Starting phenix.real_space_refine on Tue Mar 3 23:09:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ni2_9375/03_2026/6ni2_9375.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ni2_9375/03_2026/6ni2_9375.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ni2_9375/03_2026/6ni2_9375.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ni2_9375/03_2026/6ni2_9375.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ni2_9375/03_2026/6ni2_9375.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ni2_9375/03_2026/6ni2_9375.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4506 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 21 5.16 5 C 3402 2.51 5 N 910 2.21 5 O 1042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5381 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 865 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "B" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2699 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 2, 'GLU:plan': 7, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "H" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 800 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "V" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 109 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.29, per 1000 atoms: 0.24 Number of scatterers: 5381 At special positions: 0 Unit cell: (95.68, 91.52, 109.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 6 15.00 O 1042 8.00 N 910 7.00 C 3402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 331.5 milliseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 15 sheets defined 2.8% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 98 through 109 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'H' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 23 removed outlier: 3.728A pdb=" N MET A 82 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 70 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.537A pdb=" N THR A 108 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 117 removed outlier: 3.580A pdb=" N LYS B 10 " --> pdb=" O ALA V 361 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.700A pdb=" N VAL B 164 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 168 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 53 " --> pdb=" O GLN B 85 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN B 85 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 55 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASN B 83 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 57 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 81 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS B 59 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 75 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.700A pdb=" N VAL B 164 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 168 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 183 through 188 removed outlier: 3.680A pdb=" N HIS B 198 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 274 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 272 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 218 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS B 270 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 220 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 268 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.629A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE B 231 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU B 257 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE B 233 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET B 255 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 235 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N CYS B 251 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 239 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR B 249 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 241 " --> pdb=" O ALA B 247 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 207 through 208 removed outlier: 4.629A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.511A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 343 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.557A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.094A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.094A pdb=" N GLY H 13 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR H 112 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ARG H 103 " --> pdb=" O LEU H 110 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N LEU H 110 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.659A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.926A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 465 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: 0.92 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1685 1.34 - 1.46: 1215 1.46 - 1.58: 2547 1.58 - 1.70: 22 1.70 - 1.82: 28 Bond restraints: 5497 Sorted by residual: bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.605 