Starting phenix.real_space_refine on Wed Mar 5 17:53:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wro_32734/03_2025/7wro_32734.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wro_32734/03_2025/7wro_32734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wro_32734/03_2025/7wro_32734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wro_32734/03_2025/7wro_32734.map" model { file = "/net/cci-nas-00/data/ceres_data/7wro_32734/03_2025/7wro_32734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wro_32734/03_2025/7wro_32734.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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 14 5.16 5 C 2004 2.51 5 N 541 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3179 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 916 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 796 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "R" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1467 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Time building chain proxies: 3.63, per 1000 atoms: 1.14 Number of scatterers: 3179 At special positions: 0 Unit cell: (68.48, 82.39, 84.53, 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 14 16.00 O 620 8.00 N 541 7.00 C 2004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 109 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.05 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 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: 0.68 Conformation dependent library (CDL) restraints added in 366.7 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'H' and resid 81 through 84 removed outlier: 3.613A pdb=" N LYS H 84 " --> pdb=" O ASP H 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 84' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.894A pdb=" N ASP H 109 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR H 110 " --> pdb=" O ASP H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 110' Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 383 through 390 removed outlier: 3.622A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 408 removed outlier: 4.009A pdb=" N VAL R 407 " --> pdb=" O GLY R 404 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 404 through 408' Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.878A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.680A pdb=" N SER H 97 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 77 through 79 removed outlier: 5.446A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 36 through 37 Processing sheet with id=AA4, first strand: chain 'L' and resid 66 through 67 removed outlier: 3.703A pdb=" N ALA L 105 " --> pdb=" O LEU L 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 86 through 88 removed outlier: 3.971A pdb=" N SER L 86 " --> pdb=" O SER L 93 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER L 93 " --> pdb=" O SER L 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 110 through 113 Processing sheet with id=AA7, first strand: chain 'R' and resid 396 through 402 removed outlier: 3.755A pdb=" N SER R 514 " --> pdb=" O TYR R 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'R' and resid 473 through 474 73 hydrogen bonds defined for protein. 168 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: 0.76 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1037 1.34 - 1.47: 904 1.47 - 1.60: 1298 1.60 - 1.73: 0 1.73 - 1.86: 17 Bond restraints: 3256 Sorted by residual: bond pdb=" C TYR R 505 " pdb=" N GLN R 506 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.15e+00 bond pdb=" CG1 ILE R 402 " pdb=" CD1 ILE R 402 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.37e+00 bond pdb=" CA ARG R 509 " pdb=" CB ARG R 509 " ideal model delta sigma weight residual 1.527 1.502 0.026 1.30e-02 5.92e+03 3.87e+00 bond pdb=" CB TRP L 56 " pdb=" CG TRP L 56 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.10e+00 bond pdb=" N THR H 124 " pdb=" CA THR H 124 " ideal model delta sigma weight residual 1.454 1.429 0.025 1.42e-02 4.96e+03 3.02e+00 ... (remaining 3251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 4271 2.65 - 5.31: 124 5.31 - 7.96: 16 7.96 - 10.61: 5 10.61 - 13.26: 4 Bond angle restraints: 4420 Sorted by residual: angle pdb=" CB LYS H 32 " pdb=" CG LYS H 32 " pdb=" CD LYS H 32 " ideal model delta sigma weight residual 111.30 123.47 -12.17 2.30e+00 1.89e-01 2.80e+01 angle pdb=" CA CYS R 379 " pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " ideal model delta sigma weight residual 114.40 125.41 -11.01 2.30e+00 1.89e-01 2.29e+01 angle pdb=" N SER L 70 " pdb=" CA SER L 70 " pdb=" C SER L 70 " ideal model delta sigma weight residual 110.80 101.57 9.23 2.13e+00 2.20e-01 1.88e+01 angle pdb=" C LEU L 69 " pdb=" N SER L 70 " pdb=" CA SER L 70 " ideal model delta sigma weight residual 121.54 129.28 -7.74 1.91e+00 2.74e-01 1.64e+01 angle pdb=" CA LEU R 368 " pdb=" CB LEU R 368 " pdb=" CG LEU R 368 " ideal model delta sigma weight residual 116.30 129.56 -13.26 3.50e+00 8.16e-02 1.44e+01 ... (remaining 4415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 1660 15.04 - 30.09: 192 30.09 - 45.13: 51 45.13 - 60.18: 8 60.18 - 75.22: 4 Dihedral angle restraints: 1915 sinusoidal: 736 