Starting phenix.real_space_refine on Wed Jun 11 08:51:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ze0_60019/06_2025/8ze0_60019.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ze0_60019/06_2025/8ze0_60019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ze0_60019/06_2025/8ze0_60019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ze0_60019/06_2025/8ze0_60019.map" model { file = "/net/cci-nas-00/data/ceres_data/8ze0_60019/06_2025/8ze0_60019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ze0_60019/06_2025/8ze0_60019.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.050 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 92 5.16 5 C 8528 2.51 5 N 2124 2.21 5 O 2136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12880 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3220 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 377} Restraints were copied for chains: C, B, D Time building chain proxies: 6.77, per 1000 atoms: 0.53 Number of scatterers: 12880 At special positions: 0 Unit cell: (116.5, 116.5, 98.792, 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 92 16.00 O 2136 8.00 N 2124 7.00 C 8528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.7 seconds 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3024 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 78.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.594A pdb=" N LEU A 69 " --> pdb=" O PRO A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 123 Processing helix chain 'A' and resid 128 through 164 removed outlier: 4.364A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 177 through 214 removed outlier: 3.591A pdb=" N MET A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 Processing helix chain 'A' and resid 242 through 287 removed outlier: 4.096A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 387 removed outlier: 3.978A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 421 through 444 removed outlier: 4.127A pdb=" N GLN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.595A pdb=" N LEU B 69 " --> pdb=" O PRO B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'B' and resid 128 through 164 removed outlier: 4.363A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 177 through 214 removed outlier: 3.592A pdb=" N MET B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 242 through 287 removed outlier: 4.097A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER B 321 " --> pdb=" O SER B 317 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 387 removed outlier: 3.977A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 421 through 444 removed outlier: 4.126A pdb=" N GLN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.595A pdb=" N LEU C 69 " --> pdb=" O PRO C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 123 Processing helix chain 'C' and resid 128 through 164 removed outlier: 4.364A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 177 through 214 removed outlier: 3.591A pdb=" N MET C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 242 through 287 removed outlier: 4.097A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 387 removed outlier: 3.978A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL C 385 " --> pdb=" O ARG C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 421 through 444 removed outlier: 4.126A pdb=" N GLN C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE C 442 " --> pdb=" O VAL C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.594A pdb=" N LEU D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 123 Processing helix chain 'D' and resid 128 through 164 removed outlier: 4.364A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 177 through 214 removed outlier: 3.590A pdb=" N MET D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 242 through 287 removed outlier: 4.097A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 341 removed outlier: 3.559A pdb=" N PHE D 298 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N SER D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 387 removed outlier: 3.978A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 421 through 444 removed outlier: 4.127A pdb=" N GLN D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE D 442 " --> pdb=" O VAL D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 447 No H-bonds generated for 'chain 'D' and resid 445 through 447' 964 hydrogen bonds defined for protein. 