Starting phenix.real_space_refine on Tue Mar 3 14:41:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wso_32762/03_2026/7wso_32762.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wso_32762/03_2026/7wso_32762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wso_32762/03_2026/7wso_32762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wso_32762/03_2026/7wso_32762.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wso_32762/03_2026/7wso_32762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wso_32762/03_2026/7wso_32762.map" } resolution = 3.03 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= 0.128 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 33 5.16 5 C 3955 2.51 5 N 1042 2.21 5 O 1174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 6204 Number of models: 1 Model: "" Number of chains: 4 Chain: "K" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2003 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 233} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1076 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 125} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1997 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 233} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 135} Time building chain proxies: 1.53, per 1000 atoms: 0.25 Number of scatterers: 6204 At special positions: 0 Unit cell: (67.1, 91.3, 172.7, 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 33 16.00 O 1174 8.00 N 1042 7.00 C 3955 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS K 265 " - pdb=" SG CYS K 325 " distance=2.04 Simple disulfide: pdb=" SG CYS K 371 " - pdb=" SG CYS K 429 " distance=2.05 Simple disulfide: pdb=" SG CYS K 457 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 106 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS C 136 " distance=2.06 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 325 " distance=2.04 Simple disulfide: pdb=" SG CYS B 371 " - pdb=" SG CYS B 429 " distance=2.05 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 122 " 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=0, symmetry=0 Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 351.7 milliseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1476 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 16 sheets defined 20.8% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'K' and resid 313 through 318 removed outlier: 3.616A pdb=" N TRP K 317 " --> pdb=" O LEU K 313 " (cutoff:3.500A) Processing helix chain 'K' and resid 358 through 364 removed outlier: 3.732A pdb=" N LEU K 362 " --> pdb=" O ARG K 359 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR K 363 " --> pdb=" O ASP K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 418 through 423 removed outlier: 3.618A pdb=" N GLN K 423 " --> pdb=" O SER K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 440 removed outlier: 3.875A pdb=" N TYR K 440 " --> pdb=" O HIS K 437 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 492 removed outlier: 4.641A pdb=" N THR K 473 " --> pdb=" O TRP K 469 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE K 474 " --> pdb=" O THR K 470 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N PHE K 475 " --> pdb=" O THR K 471 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE K 492 " --> pdb=" O THR K 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.801A pdb=" N HIS A 36 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 168 removed outlier: 3.874A pdb=" N THR A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 4.067A pdb=" N LEU A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 removed outlier: 3.648A pdb=" N TRP B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 313 through 318' Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 436 through 440 removed outlier: 3.845A pdb=" N HIS B 439 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 440 " --> pdb=" O HIS B 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 436 through 440' Processing helix chain 'B' and resid 465 through 471 removed outlier: 3.800A pdb=" N TRP B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 490 removed outlier: 3.606A pdb=" N ILE B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 489 " --> pdb=" O TYR B 485 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.622A pdb=" N ASN C 117 " --> pdb=" O PHE C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 182 removed outlier: 3.770A pdb=" N ARG C 154 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 173 " --> pdb=" O ILE C 169 " (cutoff:3.500A) Proline residue: C 176 - end of helix removed outlier: 3.948A pdb=" N ASP C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 