0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.717 1.625 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O1P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.525 1.610 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O2P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.528 1.607 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O2P TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.528 1.605 -0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 5492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 7216 3.13 - 6.26: 240 6.26 - 9.40: 27 9.40 - 12.53: 3 12.53 - 15.66: 2 Bond angle restraints: 7488 Sorted by residual: angle pdb=" N GLU B 156 " pdb=" CA GLU B 156 " pdb=" C GLU B 156 " ideal model delta sigma weight residual 110.24 117.78 -7.54 1.41e+00 5.03e-01 2.86e+01 angle pdb=" C THR B 74 " pdb=" N PHE B 75 " pdb=" CA PHE B 75 " ideal model delta sigma weight residual 122.29 130.49 -8.20 1.65e+00 3.67e-01 2.47e+01 angle pdb=" C GLN B 189 " pdb=" N PHE B 190 " pdb=" CA PHE B 190 " ideal model delta sigma weight residual 122.07 112.79 9.28 2.01e+00 2.48e-01 2.13e+01 angle pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " pdb=" CG LEU A 85 " ideal model delta sigma weight residual 116.30 100.64 15.66 3.50e+00 8.16e-02 2.00e+01 angle pdb=" N PHE B 75 " pdb=" CA PHE B 75 " pdb=" C PHE B 75 " ideal model delta sigma weight residual 109.23 102.62 6.61 1.55e+00 4.16e-01 1.82e+01 ... (remaining 7483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.64: 3059 13.64 - 27.29: 185 27.29 - 40.93: 30 40.93 - 54.58: 7 54.58 - 68.22: 4 Dihedral angle restraints: 3285 sinusoidal: 1239 harmonic: 2046 Sorted by residual: dihedral pdb=" CA ALA A 51 " pdb=" C ALA A 51 " pdb=" N THR A 52 " pdb=" CA THR A 52 " ideal model delta harmonic sigma weight residual 180.00 144.84 35.16 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" CA TYR A 59 " pdb=" C TYR A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA SER A 50 " pdb=" C SER A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 3282 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 641 0.077 - 0.154: 188 0.154 - 0.231: 23 0.231 - 0.308: 2 0.308 - 0.385: 2 Chirality restraints: 856 Sorted by residual: chirality pdb=" CB VAL B 164 " pdb=" CA VAL B 164 " pdb=" CG1 VAL B 164 " pdb=" CG2 VAL B 164 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA GLU B 156 " pdb=" N GLU B 156 " pdb=" C GLU B 156 " pdb=" CB GLU B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA VAL B 164 " pdb=" N VAL B 164 " pdb=" C VAL B 164 " pdb=" CB VAL B 164 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 853 not shown) Planarity restraints: 951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 9 " 0.028 2.00e-02 2.50e+03 2.35e-02 9.65e+00 pdb=" CG PHE B 9 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 9 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 9 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 9 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 9 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 9 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 113 " 0.022 2.00e-02 2.50e+03 2.04e-02 8.32e+00 pdb=" CG TYR B 113 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 113 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 113 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 113 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 113 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 113 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 113 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 21 " 0.019 2.00e-02 2.50e+03 1.97e-02 7.76e+00 pdb=" CG TYR B 21 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 21 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 21 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 21 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 21 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 21 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR B 21 " -0.005 2.00e-02 2.50e+03 ... (remaining 948 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1065 2.78 - 3.31: 4502 3.31 - 3.84: 8646 3.84 - 4.37: 9354 4.37 - 4.90: 16512 Nonbonded interactions: 40079 Sorted by model distance: nonbonded pdb=" OD1 ASP B 204 " pdb=" OH TYR B 208 " model vdw 2.245 3.040 nonbonded pdb=" O ASP A 89 " pdb=" OH TYR A 93 " model vdw 2.256 3.040 nonbonded pdb=" OG SEP V 363 " pdb=" N SEP V 364 " model vdw 2.314 3.120 nonbonded pdb=" O ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.318 3.040 nonbonded pdb=" OD1 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.337 3.040 ... (remaining 40074 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.350 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 0.121 5500 Z= 0.431 Angle : 1.328 15.660 7492 Z= 0.729 Chirality : 0.070 0.385 856 Planarity : 0.007 0.055 951 Dihedral : 9.614 68.220 1967 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.74 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.31), residues: 682 helix: -0.31 (1.30), residues: 