: 0.7607 (pp20) outliers start: 21 outliers final: 13 residues processed: 297 average time/residue: 0.2054 time to fit residues: 95.4762 Evaluate side-chains 176 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 191 ASN A 226 ASN A 243 ASN B 136 ASN B 191 ASN B 226 ASN B 243 ASN C 136 ASN C 191 ASN C 226 ASN C 243 ASN D 136 ASN D 191 ASN D 226 ASN D 243 ASN E 136 ASN E 191 ASN E 226 ASN E 243 ASN F 136 ASN F 191 ASN F 226 ASN F 243 ASN G 136 ASN G 191 ASN G 226 ASN G 243 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13636 Z= 0.271 Angle : 0.631 6.376 18571 Z= 0.326 Chirality : 0.045 0.136 2156 Planarity : 0.005 0.042 2415 Dihedral : 5.853 64.557 1878 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 4.13 % Allowed : 17.60 % Favored : 78.27 % 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: -4.87 (0.17), residues: 1722 helix: 0.93 (0.42), residues: 140 sheet: -3.21 (0.16), residues: 784 loop : -4.01 (0.17), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP D 203 HIS 0.002 0.001 HIS D 162 PHE 0.016 0.002 PHE F 135 TYR 0.017 0.002 TYR F 244 ARG 0.001 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 184 time to evaluate : 1.431 Fit side-chains REVERT: A 64 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8594 (mp) REVERT: A 68 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8253 (mttp) REVERT: A 205 GLU cc_start: 0.8095 (pp20) cc_final: 0.7361 (pt0) REVERT: C 64 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8646 (mp) REVERT: C 68 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8303 (mttp) REVERT: C 81 GLU cc_start: 0.7239 (pm20) cc_final: 0.6999 (pm20) REVERT: C 130 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8183 (mtpp) REVERT: C 205 GLU cc_start: 0.8175 (pp20) cc_final: 0.7686 (pt0) REVERT: D 68 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8430 (mttp) REVERT: D 130 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8237 (mtmm) REVERT: D 205 GLU cc_start: 0.8229 (pp20) cc_final: 0.7550 (pp20) REVERT: E 68 LYS cc_start: 0.8737 (mtpt) cc_final: 0.8338 (mttp) REVERT: E 130 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8263 (mtpp) REVERT: E 205 GLU cc_start: 0.8124 (pp20) cc_final: 0.7531 (pt0) REVERT: F 68 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8244 (mttp) REVERT: F 187 ASN cc_start: 0.8420 (p0) cc_final: 0.8051 (p0) REVERT: F 205 GLU cc_start: 0.8052 (pp20) cc_final: 0.7397 (pt0) REVERT: G 39 MET cc_start: 0.4882 (mmm) cc_final: 0.4682 (mmp) REVERT: G 68 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8315 (mttp) REVERT: G 130 LYS cc_start: 0.8547 (mtmm) cc_final: 0.8128 (mtpp) REVERT: G 205 GLU cc_start: 0.8102 (pp20) cc_final: 0.7663 (pp20) outliers start: 61 outliers final: 40 residues processed: 240 average time/residue: 0.1962 time to fit residues: 73.4267 Evaluate side-chains 213 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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: 0.8072 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 13636 Z= 0.286 Angle : 0.604 6.169 18571 Z= 0.312 Chirality : 0.045 0.136 2156 Planarity : 0.004 0.040 2415 Dihedral : 5.416 33.808 1874 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 5.89 % Allowed : 17.26 % Favored : 76.84 % 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: -4.46 (0.18), residues: 1722 helix: 1.66 (0.47), residues: 140 sheet: -3.00 (0.17), residues: 798 loop : -3.75 (0.18), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 203 HIS 0.002 0.001 HIS G 162 PHE 0.020 0.002 PHE D 135 TYR 0.015 0.002 TYR F 84 ARG 0.001 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 179 time to evaluate : 1.472 Fit side-chains REVERT: A 64 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8607 (mp) REVERT: A 68 