2880 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: 3.48 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3912 1.34 - 1.46: 3209 1.46 - 1.58: 5935 1.58 - 1.70: 0 1.70 - 1.81: 148 Bond restraints: 13204 Sorted by residual: bond pdb=" CA TYR B 234 " pdb=" CB TYR B 234 " ideal model delta sigma weight residual 1.530 1.548 -0.017 1.69e-02 3.50e+03 1.07e+00 bond pdb=" CA TYR A 234 " pdb=" CB TYR A 234 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.89e-01 bond pdb=" CA TYR C 234 " pdb=" CB TYR C 234 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.83e-01 bond pdb=" CA TYR D 234 " pdb=" CB TYR D 234 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.69e-02 3.50e+03 9.27e-01 bond pdb=" CA VAL D 410 " pdb=" CB VAL D 410 " ideal model delta sigma weight residual 1.531 1.541 -0.010 1.11e-02 8.12e+03 7.82e-01 ... (remaining 13199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 17553 1.60 - 3.20: 274 3.20 - 4.80: 54 4.80 - 6.40: 11 6.40 - 8.00: 16 Bond angle restraints: 17908 Sorted by residual: angle pdb=" C ASP B 233 " pdb=" N TYR B 234 " pdb=" CA TYR B 234 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C ASP D 233 " pdb=" N TYR D 234 " pdb=" CA TYR D 234 " ideal model delta sigma weight residual 121.54 128.00 -6.46 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C ASP C 233 " pdb=" N TYR C 234 " pdb=" CA TYR C 234 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C ASP A 233 " pdb=" N TYR A 234 " pdb=" CA TYR A 234 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.12e+01 angle pdb=" N TRP B 152 " pdb=" CA TRP B 152 " pdb=" C TRP B 152 " ideal model delta sigma weight residual 109.81 115.22 -5.41 2.21e+00 2.05e-01 6.00e+00 ... (remaining 17903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 6581 16.88 - 33.76: 895 33.76 - 50.63: 284 50.63 - 67.51: 48 67.51 - 84.39: 16 Dihedral angle restraints: 7824 sinusoidal: 3156 harmonic: 4668 Sorted by residual: dihedral pdb=" CG ARG A 364 " pdb=" CD ARG A 364 " pdb=" NE ARG A 364 " pdb=" CZ ARG A 364 " ideal model delta sinusoidal sigma weight residual -180.00 -137.14 -42.86 2 1.50e+01 4.44e-03 9.87e+00 dihedral pdb=" CG ARG D 364 " pdb=" CD ARG D 364 " pdb=" NE ARG D 364 " pdb=" CZ ARG D 364 " ideal model delta sinusoidal sigma weight residual -180.00 -137.15 -42.85 2 1.50e+01 4.44e-03 9.87e+00 dihedral pdb=" CG ARG B 364 " pdb=" CD ARG B 364 " pdb=" NE ARG B 364 " pdb=" CZ ARG B 364 " ideal model delta sinusoidal sigma weight residual -180.00 -137.15 -42.85 2 1.50e+01 4.44e-03 9.87e+00 ... (remaining 7821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1288 0.028 - 0.056: 501 0.056 - 0.084: 195 0.084 - 0.113: 68 0.113 - 0.141: 16 Chirality restraints: 2068 Sorted by residual: chirality pdb=" CA TYR A 234 " pdb=" N TYR A 234 " pdb=" C TYR A 234 " pdb=" CB TYR A 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA TYR D 234 " pdb=" N TYR D 234 " pdb=" C TYR D 234 " pdb=" CB TYR D 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA TYR C 234 " pdb=" N TYR C 234 " pdb=" C TYR C 234 " pdb=" CB TYR C 234 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2065 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 152 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO D 153 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 153 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 152 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO A 153 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 152 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO B 153 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 153 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 153 " -0.030 5.00e-02 4.00e+02 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2976 2.78 - 3.31: 12547 3.31 - 3.84: 22524 3.84 - 4.37: 25245 4.37 - 4.90: 43694 Nonbonded interactions: 106986 Sorted by model distance: nonbonded pdb=" OD2 ASP A 316 " pdb=" OG SER A 413 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP D 316 " pdb=" OG SER D 413 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP C 316 " pdb=" OG SER C 413 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP B 316 " pdb=" OG SER B 413 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASN B 225 " pdb=" OH TYR B 241 " model vdw 2.317 3.040 ... (remaining 106981 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.100 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.002 0.027 13204 Z= 0.123 Angle : 0.553 8.005 17908 Z= 0.292 Chirality : 0.037 0.141 2068 Planarity : 0.004 0.054 2184 Dihedral : 17.024 84.391 4800 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.31 % Favored : 97.44 % Rotamer: Outliers : 0.28 % Allowed : 22.82 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.20), residues: 1560 helix: 2.41 (0.14), residues: 1168 sheet: None (None), residues: 0 loop : -1.18 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 394 HIS 0.001 0.000 HIS B 290 PHE 0.020 0.001 PHE D 354 TYR 0.013 0.001 TYR B 227 ARG 0.003 0.000 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.07913 ( 964) hydrogen bonds : angle 4.10668 ( 2880) covalent geometry : bond 0.00231 (13204) covalent geometry : angle 0.55307 (17908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 394 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 394 average time/residue: 0.7780 time to fit residues: 347.4889 Evaluate side-chains 260 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 231 ASN B 71 GLN B 231 ASN C 71 GLN C 231 ASN D 71 