12 sheet: -0.88 (0.30), residues: 271 loop : -1.06 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG H 101 TYR 0.051 0.005 TYR B 113 PHE 0.054 0.005 PHE B 9 TRP 0.045 0.004 TRP A 36 HIS 0.012 0.004 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00957 ( 5497) covalent geometry : angle 1.32666 ( 7488) SS BOND : bond 0.01335 ( 2) SS BOND : angle 2.64714 ( 4) hydrogen bonds : bond 0.30825 ( 162) hydrogen bonds : angle 9.89892 ( 465) Misc. bond : bond 0.00019 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6443 (tpt-90) cc_final: 0.6017 (tpp80) REVERT: A 64 LYS cc_start: 0.8636 (ptpt) cc_final: 0.8060 (ptpp) REVERT: A 67 PHE cc_start: 0.7543 (m-10) cc_final: 0.7182 (m-10) REVERT: A 85 LEU cc_start: 0.7294 (mt) cc_final: 0.7092 (mt) REVERT: B 42 LEU cc_start: 0.7307 (tp) cc_final: 0.6996 (pp) REVERT: B 77 LYS cc_start: 0.8015 (tppt) cc_final: 0.7526 (mmtm) REVERT: B 232 LYS cc_start: 0.6625 (mttt) cc_final: 0.5652 (tttt) REVERT: H 48 LEU cc_start: 0.9402 (mt) cc_final: 0.9088 (tp) REVERT: H 71 PHE cc_start: 0.8089 (m-10) cc_final: 0.7622 (m-10) REVERT: L 25 ARG cc_start: 0.8411 (ttm170) cc_final: 0.8168 (mtm-85) REVERT: L 28 GLN cc_start: 0.8998 (tt0) cc_final: 0.8638 (mt0) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0967 time to fit residues: 18.3377 Evaluate side-chains 76 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0030 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.109548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.093644 restraints weight = 19123.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.096181 restraints weight = 11552.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.097967 restraints weight = 8001.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.099206 restraints weight = 6069.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.100004 restraints weight = 4935.762| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5500 Z= 0.139 Angle : 0.736 10.547 7492 Z= 0.378 Chirality : 0.047 0.153 856 Planarity : 0.005 0.056 951 Dihedral : 6.580 54.513 780 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.93 % Allowed : 14.04 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.31), residues: 682 helix: 0.67 (1.49), residues: 12 sheet: -0.05 (0.31), residues: 262 loop : -0.62 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 67 TYR 0.032 0.002 TYR H 57 PHE 0.014 0.002 PHE A 29 TRP 0.013 0.001 TRP A 36 HIS 0.008 0.002 HIS B 159 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5497) covalent geometry : angle 0.73452 ( 7488) SS BOND : bond 0.00933 ( 2) SS BOND : angle 1.89703 ( 4) hydrogen bonds : bond 0.04103 ( 162) hydrogen bonds : angle 7.09784 ( 465) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.6605 (tpt-90) cc_final: 0.6204 (tpp80) REVERT: A 64 LYS cc_start: 0.8484 (ptpt) cc_final: 0.8248 (ptpp) REVERT: A 75 LYS cc_start: 0.8479 (tttt) cc_final: 0.8225 (ttmt) REVERT: A 82 MET cc_start: 0.7990 (mtp) cc_final: 0.7233 (mtp) REVERT: B 77 LYS cc_start: 0.8048 (tppt) cc_final: 0.7621 (mmtm) REVERT: B 202 SER cc_start: 0.7444 (p) cc_final: 0.6800 (t) REVERT: B 217 ASN cc_start: 0.7163 (t0) cc_final: 0.6929 (p0) REVERT: H 50 TRP cc_start: 0.8803 (t60) cc_final: 0.8522 (t60) REVERT: H 51 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8188 (m) REVERT: H 76 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6343 (p0) REVERT: H 86 MET cc_start: 0.6872 (mtm) cc_final: 0.6595 (ttp) REVERT: L 28 GLN cc_start: 0.8790 (tt0) cc_final: 0.8509 (mt0) REVERT: L 82 GLU cc_start: 0.8321 (pm20) cc_final: 0.8045 (pp20) outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 0.0884 time to fit residues: 12.3573 Evaluate side-chains 84 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.111966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.096626 restraints weight = 19423.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.099016 restraints weight = 11631.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.100838 restraints weight = 8047.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.102114 restraints weight = 6044.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.102975 restraints weight = 4863.617| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5500 Z= 0.164 Angle : 0.674 8.382 7492 Z= 0.349 Chirality : 0.045 0.147 856 Planarity : 0.005 0.047 951 Dihedral : 6.480 56.804 780 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.86 % Allowed : 11.93 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.32), residues: 682 helix: 1.32 (1.54), residues: 12 sheet: 0.22 (0.31), residues: 276 loop : -0.51 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 25 TYR 0.022 0.002 TYR H 83 PHE 0.015 0.002 PHE A 67 TRP 0.013 0.001 TRP A 36 HIS 0.006 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 5497) covalent geometry : angle 0.67324 ( 7488) SS BOND : bond 0.00913 ( 2) SS BOND : angle 1.27654 ( 4) hydrogen bonds : bond 0.03747 ( 162) hydrogen bonds : angle 6.26435 ( 465) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.204 Fit