Starting phenix.real_space_refine on Wed Jun 11 18:33:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rb9_4789/06_2025/6rb9_4789.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rb9_4789/06_2025/6rb9_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/cci-nas-00/data/ceres_data/6rb9_4789/06_2025/6rb9_4789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rb9_4789/06_2025/6rb9_4789.map" model { file = "/net/cci-nas-00/data/ceres_data/6rb9_4789/06_2025/6rb9_4789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rb9_4789/06_2025/6rb9_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-5710/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: 4.49, 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: 3.24 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: 1.18 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: 2.45 Time building geometry restraints manager: 3.84 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.730 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: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 26.410 Find NCS groups from input model: 0.290 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.940 ------------------------------------------------------------------------------- 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= 0.416 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 Details of bonding type rmsd hydrogen bonds : bond 0.19211 ( 105) hydrogen bonds : angle 8.19573 ( 588) covalent geometry : bond 0.00976 (13636) covalent geometry : angle 0.82375 (18571) *********************** 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 to be fit. rotamer outliers: 21 poor density : 276 time to evaluate : 1.483 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: 0.1979 time to fit residues: 91.6481 Evaluate side-chains 176 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.619 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.096551 restraints weight = 17455.118| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.97 r_work: 0.3128 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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= 0.173 Angle : 0.631 6.376 18571 Z= 0.326 Chirality : 0.045 0.136 2156 Planarity : 0.005 0.042 2415 Dihedral : 5.853 64.556 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 Details of bonding type rmsd hydrogen bonds : bond 0.02765 ( 105) hydrogen bonds : angle 2.14117 ( 588) covalent geometry : bond 0.00409 (13636) covalent geometry : angle 0.63058 (18571) *********************** 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 to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 1.451 Fit side-chains REVERT: A 64 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8759 (mp) REVERT: A 68 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8349 (mttp) REVERT: A 205 GLU cc_start: 0.8179 (pp20) cc_final: 0.7578 (pt0) REVERT: C 64 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8791 (mp) REVERT: C 68 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8416 (mttp) REVERT: C 81 GLU cc_start: 0.7922 (pm20) cc_final: 0.7537 (pm20) REVERT: C 130 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8179 (mtpp) REVERT: C 205 GLU cc_start: 0.8253 (pp20) cc_final: 0.7884 (pt0) REVERT: D 68 LYS cc_start: 0.9088 (mtpt) cc_final: 0.8461 (mttp) REVERT: D 130 LYS cc_start: 0.8512 (mtmm) cc_final: 0.8105 (mtmm) REVERT: D 205 GLU cc_start: 0.8273 (pp20) cc_final: 0.7371 (pp20) REVERT: E 68 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8384 (mttp) REVERT: E 81 GLU cc_start: 0.8159 (pm20) cc_final: 0.7872 (pm20) REVERT: E 130 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8261 (mtpp) REVERT: E 205 GLU cc_start: 0.8202 (pp20) cc_final: 0.7709 (pt0) REVERT: F 68 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8290 (mttp) REVERT: F 187 ASN cc_start: 0.8688 (p0) cc_final: 0.8366 (p0) REVERT: F 205 GLU cc_start: 0.8137 (pp20) cc_final: 0.7606 (pt0) REVERT: G 39 MET cc_start: 0.4867 (mmm) cc_final: 0.4605 (mmp) REVERT: G 68 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8405 (mttp) REVERT: G 130 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8155 (mtpp) REVERT: G 205 GLU cc_start: 0.8232 (pp20) cc_final: 0.7487 (pp20) outliers start: 61 outliers final: 40 residues processed: 240 average time/residue: 0.2066 time to fit residues: 76.8309 Evaluate side-chains 215 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 136 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 chunk 117 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101435 restraints weight = 17120.981| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.80 r_work: 0.3218 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13636 Z= 0.119 Angle : 0.556 6.584 18571 Z= 0.290 Chirality : 0.044 0.133 2156 Planarity : 0.004 0.041 2415 Dihedral : 5.070 28.620 1874 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.33 % Allowed : 17.33 % Favored : 78.33 % 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: -4.39 (0.19), residues: 1722 helix: 1.63 (0.46), residues: 140 sheet: -2.87 (0.17), residues: 784 loop : -3.79 (0.18), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 