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.082596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064910 restraints weight = 31741.283| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.72 r_work: 0.2892 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13204 Z= 0.163 Angle : 0.631 9.512 17908 Z= 0.317 Chirality : 0.041 0.142 2068 Planarity : 0.005 0.052 2184 Dihedral : 3.611 11.841 1754 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.92 % Favored : 97.82 % Rotamer: Outliers : 4.08 % Allowed : 24.93 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.20), residues: 1560 helix: 2.29 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.91 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 347 HIS 0.005 0.001 HIS D 118 PHE 0.024 0.001 PHE D 224 TYR 0.015 0.002 TYR B 262 ARG 0.007 0.000 ARG C 392 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 964) hydrogen bonds : angle 3.97976 ( 2880) covalent geometry : bond 0.00355 (13204) covalent geometry : angle 0.63110 (17908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 LEU cc_start: 0.9424 (tp) cc_final: 0.9201 (tm) REVERT: A 196 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8938 (tp30) REVERT: B 106 ILE cc_start: 0.9603 (OUTLIER) cc_final: 0.9372 (mp) REVERT: B 109 SER cc_start: 0.9124 (p) cc_final: 0.8782 (p) REVERT: C 71 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8637 (tp40) REVERT: C 253 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8448 (t0) outliers start: 58 outliers final: 18 residues processed: 312 average time/residue: 0.7411 time to fit residues: 265.7350 Evaluate side-chains 271 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 71 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 253 ASN Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 123 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN B 253 ASN C 71 GLN D 71 GLN D 253 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.079713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.061964 restraints weight = 32425.805| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.72 r_work: 0.2825 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 13204 Z= 0.236 Angle : 0.658 11.416 17908 Z= 0.333 Chirality : 0.042 0.204 2068 Planarity : 0.005 0.060 2184 Dihedral : 3.637 17.199 1752 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.99 % Favored : 97.76 % Rotamer: Outliers : 4.51 % Allowed : 24.15 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.20), residues: 1560 helix: 2.40 (0.14), residues: 1180 sheet: None (None), residues: 0 loop : -0.88 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 347 HIS 0.004 0.001 HIS D 118 PHE 0.019 0.002 PHE A 224 TYR 0.016 0.002 TYR D 208 ARG 0.004 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 964) hydrogen bonds : angle 4.04994 ( 2880) covalent geometry : bond 0.00527 (13204) covalent geometry : angle 0.65796 (17908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 254 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.9605 (mp) cc_final: 0.9371 (mp) REVERT: A 184 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9317 (mm) REVERT: A 313 GLU cc_start: 0.9101 (tp30) cc_final: 0.8776 (tp30) REVERT: A 428 MET cc_start: 0.9593 (ttt) cc_final: 0.9211 (ttt) REVERT: B 71 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8693 (tp40) REVERT: B 231 ASN cc_start: 0.8533 (t0) cc_final: 0.8256 (t0) REVERT: C 106 ILE cc_start: 0.9670 (mp) cc_final: 0.9467 (mp) REVERT: C 231 ASN cc_start: 0.8512 (t0) cc_final: 0.8288 (t0) REVERT: D 106 ILE cc_start: 0.9702 (mp) cc_final: 0.9502 (mp) REVERT: D 232 TYR cc_start: 0.8365 (m-80) cc_final: 0.8145 (m-80) REVERT: D 440 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9080 (mm) REVERT: D 441 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8841 (mm-40) REVERT: D 442 PHE cc_start: 0.8153 (m-80) cc_final: 0.7641 (m-80) outliers start: 64 outliers final: 19 residues processed: 301 average time/residue: 0.6917 time to fit residues: 240.6221 Evaluate side-chains 251 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 71 GLN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 253 ASN Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN C 71 GLN D 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.063117 restraints weight = 31202.531| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.74 r_work: 0.2852 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13204 Z= 0.129 Angle : 0.600 11.491 17908 Z= 0.299 Chirality : 0.040 0.274 2068 Planarity : 0.004 0.042 2184 Dihedral : 3.570 12.561 1752 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.86 % Favored : 97.88 % Rotamer: Outliers : 3.73 % Allowed : 23.80 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.20), residues: 1560 helix: 2.45 (0.14), residues: 1180 sheet: None (None), residues: 0 loop : -0.91 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 347 HIS 0.003 0.001 HIS A 118 PHE 0.014 0.001 PHE D 64 TYR 0.017 0.002 TYR D 234 ARG 0.004 0.000 ARG