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8259 (mttp) REVERT: A 154 ASN cc_start: 0.8353 (p0) cc_final: 0.8092 (p0) REVERT: A 205 GLU cc_start: 0.8113 (pp20) cc_final: 0.7342 (pt0) REVERT: A 230 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7822 (pp) REVERT: B 154 ASN cc_start: 0.8304 (p0) cc_final: 0.8055 (p0) REVERT: B 230 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8010 (pp) REVERT: C 64 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8647 (mp) REVERT: C 68 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8260 (mttp) REVERT: C 81 GLU cc_start: 0.7316 (pm20) cc_final: 0.7045 (pm20) REVERT: C 130 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8175 (mtpp) REVERT: C 154 ASN cc_start: 0.8328 (p0) cc_final: 0.8091 (p0) REVERT: C 205 GLU cc_start: 0.8147 (pp20) cc_final: 0.7611 (pt0) REVERT: C 230 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7900 (pp) REVERT: D 68 LYS cc_start: 0.8823 (mtpt) cc_final: 0.8463 (mttp) REVERT: D 154 ASN cc_start: 0.8329 (p0) cc_final: 0.8100 (p0) REVERT: D 205 GLU cc_start: 0.8271 (pp20) cc_final: 0.7532 (pp20) REVERT: D 230 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7803 (pp) REVERT: E 68 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8337 (mttp) REVERT: E 130 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8161 (mttm) REVERT: E 205 GLU cc_start: 0.8172 (pp20) cc_final: 0.7372 (pt0) REVERT: E 236 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8116 (pt) REVERT: F 68 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8230 (mttp) REVERT: F 187 ASN cc_start: 0.8413 (p0) cc_final: 0.8033 (p0) REVERT: F 205 GLU cc_start: 0.8138 (pp20) cc_final: 0.7401 (pt0) REVERT: G 68 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8341 (mttp) REVERT: G 130 LYS cc_start: 0.8593 (mtmm) cc_final: 0.8130 (mtpp) REVERT: G 154 ASN cc_start: 0.8330 (p0) cc_final: 0.8034 (p0) REVERT: G 205 GLU cc_start: 0.8098 (pp20) cc_final: 0.7648 (pp20) outliers start: 87 outliers final: 65 residues processed: 257 average time/residue: 0.1871 time to fit residues: 76.7464 Evaluate side-chains 236 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 164 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 153 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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: 0.8065 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13636 Z= 0.276 Angle : 0.585 6.262 18571 Z= 0.302 Chirality : 0.045 0.135 2156 Planarity : 0.004 0.045 2415 Dihedral : 5.331 34.716 1874 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 6.50 % Allowed : 18.35 % Favored : 75.15 % 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: -4.16 (0.19), residues: 1722 helix: 2.35 (0.47), residues: 133 sheet: -2.79 (0.17), residues: 784 loop : -3.62 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 203 HIS 0.002 0.001 HIS D 162 PHE 0.020 0.002 PHE D 135 TYR 0.016 0.002 TYR E 84 ARG 0.002 0.000 ARG F 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 176 time to evaluate : 1.606 Fit side-chains REVERT: A 64 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 68 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8261 (mttp) REVERT: A 154 ASN cc_start: 0.8305 (p0) cc_final: 0.8017 (p0) REVERT: A 205 GLU cc_start: 0.8155 (pp20) cc_final: 0.7949 (pp20) REVERT: A 230 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7814 (pp) REVERT: B 23 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7489 (mm) REVERT: B 154 ASN cc_start: 0.8266 (p0) cc_final: 0.8005 (p0) REVERT: B 230 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7964 (pp) REVERT: C 68 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8219 (mttp) REVERT: C 81 GLU cc_start: 0.7302 (pm20) cc_final: 0.7050 (pm20) REVERT: C 130 