243 through 247 Processing sheet with id=AA2, first strand: chain 'K' and resid 286 through 287 Processing sheet with id=AA3, first strand: chain 'K' and resid 351 through 355 removed outlier: 3.572A pdb=" N THR K 370 " --> pdb=" O LEU K 355 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE K 408 " --> pdb=" O GLY K 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 351 through 355 removed outlier: 3.572A pdb=" N THR K 370 " --> pdb=" O LEU K 355 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N PHE K 408 " --> pdb=" O GLY K 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 390 through 391 Processing sheet with id=AA6, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.005A pdb=" N LEU A 42 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 102 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL A 64 " --> pdb=" O PRO A 83 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP A 66 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.005A pdb=" N LEU A 42 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 102 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA9, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AB1, first strand: chain 'B' and resid 286 through 288 removed outlier: 4.553A pdb=" N TRP B 281 " --> pdb=" O VAL B 288 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 351 through 355 removed outlier: 5.968A pdb=" N PHE B 408 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 351 through 355 removed outlier: 5.968A pdb=" N PHE B 408 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 390 through 391 Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 49 Processing sheet with id=AB6, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AB7, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.727A pdb=" N GLY C 118 " --> pdb=" O LEU C 140 " (cutoff:3.500A) 280 hydrogen bonds defined for protein. 720 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: 0.96 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1422 1.33 - 1.46: 2020 1.46 - 1.60: 2872 1.60 - 1.73: 0 1.73 - 1.86: 46 Bond restraints: 6360 Sorted by residual: bond pdb=" CB VAL A 105 " pdb=" CG1 VAL A 105 " ideal model delta sigma weight residual 1.521 1.394 0.127 3.30e-02 9.18e+02 1.47e+01 bond pdb=" CB PRO A 77 " pdb=" CG PRO A 77 " ideal model delta sigma weight residual 1.506 1.364 0.142 3.90e-02 6.57e+02 1.33e+01 bond pdb=" CB PRO C 50 " pdb=" CG PRO C 50 " ideal model delta sigma weight residual 1.506 1.367 0.139 3.90e-02 6.57e+02 1.27e+01 bond pdb=" CB GLN C 48 " pdb=" CG GLN C 48 " ideal model delta sigma weight residual 1.520 1.426 0.094 3.00e-02 1.11e+03 9.76e+00 bond pdb=" CB PRO B 357 " pdb=" CG PRO B 357 " ideal model delta sigma weight residual 1.492 1.347 0.145 5.00e-02 4.00e+02 8.37e+00 ... (remaining 6355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 8515 3.95 - 7.90: 125 7.90 - 11.86: 12 11.86 - 15.81: 0 15.81 - 19.76: 2 Bond angle restraints: 8654 Sorted by residual: angle pdb=" CA LEU B 447 " pdb=" CB LEU B 447 " pdb=" CG LEU B 447 " ideal model delta sigma weight residual 116.30 136.06 -19.76 3.50e+00 8.16e-02 3.19e+01 angle pdb=" CA TYR B 411 " pdb=" CB TYR B 411 " pdb=" CG TYR B 411 " ideal model delta sigma weight residual 113.90 124.01 -10.11 1.80e+00 3.09e-01 3.16e+01 angle pdb=" CA LEU K 410 " pdb=" CB LEU K 410 " pdb=" CG LEU K 410 " ideal model delta sigma weight residual 116.30 134.75 -18.45 3.50e+00 8.16e-02 2.78e+01 angle pdb=" N LYS A 141 " pdb=" CA LYS A 141 " pdb=" C LYS A 141 " ideal model delta sigma weight residual 113.55 107.09 6.46 1.26e+00 6.30e-01 2.63e+01 angle pdb=" N ALA K 458 " pdb=" CA ALA K 458 " pdb=" C ALA K 458 " ideal model delta sigma weight residual 110.80 120.98 -10.18 2.13e+00 2.20e-01 2.28e+01 ... (remaining 8649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 3594 15.02 - 30.03: 187 30.03 - 45.05: 51 45.05 - 60.07: 9 60.07 - 75.08: 6 Dihedral angle restraints: 3847 sinusoidal: 1568 harmonic: 2279 Sorted by residual: dihedral pdb=" CA CYS K 457 " pdb=" C CYS K 457 " pdb=" N ALA K 458 " pdb=" CA ALA K 458 " ideal model delta harmonic sigma weight residual 180.00 140.57 39.43 0 5.00e+00 4.00e-02 6.22e+01 dihedral pdb=" CA GLU B 454 " pdb=" C GLU B 454 " pdb=" N GLU B 455 " pdb=" CA GLU B 455 " ideal model delta harmonic sigma weight residual -180.00 -142.25 -37.75 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA PRO A 128 " pdb=" C PRO A 128 " pdb=" N PRO A 129 " pdb=" CA PRO A 129 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 3844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 618 0.060 - 0.120: 258 0.120 - 0.180: 72 0.180 - 0.241: 16 0.241 - 0.301: 2 Chirality restraints: 