D 423 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 964) hydrogen bonds : angle 3.91236 ( 2880) covalent geometry : bond 0.00273 (13204) covalent geometry : angle 0.59963 (17908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9323 (mm) REVERT: B 231 ASN cc_start: 0.8583 (t0) cc_final: 0.8373 (t0) REVERT: D 432 ILE cc_start: 0.9591 (mt) cc_final: 0.9318 (mp) REVERT: D 440 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9081 (mm) REVERT: D 441 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8841 (mm-40) outliers start: 53 outliers final: 19 residues processed: 279 average time/residue: 0.7595 time to fit residues: 242.2033 Evaluate side-chains 244 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 53 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 33 optimal weight: 0.1980 chunk 62 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 253 ASN B 71 GLN C 71 GLN C 253 ASN D 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.079554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.061654 restraints weight = 31764.750| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.74 r_work: 0.2815 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13204 Z= 0.177 Angle : 0.622 12.351 17908 Z= 0.310 Chirality : 0.042 0.265 2068 Planarity : 0.004 0.042 2184 Dihedral : 3.534 13.220 1752 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.92 % Favored : 97.82 % Rotamer: Outliers : 4.08 % Allowed : 23.94 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.21), residues: 1560 helix: 2.62 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.88 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 355 HIS 0.004 0.001 HIS A 118 PHE 0.016 0.001 PHE B 224 TYR 0.021 0.002 TYR D 208 ARG 0.005 0.000 ARG D 381 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 964) hydrogen bonds : angle 3.88787 ( 2880) covalent geometry : bond 0.00393 (13204) covalent geometry : angle 0.62150 (17908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 237 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.9689 (tm) cc_final: 0.9469 (tm) REVERT: A 231 ASN cc_start: 0.8700 (t0) cc_final: 0.8406 (t0) REVERT: A 342 PHE cc_start: 0.9183 (m-80) cc_final: 0.8955 (m-80) REVERT: B 231 ASN cc_start: 0.8715 (t0) cc_final: 0.8446 (t0) REVERT: B 428 MET cc_start: 0.9657 (ttt) cc_final: 0.9289 (ttt) REVERT: C 115 MET cc_start: 0.9557 (tpt) cc_final: 0.9284 (tpp) REVERT: C 442 PHE cc_start: 0.8408 (m-80) cc_final: 0.7748 (m-80) REVERT: D 76 MET cc_start: 0.8706 (mtp) cc_final: 0.8457 (ttt) REVERT: D 428 MET cc_start: 0.9651 (ttt) cc_final: 0.9268 (ttt) REVERT: D 440 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9156 (mm) REVERT: D 441 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8771 (mm-40) outliers start: 58 outliers final: 23 residues processed: 275 average time/residue: 0.8875 time to fit residues: 281.0406 Evaluate side-chains 244 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 140 optimal weight: 0.0270 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 253 ASN B 71 GLN C 71 GLN C 253 ASN D 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.080829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.063150 restraints weight = 32543.330| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.81 r_work: 0.2839 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13204 Z= 0.124 Angle : 0.644 13.403 17908 Z= 0.309 Chirality : 0.041 0.322 2068 Planarity : 0.004 0.039 2184 Dihedral : 3.516 12.782 1752 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.31 % Favored : 97.44 % Rotamer: Outliers : 3.94 % Allowed : 25.07 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.21), residues: 1560 helix: 2.61 (0.14), residues: 1176 sheet: None (None), residues: 0 loop : -0.83 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 355 HIS 0.004 0.001 HIS A 118 PHE 0.014 0.001 PHE D 64 TYR 0.018 0.001 TYR D 227 ARG 0.008 0.000 ARG C 423 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 964) hydrogen bonds : angle 3.81556 ( 2880) covalent geometry : bond 0.00256 (13204) covalent geometry : angle 0.64363 (17908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ILE cc_start: 0.9546 (mp) cc_final: 0.9337 (mp) REVERT: A 231 ASN cc_start: 0.8807 (t0) cc_final: 0.8546 (t0) REVERT: A 428 MET cc_start: 0.9648 (ttt) cc_final: 0.9238 (ttt) REVERT: B 184 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9303 (mm) REVERT: B 231 ASN cc_start: 0.8802 (t0) cc_final: 0.8461 (t0) REVERT: B 428 MET cc_start: 0.9664 (ttt) cc_final: 0.9299 (ttt) REVERT: D 76 MET cc_start: 0.8652 (mtp) cc_final: 0.8402 (ttt) REVERT: D 428 MET cc_start: 0.9666 (ttt) cc_final: 0.9220 (ttt) REVERT: D 432 ILE cc_start: 0.9634 (mt) cc_final: 0.9395 (mp) REVERT: D 440 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9101 (mm) REVERT: D 441 GLN cc_start: 0.8962 (mm-40) cc_final: 0.8596 (mm-40) outliers start: 56 outliers final: 24 residues processed: 277 average time/residue: 0.9399 time to fit