side-chains REVERT: A 67 PHE cc_start: 0.7402 (m-10) cc_final: 0.7093 (m-10) REVERT: A 82 MET cc_start: 0.7881 (mtp) cc_final: 0.7405 (mtp) REVERT: H 32 VAL cc_start: 0.7876 (p) cc_final: 0.7625 (t) REVERT: H 50 TRP cc_start: 0.8865 (t60) cc_final: 0.8650 (t60) REVERT: H 55 SER cc_start: 0.8807 (t) cc_final: 0.8566 (m) REVERT: L 28 GLN cc_start: 0.8861 (tt0) cc_final: 0.8598 (mt0) outliers start: 22 outliers final: 15 residues processed: 91 average time/residue: 0.0673 time to fit residues: 8.3250 Evaluate side-chains 79 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 40 optimal weight: 0.2980 chunk 55 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 HIS ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.109833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.094842 restraints weight = 19480.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.097176 restraints weight = 11777.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.098939 restraints weight = 8167.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.100114 restraints weight = 6162.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.100887 restraints weight = 4976.194| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5500 Z= 0.206 Angle : 0.701 7.563 7492 Z= 0.361 Chirality : 0.046 0.148 856 Planarity : 0.005 0.045 951 Dihedral : 6.610 58.681 780 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.56 % Allowed : 13.68 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.32), residues: 682 helix: 1.52 (1.56), residues: 12 sheet: 0.28 (0.32), residues: 270 loop : -0.52 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 45 TYR 0.022 0.002 TYR H 83 PHE 0.011 0.002 PHE B 277 TRP 0.016 0.002 TRP A 36 HIS 0.007 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 5497) covalent geometry : angle 0.70002 ( 7488) SS BOND : bond 0.00969 ( 2) SS BOND : angle 1.32525 ( 4) hydrogen bonds : bond 0.03800 ( 162) hydrogen bonds : angle 5.99187 ( 465) Misc. bond : bond 0.00039 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 67 PHE cc_start: 0.7481 (m-10) cc_final: 0.7184 (m-10) REVERT: A 82 MET cc_start: 0.7914 (mtp) cc_final: 0.7523 (mtp) REVERT: H 32 VAL cc_start: 0.7678 (p) cc_final: 0.7439 (t) REVERT: H 55 SER cc_start: 0.8885 (t) cc_final: 0.8588 (m) REVERT: H 79 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8559 (mtmm) REVERT: L 28 GLN cc_start: 0.8910 (tt0) cc_final: 0.8666 (mt0) outliers start: 26 outliers final: 20 residues processed: 85 average time/residue: 0.0654 time to fit residues: 7.7390 Evaluate side-chains 85 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 35 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.110478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.095350 restraints weight = 19900.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.097738 restraints weight = 12042.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.099479 restraints weight = 8326.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.100575 restraints weight = 6278.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.101518 restraints weight = 5109.623| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5500 Z= 0.156 Angle : 0.648 7.188 7492 Z= 0.331 Chirality : 0.044 0.141 856 Planarity : 0.004 0.040 951 Dihedral : 6.365 57.576 780 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.21 % Allowed : 15.44 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.32), residues: 682 helix: 1.75 (1.63), residues: 12 sheet: 0.40 (0.32), residues: 272 loop : -0.47 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 45 TYR 0.015 0.002 TYR H 83 PHE 0.012 0.002 PHE H 71 TRP 0.015 0.002 TRP A 36 HIS 0.005 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5497) covalent geometry : angle 0.64734 ( 7488) SS BOND : bond 0.00837 ( 2) SS BOND : angle 1.13705 ( 4) hydrogen bonds : bond 0.03420 ( 162) hydrogen bonds : angle 5.66632 ( 465) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7858 (mtp) cc_final: 0.7355 (mtp) REVERT: B 240 ASP cc_start: 0.7331 (p0) cc_final: 0.6987 (m-30) REVERT: B 243 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.5270 (pt) REVERT: H 32 VAL cc_start: 0.7599 (p) cc_final: 0.7353 (t) REVERT: H 55 SER cc_start: 0.8828 (t) cc_final: 0.8604 (m) REVERT: H 79 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8330 (mtmm) outliers start: 24 outliers final: 19 residues processed: 87 average time/residue: 0.0634 time to fit residues: 7.5212 Evaluate side-chains 83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 19 optimal weight: 0.0270 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.107739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.092939 restraints weight = 20064.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.095186 restraints weight = 12288.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.096836 restraints weight = 8569.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.097892 restraints weight = 6498.