966 Sorted by residual: chirality pdb=" CG LEU K 414 " pdb=" CB LEU K 414 " pdb=" CD1 LEU K 414 " pdb=" CD2 LEU K 414 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CG LEU C 107 " pdb=" CB LEU C 107 " pdb=" CD1 LEU C 107 " pdb=" CD2 LEU C 107 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB ILE B 381 " pdb=" CA ILE B 381 " pdb=" CG1 ILE B 381 " pdb=" CG2 ILE B 381 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 963 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 104 " 0.030 2.00e-02 2.50e+03 2.81e-02 1.58e+01 pdb=" CG TYR A 104 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 104 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 104 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 104 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 104 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 104 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR A 104 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 78 " 0.035 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRP C 78 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 78 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 78 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP C 78 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 78 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 78 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 78 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 78 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 78 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 86 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO A 87 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " 0.042 5.00e-02 4.00e+02 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1996 2.86 - 3.37: 4632 3.37 - 3.88: 9122 3.88 - 4.39: 9713 4.39 - 4.90: 18455 Nonbonded interactions: 43918 Sorted by model distance: nonbonded pdb=" O SER C 71 " pdb=" NE2 GLN C 124 " model vdw 2.351 3.120 nonbonded pdb=" O MET C 163 " pdb=" OG1 THR C 166 " model vdw 2.388 3.040 nonbonded pdb=" O SER K 486 " pdb=" OG1 THR K 490 " model vdw 2.397 3.040 nonbonded pdb=" O GLN K 315 " pdb=" ND2 ASN K 319 " model vdw 2.417 3.120 nonbonded pdb=" OH TYR K 440 " pdb=" NE2 GLN K 442 " model vdw 2.427 3.120 ... (remaining 43913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'K' and (resid 241 through 491 or (resid 492 and (name N or name CA or na \ me C or name O or name CB )))) } 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: 1.090 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.530 Find NCS groups from input model: 0.070 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.014 0.145 6368 Z= 0.544 Angle : 1.303 19.760 8670 Z= 0.691 Chirality : 0.071 0.301 966 Planarity : 0.010 0.075 1111 Dihedral : 10.666 75.083 2347 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.85 % Allowed : 3.40 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.41 % 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: -2.93 (0.27), residues: 772 helix: -3.26 (0.31), residues: 124 sheet: 0.03 (0.31), residues: 277 loop : -3.14 (0.25), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG C 154 TYR 0.068 0.005 TYR A 104 PHE 0.039 0.005 PHE A 80 TRP 0.054 0.006 TRP C 78 HIS 0.016 0.004 HIS C 64 Details of bonding type rmsd covalent geometry : bond 0.01408 ( 6360) covalent geometry : angle 1.29470 ( 8654) SS BOND : bond 0.01739 ( 8) SS BOND : angle 3.69270 ( 16) hydrogen bonds : bond 0.15238 ( 242) hydrogen bonds : angle 7.58620 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7513 (m-80) cc_final: 0.7099 (m-80) REVERT: K 322 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8100 (tt0) REVERT: K 324 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7557 (tttm) REVERT: K 341 SER cc_start: 0.8997 (p) cc_final: 0.8780 (t) REVERT: K 461 GLN cc_start: 0.7845 (mm110) cc_final: 0.7469 (mp10) REVERT: K 465 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8297 (pt) REVERT: B 256 MET cc_start: 0.7588 (mtm) cc_final: 0.6680 (mmt) REVERT: B 348 ARG cc_start: 0.8527 (mtt90) cc_final: 0.8220 (mtt180) REVERT: B 390 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6814 (mt0) REVERT: C 67 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.5544 (pmt) REVERT: C 83 ASP cc_start: 0.5885 (m-30) cc_final: 0.5628 (m-30) REVERT: C 87 GLN cc_start: 0.7651 (mt0) cc_final: 0.6975 (mm110) outliers start: 6 outliers final: 1 residues processed: 134 average time/residue: 0.0948 time to fit residues: 16.1254 Evaluate side-chains 95 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain C residue 67 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 314 HIS K 329 ASN K 394 ASN K 439 HIS A 