residues: 297.2964 Evaluate side-chains 251 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 367 PHE Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 146 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN C 71 GLN ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.079693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.062204 restraints weight = 32736.177| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.75 r_work: 0.2838 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13204 Z= 0.171 Angle : 0.668 13.616 17908 Z= 0.322 Chirality : 0.042 0.344 2068 Planarity : 0.004 0.040 2184 Dihedral : 3.505 12.950 1752 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.24 % Favored : 97.50 % Rotamer: Outliers : 4.30 % Allowed : 25.00 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.20), residues: 1560 helix: 2.62 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.78 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 355 HIS 0.003 0.001 HIS A 118 PHE 0.016 0.001 PHE D 64 TYR 0.020 0.001 TYR D 227 ARG 0.003 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 964) hydrogen bonds : angle 3.83796 ( 2880) covalent geometry : bond 0.00387 (13204) covalent geometry : angle 0.66821 (17908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 228 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.9654 (tm) cc_final: 0.9425 (tm) REVERT: A 231 ASN cc_start: 0.8926 (t0) cc_final: 0.8584 (t0) REVERT: A 252 ILE cc_start: 0.8848 (tt) cc_final: 0.8587 (tp) REVERT: A 342 PHE cc_start: 0.9178 (m-80) cc_final: 0.8907 (m-80) REVERT: A 428 MET cc_start: 0.9673 (ttt) cc_final: 0.9295 (ttt) REVERT: B 184 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9294 (mm) REVERT: B 231 ASN cc_start: 0.8857 (t0) cc_final: 0.8509 (t0) REVERT: B 428 MET cc_start: 0.9696 (ttt) cc_final: 0.9354 (ttt) REVERT: D 76 MET cc_start: 0.8752 (mtp) cc_final: 0.8498 (ttt) REVERT: D 428 MET cc_start: 0.9679 (ttt) cc_final: 0.9253 (ttt) REVERT: D 432 ILE cc_start: 0.9617 (mt) cc_final: 0.9352 (mp) REVERT: D 440 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9150 (mm) REVERT: D 441 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8560 (mm-40) outliers start: 61 outliers final: 27 residues processed: 270 average time/residue: 0.8726 time to fit residues: 270.4211 Evaluate side-chains 249 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 150 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 253 ASN B 71 GLN C 71 GLN D 71 GLN D 231 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.079579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.062550 restraints weight = 33108.222| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.72 r_work: 0.2850 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13204 Z= 0.145 Angle : 0.670 14.204 17908 Z= 0.322 Chirality : 0.042 0.345 2068 Planarity : 0.004 0.041 2184 Dihedral : 3.520 13.118 1752 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.44 % Favored : 97.31 % Rotamer: Outliers : 3.31 % Allowed : 26.55 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.20), residues: 1560 helix: 2.64 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.82 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 347 HIS 0.006 0.001 HIS A 118 PHE 0.015 0.001 PHE D 64 TYR 0.021 0.001 TYR D 227 ARG 0.007 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 964) hydrogen bonds : angle 3.82944 ( 2880) covalent geometry : bond 0.00320 (13204) covalent geometry : angle 0.66952 (17908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.9002 (t0) cc_final: 0.8665 (t0) REVERT: A 252 ILE cc_start: 0.8878 (tt) cc_final: 0.8614 (tp) REVERT: A 428 MET cc_start: 0.9656 (ttt) cc_final: 0.9286 (ttt) REVERT: B 184 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9289 (mm) REVERT: B 231 ASN cc_start: 0.8902 (t0) cc_final: 0.8533 (t0) REVERT: B 428 MET cc_start: 0.9670 (ttt) cc_final: 0.9356 (ttt) REVERT: D 76 MET cc_start: 0.8777 (mtp) cc_final: 0.8561 (ttt) REVERT: D 428 MET cc_start: 0.9653 (ttt) cc_final: 0.9335 (ttt) REVERT: D 440 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9139 (mm) REVERT: D 441 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8478 (mm-40) outliers start: 47 outliers final: 22 residues processed: 263 average time/residue: 0.7698 time to fit residues: 230.9125 Evaluate side-chains 241 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 105 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 114 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN B 71 GLN C 71 GLN D 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.079345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.062284 restraints weight = 32819.471| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.73 r_work: 0.2844 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13204 Z= 0.149 Angle : 0.703 14.988 17908 Z= 0.338 Chirality : 0.043 0.370 2068 Planarity : 0.004 0.041 2184 Dihedral : 3.555 13.439 1752 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.37 % Favored : 97.37 % Rotamer: Outliers : 3.10 % Allowed : 26.97 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.20), residues: 1560 helix: 2.61 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.83 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 347 HIS 0.002 0.001 HIS A 118 PHE 0.015 0.001 PHE D 64 TYR 0.022 0.001 TYR C 227 ARG 0.006 0.000 ARG A 392 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 964) hydrogen bonds : angle 3.86398 ( 2880) covalent geometry : bond 0.00329 (13204) covalent geometry : angle 0.70347 (17908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ASN cc_start: 0.9021 (t0) cc_final: 0.8753 (t0) REVERT: A 252 ILE cc_start: 0.8859 (tt) cc_final: 0.8574 (tp) REVERT: A 428 MET cc_start: 0.9667 (ttt) cc_final: 0.9312 (ttt) REVERT: B 184 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9280 (mm) REVERT: B 231 ASN cc_start: 0.8944 (t0) cc_final: 0.8572 (t0) REVERT: B 428 MET cc_start: 0.9671 (ttt) cc_final: 0.9367 (ttt) REVERT: D 428 MET cc_start: 0.9644 (ttt) cc_final: 0.9343 (ttt) REVERT: D 440 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9135 (mm) REVERT: D 441 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8489 (mm-40) outliers start: 44 outliers final: 20 residues processed: 258 average time/residue: 0.7771 time to fit residues: 228.5048 Evaluate side-chains 238 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 142 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 231 ASN A 253 ASN B 71 GLN C 71 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 GLN D 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062486 restraints weight = 33134.967| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.73 r_work: 0.2848 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13204 Z= 0.143 Angle : 0.727 15.560 17908 Z= 0.345 Chirality : 0.043 0.392 2068 Planarity : 0.004 0.041 2184 Dihedral : 3.584 13.190 1752 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.24 % Favored : 97.50 % Rotamer: Outliers : 2.96 % Allowed : 27.39 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.20), residues: 1560 helix: 2.56 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.83 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 152 HIS 0.002 0.001 HIS B 290 PHE 0.015 0.001 PHE D 64 TYR 0.026 0.002 TYR D 227 ARG 0.002 0.000 ARG D 381 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 964) hydrogen bonds : angle 3.89562 ( 2880) covalent geometry : bond 0.00316 (13204) covalent geometry : angle 0.72704 (17908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3120 Ramachandran restraints generated. 1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 MET cc_start: 0.9540 (tpt) cc_final: 0.9276 (tpp) REVERT: A 231 ASN cc_start: 0.9045 (t0) cc_final: 0.8760 (t0) REVERT: A 252 ILE cc_start: 0.8868 (tt) cc_final: 0.8590 (tp) REVERT: A 428 MET cc_start: 0.9658 (ttt) cc_final: 0.9342 (ttt) REVERT: B 184 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9286 (mm) REVERT: B 231 ASN cc_start: 0.8950 (t0) cc_final: 0.8576 (t0) REVERT: B 428 MET cc_start: 0.9677 (ttt) cc_final: 0.9383 (ttt) REVERT: C 442 PHE cc_start: 0.8470 (m-10) cc_final: 0.8010 (m-10) REVERT: D 428 MET cc_start: 0.9637 (ttt) cc_final: 0.9345 (ttt) REVERT: D 440 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9174 (mm) outliers start: 42 outliers final: 21 residues processed: 248 average time/residue: 0.8239 time to fit residues: 232.4009 Evaluate side-chains 236 residues out of total 1420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 431 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 398 VAL Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 153 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN A 253 ASN B 71 GLN C 71 GLN C 253 ASN D 71 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.079628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.062461 restraints weight = 32881.947| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.74 r_work: 0.2846 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.132 13204 Z= 0.196 Angle : 0.947 59.197 17908 Z= 0.523 Chirality : 0.044 0.386 2068 Planarity : 0.004 0.040 2184 Dihedral : 3.576 13.060 1752 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.18 % Favored : 97.56 % Rotamer: Outliers : 2.39 % Allowed : 28.38 % Favored : 69.23 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.20), residues: 1560 helix: 2.54 (0.14), residues: 1172 sheet: None (None), residues: 0 loop : -0.83 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 152 HIS 0.002 0.001 HIS B 290 PHE 0.015 0.001 PHE D 64 TYR 0.019 0.001 TYR C 227 ARG 0.003 0.000 ARG C 392 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 964) hydrogen bonds : angle 3.90845 ( 2880) covalent geometry : bond 0.00407 (13204) covalent geometry : angle 0.94656 (17908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10453.06 seconds wall clock time: 184 minutes 21.82 seconds (11061.82 seconds total)