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.098823 restraints weight = 5335.200| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5500 Z= 0.233 Angle : 0.734 7.521 7492 Z= 0.379 Chirality : 0.047 0.238 856 Planarity : 0.005 0.039 951 Dihedral : 6.782 60.906 780 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.86 % Allowed : 17.02 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.32), residues: 682 helix: 1.72 (1.62), residues: 12 sheet: 0.30 (0.31), residues: 286 loop : -0.71 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 76 TYR 0.018 0.002 TYR H 83 PHE 0.014 0.002 PHE B 190 TRP 0.017 0.002 TRP A 36 HIS 0.006 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 5497) covalent geometry : angle 0.73356 ( 7488) SS BOND : bond 0.01002 ( 2) SS BOND : angle 1.23313 ( 4) hydrogen bonds : bond 0.04078 ( 162) hydrogen bonds : angle 5.84611 ( 465) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 203 LEU cc_start: 0.8883 (mp) cc_final: 0.8611 (mp) REVERT: H 32 VAL cc_start: 0.7533 (p) cc_final: 0.7320 (t) REVERT: H 55 SER cc_start: 0.8852 (t) cc_final: 0.8608 (m) outliers start: 22 outliers final: 21 residues processed: 82 average time/residue: 0.0658 time to fit residues: 7.4301 Evaluate side-chains 87 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 65 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.110100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.095110 restraints weight = 19755.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.097406 restraints weight = 12033.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.099113 restraints weight = 8352.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.100318 restraints weight = 6310.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.101137 restraints weight = 5076.717| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5500 Z= 0.137 Angle : 0.651 9.488 7492 Z= 0.328 Chirality : 0.045 0.238 856 Planarity : 0.004 0.038 951 Dihedral : 6.288 57.276 780 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.68 % Allowed : 17.37 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.32), residues: 682 helix: 1.98 (1.67), residues: 12 sheet: 0.45 (0.32), residues: 272 loop : -0.67 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 25 TYR 0.014 0.002 TYR A 59 PHE 0.013 0.002 PHE A 67 TRP 0.018 0.002 TRP A 36 HIS 0.004 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5497) covalent geometry : angle 0.65103 ( 7488) SS BOND : bond 0.00795 ( 2) SS BOND : angle 1.09145 ( 4) hydrogen bonds : bond 0.03268 ( 162) hydrogen bonds : angle 5.44255 ( 465) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 240 ASP cc_start: 0.7206 (p0) cc_final: 0.6670 (m-30) REVERT: B 243 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.5298 (pt) REVERT: B 321 TYR cc_start: 0.6515 (m-10) cc_final: 0.6270 (m-10) outliers start: 21 outliers final: 19 residues processed: 85 average time/residue: 0.0650 time to fit residues: 7.6109 Evaluate side-chains 82 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.110157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.095150 restraints weight = 19365.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.097464 restraints weight = 11958.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.099038 restraints weight = 8409.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.100234 restraints weight = 6484.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.100993 restraints weight = 5301.920| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5500 Z= 0.115 Angle : 0.635 9.358 7492 Z= 0.318 Chirality : 0.044 0.241 856 Planarity : 0.004 0.038 951 Dihedral : 6.033 56.266 780 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 3.86 % Allowed : 17.54 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.33), residues: 682 helix: 2.03 (1.66), residues: 12 sheet: 0.58 (0.31), residues: 281 loop : -0.52 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 25 TYR 0.013 0.001 TYR H 57 PHE 0.021 0.002 PHE H 71 TRP 0.018 0.002 TRP A 36 HIS 0.002 0.001 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5497) covalent geometry : angle 0.63518 ( 7488) SS BOND : bond 0.00749 ( 2) SS BOND : angle 0.92844 ( 4) hydrogen bonds : bond 0.03106 ( 162) hydrogen bonds : angle 5.24724 ( 465) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8490 (tttt) cc_final: 0.8116 (tptt) REVERT: B 240 ASP cc_start: 0.7034 (p0) cc_final: 0.6609 (m-30) REVERT: B 243 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.5175 (pt) REVERT: B 326 LYS cc_start: 0.7420 (tttt) cc_final: 0.7054 (tttt) outliers start: 22 outliers final: 18 residues processed: 82 average time/residue: 0.0724 time to fit residues: 7.9832 Evaluate side-chains 82 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 33 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.107174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.092672 restraints weight = 19933.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.094884 restraints weight = 12250.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.096522 restraints weight = 8512.