36 HIS A 127 GLN B 272 HIS B 329 ASN B 394 ASN B 425 ASN B 439 HIS B 442 GLN C 48 GLN C 68 ASN C 165 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.193357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113657 restraints weight = 7177.797| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.92 r_work: 0.2967 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6368 Z= 0.119 Angle : 0.590 8.212 8670 Z= 0.306 Chirality : 0.044 0.148 966 Planarity : 0.006 0.060 1111 Dihedral : 5.599 47.583 837 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.84 % Allowed : 7.08 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.73 (0.29), residues: 772 helix: -1.31 (0.43), residues: 130 sheet: 0.58 (0.32), residues: 282 loop : -2.61 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 143 TYR 0.014 0.001 TYR A 104 PHE 0.012 0.001 PHE B 475 TRP 0.013 0.001 TRP B 469 HIS 0.005 0.001 HIS K 314 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6360) covalent geometry : angle 0.58724 ( 8654) SS BOND : bond 0.00756 ( 8) SS BOND : angle 1.38119 ( 16) hydrogen bonds : bond 0.03955 ( 242) hydrogen bonds : angle 4.54960 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7561 (m-80) cc_final: 0.7119 (m-80) REVERT: K 316 ASP cc_start: 0.7925 (m-30) cc_final: 0.7489 (t70) REVERT: K 322 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8103 (tt0) REVERT: K 324 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7499 (tttm) REVERT: K 341 SER cc_start: 0.8881 (p) cc_final: 0.8617 (t) REVERT: K 462 ASP cc_start: 0.7752 (p0) cc_final: 0.7521 (p0) REVERT: A 136 MET cc_start: 0.6516 (pmt) cc_final: 0.5592 (mpp) REVERT: B 256 MET cc_start: 0.7494 (mtm) cc_final: 0.6552 (mmt) REVERT: B 292 LYS cc_start: 0.6953 (ttmt) cc_final: 0.6238 (mttm) REVERT: B 324 LYS cc_start: 0.7617 (ttmt) cc_final: 0.7069 (ttpp) REVERT: B 348 ARG cc_start: 0.8638 (mtt90) cc_final: 0.8260 (mtt180) REVERT: C 87 GLN cc_start: 0.7968 (mt0) cc_final: 0.7535 (mm110) REVERT: C 93 LYS cc_start: 0.8705 (mptt) cc_final: 0.8455 (mmtt) outliers start: 13 outliers final: 7 residues processed: 114 average time/residue: 0.0946 time to fit residues: 13.8705 Evaluate side-chains 92 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 434 GLU Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 147 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 8.9990 chunk 59 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 0.0370 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.0470 chunk 42 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 overall best weight: 0.8338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 314 HIS K 393 ASN A 117 GLN B 365 ASN C 68 ASN C 165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.189681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.116136 restraints weight = 7078.410| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.30 r_work: 0.2992 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6368 Z= 0.134 Angle : 0.596 7.444 8670 Z= 0.306 Chirality : 0.045 0.158 966 Planarity : 0.005 0.052 1111 Dihedral : 5.336 44.914 835 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.41 % Allowed : 9.63 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.30 (0.30), residues: 772 helix: -0.61 (0.46), residues: 130 sheet: 0.83 (0.32), residues: 282 loop : -2.48 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.016 0.001 TYR B 411 PHE 0.014 0.001 PHE K 376 TRP 0.010 0.001 TRP B 469 HIS 0.004 0.001 HIS A 36 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6360) covalent geometry : angle 0.59263 ( 8654) SS BOND : bond 0.00762 ( 8) SS BOND : angle 1.52137 ( 16) hydrogen bonds : bond 0.04080 ( 242) hydrogen bonds : angle 4.24103 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: K 258 SER cc_start: 0.8633 (m) cc_final: 0.7999 (t) REVERT: K 282 TYR cc_start: 0.7554 (m-80) cc_final: 0.7132 (m-80) REVERT: K 319 ASN cc_start: 0.8508 (m-40) cc_final: 0.7901 (m110) REVERT: K 322 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8168 (tt0) REVERT: K 324 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7524 (tttm) REVERT: K 341 SER cc_start: 0.8808 (p) cc_final: 0.8581 (t) REVERT: A 95 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8516 (m-40) REVERT: A 136 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.5763 (mpp) REVERT: B 256 MET cc_start: 0.7475 (mtm) cc_final: 0.6472 (mmt) REVERT: B 292 LYS cc_start: 0.6755 (ttmt) cc_final: 0.6075 (mttm) REVERT: B 324 LYS cc_start: 0.7602 (ttmt) cc_final: 0.6764 (tptt) REVERT: B 348 ARG cc_start: 0.8650 (mtt90) cc_final: 0.8362 (mtt180) REVERT: B 388 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8183 (t0) REVERT: B 404 