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8227 (mtpp) REVERT: C 154 ASN cc_start: 0.8299 (p0) cc_final: 0.8063 (p0) REVERT: C 230 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7792 (pp) REVERT: D 68 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8429 (mttp) REVERT: D 154 ASN cc_start: 0.8225 (p0) cc_final: 0.8008 (p0) REVERT: D 205 GLU cc_start: 0.8252 (pp20) cc_final: 0.7483 (pp20) REVERT: D 230 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7748 (pp) REVERT: E 68 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8319 (mttp) REVERT: E 154 ASN cc_start: 0.8364 (p0) cc_final: 0.8096 (p0) REVERT: E 178 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7481 (tt0) REVERT: E 205 GLU cc_start: 0.8178 (pp20) cc_final: 0.7411 (pt0) REVERT: E 236 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8046 (pt) REVERT: F 68 LYS cc_start: 0.8607 (mtpt) cc_final: 0.8189 (mttp) REVERT: F 187 ASN cc_start: 0.8390 (p0) cc_final: 0.7995 (p0) REVERT: F 205 GLU cc_start: 0.8159 (pp20) cc_final: 0.7335 (pp20) REVERT: G 68 LYS cc_start: 0.8732 (mtpt) cc_final: 0.8313 (mttp) REVERT: G 130 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8091 (mtpp) REVERT: G 154 ASN cc_start: 0.8343 (p0) cc_final: 0.8025 (p0) REVERT: G 205 GLU cc_start: 0.8145 (pp20) cc_final: 0.7667 (pp20) outliers start: 96 outliers final: 78 residues processed: 263 average time/residue: 0.1872 time to fit residues: 78.0430 Evaluate side-chains 242 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 157 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 230 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 120 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13636 Z= 0.296 Angle : 0.591 7.257 18571 Z= 0.304 Chirality : 0.045 0.138 2156 Planarity : 0.004 0.040 2415 Dihedral : 5.321 35.663 1874 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 7.45 % Allowed : 19.30 % Favored : 73.26 % 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: -4.02 (0.19), residues: 1722 helix: 2.54 (0.48), residues: 133 sheet: -2.71 (0.18), residues: 784 loop : -3.52 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 203 HIS 0.002 0.001 HIS D 162 PHE 0.020 0.002 PHE D 135 TYR 0.015 0.002 TYR F 244 ARG 0.001 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3444 Ramachandran restraints generated. 1722 Oldfield, 0 Emsley, 1722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 163 time to evaluate : 1.516 Fit side-chains REVERT: A 64 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 68 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8275 (mttp) REVERT: A 154 ASN cc_start: 0.8289 (p0) cc_final: 0.7993 (p0) REVERT: A 205 GLU cc_start: 0.8184 (pp20) cc_final: 0.7963 (pp20) REVERT: A 230 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7783 (pp) REVERT: B 23 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7487 (mm) REVERT: B 154 ASN cc_start: 0.8265 (p0) cc_final: 0.8002 (p0) REVERT: B 230 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7921 (pp) REVERT: C 68 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8225 (mttp) REVERT: C 130 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8162 (mtpp) REVERT: C 154 ASN cc_start: 0.8305 (p0) cc_final: 0.8052 (p0) REVERT: C 230 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7802 (pp) REVERT: D 64 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8499 (mm) REVERT: D 68 LYS cc_start: 0.8804 (mtpt) cc_final: 0.8435 (mttp) REVERT: D 154 ASN cc_start: 0.8215 (p0) cc_final: 0.7985 (p0) REVERT: D 205 GLU cc_start: 0.8269 (pp20) cc_final: 0.7577 (pp20) REVERT: D 230 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7708 (pp) REVERT: E 68 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8336 (mttp) REVERT: E 154 ASN cc_start: 0.8353 (p0) cc_final: 0.8089 (p0) REVERT: E 205 GLU cc_start: 0.8210 (pp20) cc_final: 0.7370 (pp20) REVERT: F 47 MET cc_start: 0.2924 (mmp) cc_final: 0.2439 (mmp) REVERT: F 68 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8213 (mttp) REVERT: F 187 ASN cc_start: 0.8378 (p0) cc_final: 0.8018 (p0) REVERT: F 205 GLU cc_start: 0.8192 (pp20) cc_final: 0.7387 (pp20) REVERT: G 39 MET cc_start: 0.4491 (mmm) cc_final: 0.4270 (mmm) REVERT: G 47 MET cc_start: 0.2891 (mmp) cc_final: 0.2587 (mmp) REVERT: G 68 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8338 (mttp) REVERT: G 130 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8057 (mttm) REVERT: G 154 ASN cc_start: 0.8339 (p0) cc_final: 0.8023 (p0) REVERT: G 205 GLU cc_start: 0.8172 (pp20) cc_final: 0.7667 (pp20) outliers start: 110 outliers final: 89 residues processed: 265 average time/residue: 0.1820 time to fit residues: 77.4757 Evaluate side-chains 259 residues out of total 1540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 163 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 23 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 151 THR Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 171 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 229 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 236 ILE Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 155 THR Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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: 51.121 > 50: distance: 88 - 94: 3.195 distance: 94 - 95: 4.754 distance: 95 - 96: 5.356 distance: 95 - 98: 5.213 distance: 96 - 97: 20.725 distance: 96 - 105: 6.360 distance: 99 - 100: 5.300 distance: 99 - 101: 7.470 distance: 100 - 102: 6.796 distance: 101 - 103: 8.547 distance: 102 - 104: 9.454 distance: 103 - 104: 9.063 distance: 105 - 106: 12.654 distance: 106 - 107: 13.632 distance: 106 - 109: 9.338 distance: 107 - 108: 17.409 distance: 107 - 117: 27.285 distance: 109 - 110: 8.617 distance: 110 - 111: 6.683 distance: 111 - 113: 5.527 distance: 113 - 115: 4.741 distance: 114 - 115: 4.868 distance: 115 - 116: 7.986 distance: 117 - 118: 6.957 distance: 118 - 119: 9.547 distance: 118 - 121: 10.450 distance: 119 - 120: 3.951 distance: 119 - 125: 4.263 distance: 121 - 122: 4.371 distance: 121 - 123: 15.348 distance: 122 - 124: 16.644 distance: 125 - 126: 3.079 distance: 126 - 127: 11.547 distance: 126 - 129: 3.591 distance: 127 - 128: 20.973 distance: 127 - 133: 10.925 distance: 129 - 130: 8.098 distance: 130 - 131: 7.865 distance: 130 - 132: 7.181 distance: 133 - 134: 10.132 distance: 134 - 135: 17.809 distance: 134 - 137: 10.595 distance: 135 - 136: 4.067 distance: 135 - 141: 12.806 distance: 137 - 138: 6.923 distance: 138 - 139: 18.898 distance: 141 - 142: 11.609 distance: 141 - 147: 9.752 distance: 142 - 143: 19.692 distance: 142 - 145: 28.481 distance: 143 - 144: 15.965 distance: 143 - 148: 23.574 distance: 145 - 146: 15.409 distance: 146 - 147: 28.097 distance: 148 - 149: 14.947 distance: 149 - 150: 17.155 distance: 149 - 152: 10.600 distance: 150 - 151: 15.478 distance: 150 - 157: 20.697 distance: 152 - 153: 21.426 distance: 153 - 154: 13.704 distance: 154 - 155: 11.252 distance: 155 - 156: 8.828 distance: 157 - 158: 8.489 distance: 158 - 159: 10.688 distance: 158 - 161: 11.604 distance: 159 - 160: 14.351 distance: 159 - 164: 3.226 distance: 161 - 162: 20.454 distance: 161 - 163: 23.595 distance: 164 - 165: 6.158 distance: 165 - 166: 7.955 distance: 165 - 168: 18.833 distance: 166 - 167: 5.135 distance: 166 - 173: 14.757 distance: 168 - 169: 9.172 distance: 169 - 170: 6.089 distance: 173 - 174: 6.618 distance: 174 - 175: 7.151 distance: 174 - 177: 14.058 distance: 175 - 176: 16.466 distance: 177 - 178: 14.888 distance: 178 - 179: 19.691 distance: 178 - 180: 14.296