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.097667 restraints weight = 6465.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.098378 restraints weight = 5215.606| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 5500 Z= 0.242 Angle : 0.742 8.519 7492 Z= 0.381 Chirality : 0.046 0.223 856 Planarity : 0.005 0.039 951 Dihedral : 6.617 61.323 780 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.86 % Allowed : 17.72 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.32), residues: 682 helix: 2.03 (1.70), residues: 12 sheet: 0.26 (0.32), residues: 267 loop : -0.78 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 22 TYR 0.017 0.002 TYR H 83 PHE 0.019 0.003 PHE A 67 TRP 0.021 0.003 TRP A 36 HIS 0.005 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 5497) covalent geometry : angle 0.74225 ( 7488) SS BOND : bond 0.00954 ( 2) SS BOND : angle 1.07156 ( 4) hydrogen bonds : bond 0.03976 ( 162) hydrogen bonds : angle 5.67495 ( 465) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.4415 (tpp) cc_final: 0.4141 (tpp) REVERT: A 37 TYR cc_start: 0.6649 (m-80) cc_final: 0.6131 (m-10) REVERT: A 75 LYS cc_start: 0.8508 (tttt) cc_final: 0.8146 (tptt) REVERT: B 203 LEU cc_start: 0.8855 (mp) cc_final: 0.8597 (mp) REVERT: B 243 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.5145 (pt) REVERT: B 326 LYS cc_start: 0.7438 (tttt) cc_final: 0.7036 (tttt) outliers start: 22 outliers final: 20 residues processed: 81 average time/residue: 0.0684 time to fit residues: 7.5223 Evaluate side-chains 83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 251 CYS Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 25 CYS Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.0020 chunk 52 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.111046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.096144 restraints weight = 19468.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.098475 restraints weight = 11872.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.100197 restraints weight = 8201.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.101395 restraints weight = 6199.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.102137 restraints weight = 4989.023| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5500 Z= 0.115 Angle : 0.666 7.698 7492 Z= 0.332 Chirality : 0.044 0.231 856 Planarity : 0.004 0.038 951 Dihedral : 6.018 54.798 780 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.16 % Allowed : 18.25 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.33), residues: 682 helix: 2.11 (1.70), residues: 12 sheet: 0.55 (0.31), residues: 277 loop : -0.52 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 41 TYR 0.013 0.001 TYR H 57 PHE 0.012 0.002 PHE B 268 TRP 0.021 0.002 TRP A 36 HIS 0.002 0.000 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5497) covalent geometry : angle 0.66546 ( 7488) SS BOND : bond 0.00717 ( 2) SS BOND : angle 0.95136 ( 4) hydrogen bonds : bond 0.03132 ( 162) hydrogen bonds : angle 5.24911 ( 465) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.6485 (m-80) cc_final: 0.5945 (m-80) REVERT: A 75 LYS cc_start: 0.8419 (tttt) cc_final: 0.7587 (tptt) REVERT: B 240 ASP cc_start: 0.6961 (p0) cc_final: 0.6637 (m-30) REVERT: B 326 LYS cc_start: 0.7331 (tttt) cc_final: 0.6981 (tttt) outliers start: 18 outliers final: 17 residues processed: 83 average time/residue: 0.0745 time to fit residues: 8.2519 Evaluate side-chains 83 residues out of total 601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 61 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.109258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.094408 restraints weight = 19631.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.096657 restraints weight = 12064.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.098344 restraints weight = 8427.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.099390 restraints weight = 6399.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.100253 restraints weight = 5237.929| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5500 Z= 0.170 Angle : 0.695 9.429 7492 Z= 0.352 Chirality : 0.045 0.202 856 Planarity : 0.004 0.040 951 Dihedral : 6.172 58.477 780 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.86 % Allowed : 18.42 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.11 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.33), residues: 682 helix: 2.20 (1.71), residues: 12 sheet: 0.40 (0.31), residues: 284 loop : -0.49 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 41 TYR 0.014 0.001 TYR H 83 PHE 0.022 0.002 PHE A 27 TRP 0.016 0.002 TRP A 36 HIS 0.005 0.001 HIS A 44 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5497) covalent geometry : angle 0.69469 ( 7488) SS BOND : bond 0.00844 ( 2) SS BOND : angle 0.92673 ( 4) hydrogen bonds : bond 0.03502 ( 162) hydrogen bonds : angle 5.38860 ( 465) Misc. bond : bond 0.00011 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1061.97 seconds wall clock time: 19 minutes 2.27 seconds (1142.27 seconds total)