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8313 (p) REVERT: B 461 GLN cc_start: 0.6162 (OUTLIER) cc_final: 0.5360 (pp30) REVERT: C 87 GLN cc_start: 0.8004 (mt0) cc_final: 0.7509 (mm110) REVERT: C 93 LYS cc_start: 0.8737 (mptt) cc_final: 0.8457 (mmtt) outliers start: 17 outliers final: 9 residues processed: 103 average time/residue: 0.0843 time to fit residues: 11.4765 Evaluate side-chains 105 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 95 ASN Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 27 optimal weight: 0.4980 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 59 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 365 ASN C 68 ASN C 165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.188052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.107578 restraints weight = 7055.519| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.83 r_work: 0.2964 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6368 Z= 0.154 Angle : 0.615 7.791 8670 Z= 0.317 Chirality : 0.045 0.161 966 Planarity : 0.005 0.051 1111 Dihedral : 5.339 40.882 835 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.83 % Allowed : 11.05 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.05 (0.30), residues: 772 helix: -0.29 (0.47), residues: 131 sheet: 0.95 (0.31), residues: 290 loop : -2.42 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.017 0.001 TYR B 411 PHE 0.017 0.001 PHE K 376 TRP 0.011 0.001 TRP C 78 HIS 0.005 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 6360) covalent geometry : angle 0.61228 ( 8654) SS BOND : bond 0.00809 ( 8) SS BOND : angle 1.48161 ( 16) hydrogen bonds : bond 0.04177 ( 242) hydrogen bonds : angle 4.16045 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7601 (m-80) cc_final: 0.7281 (m-80) REVERT: K 322 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8269 (tt0) REVERT: K 323 TYR cc_start: 0.8411 (m-80) cc_final: 0.8209 (m-80) REVERT: K 324 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7680 (tttm) REVERT: K 338 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6692 (mttm) REVERT: K 341 SER cc_start: 0.8844 (p) cc_final: 0.8624 (t) REVERT: K 346 GLN cc_start: 0.8658 (tp40) cc_final: 0.8326 (tt0) REVERT: K 465 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8397 (pp) REVERT: A 136 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5714 (mpp) REVERT: B 256 MET cc_start: 0.7597 (mtm) cc_final: 0.6521 (mmt) REVERT: B 292 LYS cc_start: 0.6978 (ttmt) cc_final: 0.6260 (mttm) REVERT: B 324 LYS cc_start: 0.7585 (ttmt) cc_final: 0.6767 (tptt) REVERT: B 348 ARG cc_start: 0.8741 (mtt90) cc_final: 0.8478 (mtt180) REVERT: B 404 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 461 GLN cc_start: 0.6197 (OUTLIER) cc_final: 0.5417 (pp30) REVERT: C 87 GLN cc_start: 0.8154 (mt0) cc_final: 0.7628 (mm110) REVERT: C 93 LYS cc_start: 0.8767 (mptt) cc_final: 0.8489 (mmtt) outliers start: 20 outliers final: 11 residues processed: 98 average time/residue: 0.0869 time to fit residues: 11.2055 Evaluate side-chains 99 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 461 GLN Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 34 optimal weight: 0.0570 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 365 ASN C 68 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.188742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109890 restraints weight = 7132.597| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.15 r_work: 0.2990 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6368 Z= 0.135 Angle : 0.581 7.077 8670 Z= 0.299 Chirality : 0.044 0.160 966 Planarity : 0.005 0.051 1111 Dihedral : 5.111 37.322 835 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.69 % Allowed : 11.76 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.84 (0.30), residues: 772 helix: -0.10 (0.47), residues: 131 sheet: 1.10 (0.31), residues: 289 loop : -2.30 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.016 0.001 TYR B 411 PHE 0.014 0.001 PHE K 376 TRP 0.009 0.001 TRP C 78 HIS 0.004 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6360) covalent geometry : angle 0.57834 ( 8654) SS BOND : bond 0.00743 ( 8) SS BOND : angle 1.40080 ( 16) hydrogen bonds : bond 0.03806 ( 242) hydrogen bonds : angle 4.00281 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: K 282 TYR cc_start: 0.7547 (m-80) cc_final: 0.7265 (m-80) REVERT: K 322 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8225 (tt0) REVERT: K 324 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7609 (tttm) REVERT: K 338 LYS cc_start: 0.7033 (mmtt) cc_final: 0.6685 (mttm) REVERT: K 462 ASP cc_start: 0.8093 (p0) cc_final: 0.7219 (t0) REVERT: K 465 