203 HIS 0.002 0.001 HIS G 162 PHE 0.019 0.002 PHE D 135 TYR 0.015 0.001 TYR F 244 ARG 0.001 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.02424 ( 105) hydrogen bonds : angle 1.76644 ( 588) covalent geometry : bond 0.00280 (13636) covalent geometry : angle 0.55565 (18571) *********************** 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 269 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 205 time to evaluate : 1.528 Fit side-chains REVERT: A 64 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8405 (mp) REVERT: A 68 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8153 (mttp) REVERT: A 154 ASN cc_start: 0.8424 (p0) cc_final: 0.8205 (p0) REVERT: A 185 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8615 (mtmm) REVERT: A 205 GLU cc_start: 0.8022 (pp20) cc_final: 0.7473 (pt0) REVERT: A 230 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7205 (pp) REVERT: B 154 ASN cc_start: 0.8406 (p0) cc_final: 0.8161 (p0) REVERT: B 230 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7500 (pp) REVERT: C 64 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8500 (mp) REVERT: C 68 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8041 (mttp) REVERT: C 77 MET cc_start: 0.9056 (mmt) cc_final: 0.8384 (mmt) REVERT: C 81 GLU cc_start: 0.7850 (pm20) cc_final: 0.7349 (pm20) REVERT: C 130 LYS cc_start: 0.8484 (mtmm) cc_final: 0.7977 (mtpp) REVERT: C 154 ASN cc_start: 0.8425 (p0) cc_final: 0.8216 (p0) REVERT: C 205 GLU cc_start: 0.8060 (pp20) cc_final: 0.7784 (pt0) REVERT: C 230 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7223 (pp) REVERT: D 60 ASN cc_start: 0.7921 (t0) cc_final: 0.7712 (t0) REVERT: D 68 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8225 (mttp) REVERT: D 130 LYS cc_start: 0.8429 (mtmm) cc_final: 0.7813 (mtmm) REVERT: D 187 ASN cc_start: 0.8241 (p0) cc_final: 0.7730 (p0) REVERT: D 205 GLU cc_start: 0.8092 (pp20) cc_final: 0.7092 (pp20) REVERT: D 230 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7253 (pp) REVERT: E 68 LYS cc_start: 0.8945 (mtpt) cc_final: 0.8134 (mttp) REVERT: E 81 GLU cc_start: 0.8111 (pm20) cc_final: 0.7713 (pm20) REVERT: E 130 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8343 (mtmm) REVERT: E 154 ASN cc_start: 0.8519 (p0) cc_final: 0.8285 (p0) REVERT: E 178 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8305 (tt0) REVERT: E 187 ASN cc_start: 0.8230 (p0) cc_final: 0.7770 (p0) REVERT: E 205 GLU cc_start: 0.8067 (pp20) cc_final: 0.7560 (pt0) REVERT: F 68 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8047 (mttp) REVERT: F 77 MET cc_start: 0.9229 (mmt) cc_final: 0.8570 (mmt) REVERT: F 81 GLU cc_start: 0.8291 (pm20) cc_final: 0.8061 (pm20) REVERT: F 93 ASP cc_start: 0.8347 (m-30) cc_final: 0.8146 (m-30) REVERT: F 187 ASN cc_start: 0.8296 (p0) cc_final: 0.7902 (p0) REVERT: F 205 GLU cc_start: 0.7967 (pp20) cc_final: 0.7504 (pt0) REVERT: G 68 LYS cc_start: 0.8955 (mtpt) cc_final: 0.8178 (mttp) REVERT: G 130 LYS cc_start: 0.8515 (mtmm) cc_final: 0.7911 (mtpp) REVERT: G 154 ASN cc_start: 0.8576 (p0) cc_final: 0.8311 (p0) REVERT: G 205 GLU cc_start: 0.8031 (pp20) cc_final: 0.7815 (pt0) outliers start: 64 outliers final: 44 residues processed: 264 average time/residue: 0.2430 time to fit residues: 100.7896 Evaluate side-chains 240 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 1.748 ------------------------------------------------------------------------------- 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 171 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 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 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 188 VAL Chi-restraints excluded: chain C residue 230 LEU 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 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 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 195 VAL Chi-restraints excluded: chain E residue 230 LEU 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 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 171 VAL Chi-restraints excluded: chain G residue 188 VAL Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 116 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.133069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102001 restraints weight = 16975.248| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.87 r_work: 0.3112 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13636 Z= 0.156 Angle : 0.565 5.472 18571 Z= 0.293 Chirality : 0.044 0.140 2156 Planarity : 0.004 0.047 2415 Dihedral : 4.853 18.594 1868 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 6.23 % Allowed : 17.40 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.19), residues: 1722 helix: 2.31 (0.47), residues: 133 sheet: -2.74 (0.17), residues: 784 loop : -3.58 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 203 HIS 0.002 0.001 HIS D 162 PHE 0.019 0.002 PHE D 135 TYR 0.014 0.002 TYR E 84 ARG 0.001 0.000 ARG F 28 Details of bonding type rmsd hydrogen bonds : bond 0.02293 ( 105) hydrogen bonds : angle 1.76968 ( 588) covalent geometry : bond 0.00381 (13636) covalent geometry : angle 0.56459 (18571) *********************** 