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8250 (pp) REVERT: A 112 ASN cc_start: 0.8219 (m-40) cc_final: 0.7354 (p0) REVERT: A 136 MET cc_start: 0.6312 (OUTLIER) cc_final: 0.5669 (mpp) REVERT: B 256 MET cc_start: 0.7454 (mtm) cc_final: 0.6397 (mmt) REVERT: B 292 LYS cc_start: 0.6941 (ttmt) cc_final: 0.6455 (mttm) REVERT: B 324 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7077 (ttpp) REVERT: B 348 ARG cc_start: 0.8707 (mtt90) cc_final: 0.8491 (mtt180) REVERT: B 404 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8311 (p) REVERT: C 87 GLN cc_start: 0.8001 (mt0) cc_final: 0.7451 (mm110) REVERT: C 93 LYS cc_start: 0.8752 (mptt) cc_final: 0.8470 (mmtt) outliers start: 19 outliers final: 12 residues processed: 96 average time/residue: 0.0859 time to fit residues: 10.9079 Evaluate side-chains 96 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN B 365 ASN B 442 GLN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.188760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.111402 restraints weight = 7089.977| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.98 r_work: 0.2999 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6368 Z= 0.127 Angle : 0.574 6.821 8670 Z= 0.295 Chirality : 0.044 0.158 966 Planarity : 0.005 0.048 1111 Dihedral : 4.965 42.362 835 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.69 % Allowed : 11.76 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.62 (0.30), residues: 772 helix: 0.11 (0.47), residues: 131 sheet: 1.21 (0.31), residues: 289 loop : -2.15 (0.30), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 55 TYR 0.015 0.001 TYR B 411 PHE 0.013 0.001 PHE K 376 TRP 0.008 0.001 TRP A 34 HIS 0.004 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 6360) covalent geometry : angle 0.57210 ( 8654) SS BOND : bond 0.00695 ( 8) SS BOND : angle 1.25479 ( 16) hydrogen bonds : bond 0.03666 ( 242) hydrogen bonds : angle 3.92362 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.230 Fit side-chains REVERT: K 282 TYR cc_start: 0.7560 (m-80) cc_final: 0.7344 (m-80) REVERT: K 287 GLU cc_start: 0.6787 (tt0) cc_final: 0.6308 (pp20) REVERT: K 322 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8163 (tt0) REVERT: K 324 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7653 (tttm) REVERT: K 338 LYS cc_start: 0.6953 (mmtt) cc_final: 0.6668 (mttm) REVERT: K 462 ASP cc_start: 0.7995 (p0) cc_final: 0.7071 (t0) REVERT: A 112 ASN cc_start: 0.8200 (m-40) cc_final: 0.7350 (p0) REVERT: A 136 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.5961 (mpp) REVERT: B 256 MET cc_start: 0.7438 (mtm) cc_final: 0.6412 (mmt) REVERT: B 292 LYS cc_start: 0.6960 (ttmt) cc_final: 0.6502 (mttm) REVERT: B 348 ARG cc_start: 0.8673 (mtt90) cc_final: 0.8428 (mtt180) REVERT: B 359 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8051 (mtm-85) REVERT: B 404 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8327 (p) REVERT: C 87 GLN cc_start: 0.8003 (mt0) cc_final: 0.7455 (mm110) REVERT: C 93 LYS cc_start: 0.8745 (mptt) cc_final: 0.8470 (mmtt) outliers start: 19 outliers final: 16 residues processed: 96 average time/residue: 0.0756 time to fit residues: 9.7787 Evaluate side-chains 102 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 359 ARG Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 ASN C 68 ASN ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.185610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.106437 restraints weight = 7019.761| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.77 r_work: 0.2936 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6368 Z= 0.177 Angle : 0.638 8.519 8670 Z= 0.330 Chirality : 0.046 0.166 966 Planarity : 0.005 0.050 1111 Dihedral : 5.290 47.751 835 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.54 % Allowed : 11.19 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.63 (0.30), residues: 772 helix: 0.14 (0.47), residues: 132 sheet: 1.18 (0.31), residues: 290 loop : -2.16 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.019 0.002 TYR B 411 PHE 0.018 0.002 PHE K 376 TRP 0.011 0.001 TRP A 34 HIS 0.005 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 6360) covalent geometry : angle 0.63512 ( 8654) SS BOND : bond 0.00879 ( 8) SS BOND : angle 1.62278 ( 16) hydrogen bonds : bond 0.04341 ( 242) hydrogen bonds : angle 4.09794 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.239 Fit side-chains REVERT: K 322 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8243 (tt0) REVERT: K 324 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7667 (tttm) REVERT: K 338 LYS cc_start: 0.6995 (mmtt) cc_final: 0.6698 (mttm) REVERT: K 346 GLN cc_start: 0.8648 (tp40) cc_final: 0.8373 (tt0) REVERT: K 462 ASP cc_start: 0.8301 (p0) cc_final: 0.7408 (t0) REVERT: A 112 ASN cc_start: 0.8189 (m-40) cc_final: 0.7327 (p0) REVERT: A 136 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.5867 (mpp) REVERT: A 138 GLU cc_start: 0.8208 (tp30) cc_final: 0.7996 (tp30) REVERT: B 256 MET cc_start: 0.7562 (mtm) cc_final: 0.6509 (mmt) REVERT: B 292 LYS cc_start: 0.7107 (ttmt) cc_final: 0.6586 (mttm) REVERT: B 348 ARG cc_start: 0.8789 (mtt90) cc_final: 0.8534 (mtt180) REVERT: B 404 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8350 (p) REVERT: C 87 GLN cc_start: 0.8117 (mt0) cc_final: 0.7577 (mm110) REVERT: C 93 LYS cc_start: 0.8780 (mptt) cc_final: 0.8503 (mmtt) outliers start: 25 outliers final: 18 residues processed: 104 average time/residue: 0.0872 time to fit residues: 12.1892 Evaluate side-chains 104 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 35 optimal weight: 0.2980 chunk 14 optimal weight: 0.2980 chunk 46 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 ASN ** C 165 GLN ** 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 = 0.4100 r_free = 0.4100 target = 0.189080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.110705 restraints weight = 7056.629| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.80 r_work: 0.3035 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6368 Z= 0.105 Angle : 0.540 6.698 8670 Z= 0.276 Chirality : 0.043 0.153 966 Planarity : 0.004 0.050 1111 Dihedral : 4.771 44.581 835 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.55 % Allowed : 12.04 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.55 (0.30), residues: 772 helix: -0.00 (0.46), residues: 137 sheet: 1.30 (0.31), residues: 290 loop : -2.11 (0.30), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 143 TYR 0.012 0.001 TYR B 411 PHE 0.011 0.001 PHE K 376 TRP 0.007 0.001 TRP A 34 HIS 0.002 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 6360) covalent geometry : angle 0.53862 ( 8654) SS BOND : bond 0.00588 ( 8) SS BOND : angle 1.02053 ( 16) hydrogen bonds : bond 0.03238 ( 242) hydrogen bonds : angle 3.76615 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.235 Fit side-chains REVERT: K 322 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8223 (tt0) REVERT: K 324 LYS cc_start: 0.7841 (ttmt) cc_final: 0.7460 (tttm) REVERT: K 338 LYS cc_start: 0.6961 (mmtt) cc_final: 0.6649 (mttm) REVERT: K 462 ASP cc_start: 0.8144 (p0) cc_final: 0.7205 (t0) REVERT: A 97 ASN cc_start: 0.7816 (p0) cc_final: 0.7595 (p0) REVERT: A 112 ASN cc_start: 0.8152 (m-40) cc_final: 0.7285 (p0) REVERT: A 138 GLU cc_start: 0.8177 (tp30) cc_final: 0.7962 (tp30) REVERT: B 256 MET cc_start: 0.7485 (mtm) cc_final: 0.6456 (mmt) REVERT: B 292 LYS cc_start: 0.6960 (ttmt) cc_final: 0.6269 (mmtm) REVERT: B 348 ARG cc_start: 0.8741 (mtt90) cc_final: 0.8507 (mtt180) REVERT: B 404 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.8377 (p) REVERT: C 85 ASN cc_start: 0.8095 (m-40) cc_final: 0.7479 (p0) REVERT: C 87 GLN cc_start: 0.8082 (mt0) cc_final: 0.7532 (mm110) REVERT: C 93 LYS cc_start: 0.8776 (mptt) cc_final: 0.8516 (mmtt) outliers start: 18 outliers final: 16 residues processed: 96 average time/residue: 0.0853 time to fit residues: 10.8931 Evaluate side-chains 97 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 6 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.0060 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 ASN ** C 165 GLN ** 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 = 0.4112 r_free = 0.4112 target = 0.190203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.110378 restraints weight = 7101.310| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.84 r_work: 0.3021 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6368 Z= 0.116 Angle : 0.557 6.632 8670 Z= 0.285 Chirality : 0.043 0.156 966 Planarity : 0.004 0.048 1111 Dihedral : 4.805 45.173 835 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.41 % Allowed : 12.04 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.42 (0.30), residues: 772 helix: 0.11 (0.45), residues: 137 sheet: 1.40 (0.31), residues: 289 loop : -2.04 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 143 TYR 0.015 0.001 TYR B 411 PHE 0.011 0.001 PHE K 376 TRP 0.007 0.001 TRP A 34 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6360) covalent geometry : angle 0.55499 ( 8654) SS BOND : bond 0.00649 ( 8) SS BOND : angle 1.12486 ( 16) hydrogen bonds : bond 0.03454 ( 242) hydrogen bonds : angle 3.76717 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.241 Fit side-chains REVERT: K 322 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8204 (tt0) REVERT: K 324 LYS cc_start: 0.7846 (ttmt) cc_final: 0.7503 (tttm) REVERT: K 338 LYS cc_start: 0.7010 (mmtt) cc_final: 0.6761 (mttm) REVERT: K 462 ASP cc_start: 0.8030 (p0) cc_final: 0.7167 (t0) REVERT: A 57 ASN cc_start: 0.7080 (t0) cc_final: 0.6866 (t0) REVERT: A 97 ASN cc_start: 0.7861 (p0) cc_final: 0.7648 (p0) REVERT: A 112 ASN cc_start: 0.8150 (m-40) cc_final: 0.7296 (p0) REVERT: A 136 MET cc_start: 0.6480 (mmp) cc_final: 0.5803 (mpp) REVERT: A 138 GLU cc_start: 0.8173 (tp30) cc_final: 0.7951 (tp30) REVERT: B 256 MET cc_start: 0.7488 (mtm) cc_final: 0.6449 (mmt) REVERT: B 292 LYS cc_start: 0.6950 (ttmt) cc_final: 0.6317 (mmtm) REVERT: B 348 ARG cc_start: 0.8742 (mtt90) cc_final: 0.8522 (mtt180) REVERT: B 404 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8384 (p) REVERT: C 87 GLN cc_start: 0.8069 (mt0) cc_final: 0.7548 (mm110) REVERT: C 93 LYS cc_start: 0.8814 (mptt) cc_final: 0.8533 (mmtt) REVERT: C 134 GLN cc_start: 0.8310 (tt0) cc_final: 0.8105 (tt0) outliers start: 17 outliers final: 16 residues processed: 92 average time/residue: 0.0857 time to fit residues: 10.4603 Evaluate side-chains 97 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 ASN ** C 165 GLN ** 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 = 0.4104 r_free = 0.4104 target = 0.189405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108966 restraints weight = 7109.669| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.87 r_work: 0.2989 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6368 Z= 0.134 Angle : 0.579 7.041 8670 Z= 0.297 Chirality : 0.044 0.160 966 Planarity : 0.004 0.046 1111 Dihedral : 4.910 45.393 835 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.41 % Allowed : 12.04 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % 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: -0.39 (0.30), residues: 772 helix: 0.13 (0.45), residues: 138 sheet: 1.39 (0.31), residues: 289 loop : -1.98 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.016 0.001 TYR B 411 PHE 0.014 0.001 PHE K 376 TRP 0.008 0.001 TRP A 34 HIS 0.004 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6360) covalent geometry : angle 0.57700 ( 8654) SS BOND : bond 0.00725 ( 8) SS BOND : angle 1.29884 ( 16) hydrogen bonds : bond 0.03715 ( 242) hydrogen bonds : angle 3.85137 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.232 Fit side-chains REVERT: K 322 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8086 (tt0) REVERT: K 324 LYS cc_start: 0.7883 (ttmt) cc_final: 0.7422 (tttm) REVERT: K 462 ASP cc_start: 0.7877 (p0) cc_final: 0.7126 (t0) REVERT: A 112 ASN cc_start: 0.8153 (m-40) cc_final: 0.7339 (p0) REVERT: B 256 MET cc_start: 0.7403 (mtm) cc_final: 0.6397 (mmt) REVERT: B 292 LYS cc_start: 0.6915 (ttmt) cc_final: 0.6292 (mmtm) REVERT: B 348 ARG cc_start: 0.8662 (mtt90) cc_final: 0.8450 (mtt180) REVERT: B 404 SER cc_start: 0.8593 (OUTLIER) cc_final: 0.8343 (p) REVERT: C 87 GLN cc_start: 0.7936 (mt0) cc_final: 0.7433 (mm110) REVERT: C 93 LYS cc_start: 0.8790 (mptt) cc_final: 0.8498 (mmtt) outliers start: 17 outliers final: 16 residues processed: 91 average time/residue: 0.0793 time to fit residues: 9.5892 Evaluate side-chains 95 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 465 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 322 GLU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 147 THR Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 169 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 68 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 365 ASN ** C 165 GLN ** 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 = 0.4109 r_free = 0.4109 target = 0.189910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109702 restraints weight = 6999.395| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.84 r_work: 0.3007 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6368 Z= 0.127 Angle : 0.578 7.307 8670 Z= 0.295 Chirality : 0.044 0.160 966 Planarity : 0.004 0.046 1111 Dihedral : 4.849 44.873 835 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.41 % Allowed : 12.18 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.32 (0.30), residues: 772 helix: 0.21 (0.45), residues: 137 sheet: 1.35 (0.31), residues: 294 loop : -1.91 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 55 TYR 0.015 0.001 TYR B 411 PHE 0.013 0.001 PHE K 376 TRP 0.008 0.001 TRP A 34 HIS 0.004 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6360) covalent geometry : angle 0.57571 ( 8654) SS BOND : bond 0.00695 ( 8) SS BOND : angle 1.21439 ( 16) hydrogen bonds : bond 0.03579 ( 242) hydrogen bonds : angle 3.78493 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2241.51 seconds wall clock time: 38 minutes 51.70 seconds (2331.70 seconds total)