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 280 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 188 time to evaluate : 1.473 Fit side-chains REVERT: A 64 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8441 (mp) REVERT: A 68 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8116 (mttp) REVERT: A 154 ASN cc_start: 0.8403 (p0) cc_final: 0.8168 (p0) REVERT: A 205 GLU cc_start: 0.8026 (pp20) cc_final: 0.7468 (pt0) REVERT: A 230 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7179 (pp) REVERT: B 23 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6942 (mm) REVERT: B 154 ASN cc_start: 0.8421 (p0) cc_final: 0.8177 (p0) REVERT: B 230 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7477 (pp) REVERT: C 64 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8477 (mp) REVERT: C 68 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8038 (mttp) REVERT: C 81 GLU cc_start: 0.7899 (pm20) cc_final: 0.7414 (pm20) REVERT: C 130 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8216 (mtpp) REVERT: C 154 ASN cc_start: 0.8433 (p0) cc_final: 0.8194 (p0) REVERT: C 205 GLU cc_start: 0.7992 (pp20) cc_final: 0.7736 (pt0) REVERT: C 230 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7114 (pp) REVERT: D 68 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8215 (mttp) REVERT: D 81 GLU cc_start: 0.8381 (pm20) cc_final: 0.8123 (pm20) REVERT: D 187 ASN cc_start: 0.8138 (p0) cc_final: 0.7651 (p0) REVERT: D 205 GLU cc_start: 0.8078 (pp20) cc_final: 0.7028 (pp20) REVERT: D 230 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7057 (pp) REVERT: E 68 LYS cc_start: 0.8914 (mtpt) cc_final: 0.8074 (mttp) REVERT: E 81 GLU cc_start: 0.8150 (pm20) cc_final: 0.7726 (pm20) REVERT: E 130 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8262 (mtmm) REVERT: E 154 ASN cc_start: 0.8490 (p0) cc_final: 0.8216 (p0) REVERT: E 178 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8333 (tt0) REVERT: E 205 GLU cc_start: 0.8016 (pp20) cc_final: 0.7580 (pt0) REVERT: E 236 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7681 (pt) REVERT: F 68 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8052 (mttp) REVERT: F 187 ASN cc_start: 0.8360 (p0) cc_final: 0.8008 (p0) REVERT: F 205 GLU cc_start: 0.7993 (pp20) cc_final: 0.7528 (pt0) REVERT: G 47 MET cc_start: 0.3648 (mmp) cc_final: 0.2902 (mmm) REVERT: G 68 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8172 (mttp) REVERT: G 130 LYS cc_start: 0.8453 (mtmm) cc_final: 0.7843 (mtpp) REVERT: G 154 ASN cc_start: 0.8552 (p0) cc_final: 0.8249 (p0) REVERT: G 205 GLU cc_start: 0.8005 (pp20) cc_final: 0.7178 (pp20) outliers start: 92 outliers final: 71 residues processed: 272 average time/residue: 0.1879 time to fit residues: 81.4962 Evaluate side-chains 257 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 178 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 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 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 188 VAL Chi-restraints excluded: chain C residue 192 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 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 198 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 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 116 THR Chi-restraints excluded: chain G residue 128 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.049 > 50: distance: 36 - 39: 20.918 distance: 39 - 40: 52.007 distance: 40 - 43: 40.109 distance: 41 - 44: 17.977 distance: 44 - 45: 20.187 distance: 45 - 46: 39.176 distance: 45 - 48: 25.018 distance: 46 - 47: 38.985 distance: 46 - 51: 33.799 distance: 48 - 49: 12.389 distance: 48 - 50: 22.240 distance: 51 - 52: 35.904 distance: 52 - 53: 13.792 distance: 52 - 55: 10.007 distance: 53 - 54: 47.081 distance: 53 - 56: 22.312 distance: 56 - 57: 25.469 distance: 57 - 58: 37.569 distance: 57 - 60: 20.627 distance: 58 - 59: 35.259 distance: 58 - 64: 30.951 distance: 60 - 61: 35.717 distance: 60 - 62: 21.868 distance: 61 - 63: 33.960 distance: 64 - 65: 33.852 distance: 65 - 66: 16.825 distance: 65 - 68: 11.415 distance: 66 - 67: 23.985 distance: 66 - 72: 6.156 distance: 68 - 69: 27.269 distance: 69 - 70: 10.579 distance: 69 - 71: 11.138 distance: 72 - 73: 17.973 distance: 72 - 78: 47.861 distance: 73 - 74: 34.614 distance: 73 - 76: 26.674 distance: 74 - 75: 33.149 distance: 74 - 79: 32.271 distance: 76 - 77: 16.504 distance: 77 - 78: 17.039 distance: 79 - 80: 19.734 distance: 80 - 81: 35.769 distance: 80 - 83: 13.673 distance: 81 - 82: 33.963 distance: 81 - 88: 17.838 distance: 83 - 84: 13.880 distance: 85 - 86: 3.370 distance: 85 - 87: 14.115 distance: 88 - 89: 4.394 distance: 89 - 90: 7.737 distance: 90 - 91: 3.854 distance: 90 - 92: 7.431 distance: 92 - 93: 6.956 distance: 93 - 94: 8.033 distance: 93 - 96: 11.271 distance: 94 - 95: 15.532 distance: 94 - 100: 10.562 distance: 96 - 97: 7.041 distance: 97 - 98: 11.113 distance: 97 - 99: 4.861 distance: 100 - 101: 15.780 distance: 101 - 102: 14.953 distance: 101 - 104: 16.898 distance: 102 - 103: 24.142 distance: 102 - 108: 9.840 distance: 104 - 105: 3.300 distance: 105 - 106: 18.603 distance: 105 - 107: 12.283