harmonic: 1179 Sorted by residual: dihedral pdb=" CB CYS R 336 " pdb=" SG CYS R 336 " pdb=" SG CYS R 361 " pdb=" CB CYS R 361 " ideal model delta sinusoidal sigma weight residual 93.00 25.32 67.68 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" CA GLY L 71 " pdb=" C GLY L 71 " pdb=" N ASN L 72 " pdb=" CA ASN L 72 " ideal model delta harmonic sigma weight residual 180.00 -148.67 -31.33 0 5.00e+00 4.00e-02 3.93e+01 dihedral pdb=" CB CYS R 480 " pdb=" SG CYS R 480 " pdb=" SG CYS R 488 " pdb=" CB CYS R 488 " ideal model delta sinusoidal sigma weight residual -86.00 -132.02 46.02 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 1912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 449 0.126 - 0.252: 20 0.252 - 0.378: 0 0.378 - 0.504: 0 0.504 - 0.630: 1 Chirality restraints: 470 Sorted by residual: chirality pdb=" CB ILE R 468 " pdb=" CA ILE R 468 " pdb=" CG1 ILE R 468 " pdb=" CG2 ILE R 468 " both_signs ideal model delta sigma weight residual False 2.64 2.01 0.63 2.00e-01 2.50e+01 9.92e+00 chirality pdb=" CB VAL R 407 " pdb=" CA VAL R 407 " pdb=" CG1 VAL R 407 " pdb=" CG2 VAL R 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB ILE R 402 " pdb=" CA ILE R 402 " pdb=" CG1 ILE R 402 " pdb=" CG2 ILE R 402 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 467 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 79 " -0.052 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO L 80 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 462 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO R 463 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO R 463 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 463 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 94 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C LEU L 94 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU L 94 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA L 95 " 0.016 2.00e-02 2.50e+03 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1066 2.83 - 3.35: 2712 3.35 - 3.86: 5241 3.86 - 4.38: 6124 4.38 - 4.90: 10698 Nonbonded interactions: 25841 Sorted by model distance: nonbonded pdb=" OG SER L 46 " pdb=" OD1 ASP L 113 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR L 24 " pdb=" O VAL L 42 " model vdw 2.323 3.040 nonbonded pdb=" O PHE H 48 " pdb=" NH2 ARG H 91 " model vdw 2.328 3.120 nonbonded pdb=" OD2 ASP R 398 " pdb=" OH TYR R 423 " model vdw 2.330 3.040 nonbonded pdb=" OD1 ASP L 103 " pdb=" OH TYR L 107 " model vdw 2.342 3.040 ... (remaining 25836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.500 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 : 0.008 0.082 3256 Z= 0.513 Angle : 1.108 13.264 4420 Z= 0.599 Chirality : 0.067 0.630 470 Planarity : 0.008 0.079 579 Dihedral : 13.649 75.223 1156 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -1.94 (0.42), residues: 406 helix: -4.41 (0.54), residues: 32 sheet: -1.98 (0.45), residues: 113 loop : -0.45 (0.41), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 56 HIS 0.001 0.000 HIS H 22 PHE 0.021 0.004 PHE H 87 TYR 0.018 0.002 TYR R 380 ARG 0.018 0.002 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.6641 (tpp) cc_final: 0.6024 (tpp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1451 time to fit residues: 15.4706 Evaluate side-chains 74 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.163613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139661 restraints weight = 4353.350| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.38 r_work: 0.3566 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3256 Z= 0.292 Angle : 0.703 8.939 4420 Z= 0.364 Chirality : 0.047 0.138 470 Planarity : 0.006 0.064 579 Dihedral : 5.834 25.273 456 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.87 % Allowed : 13.29 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.44), residues: 406 helix: -4.36 (0.51), residues: 32 sheet: -1.54 (0.44), residues: 131 loop : -0.29 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 56 HIS 0.002 0.001 HIS L 55 PHE 0.021 0.002 PHE R 486 TYR 0.013 0.001 TYR R 380 ARG 0.005 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.374 Fit side-chains REVERT: R 417 LYS cc_start: 0.7960 (tppt) cc_final: 0.7170 (ttpt) REVERT: R 443 SER cc_start: 0.7859 (t) cc_final: 0.7512 (p) outliers start: 3 outliers final: 3 residues processed: 80 average time/residue: 0.1533 time to fit residues: 14.9556 Evaluate side-chains 76 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 135 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.164888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141234 restraints weight = 4228.328| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.34 r_work: 0.3551 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3256 Z= 0.223 Angle : 0.650 11.098 4420 Z= 0.329 Chirality : 0.045 0.140 470 Planarity : 0.005 0.062 579 Dihedral : 5.323 24.819 456 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.02 % Allowed : 16.76 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.43), residues: 406 helix: -4.12 (0.57), residues: 32 sheet: -1.69 (0.43), residues: 125 loop : -0.14 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 56 HIS 0.001 0.001 HIS L 55 PHE 0.013 0.001 PHE H 87 TYR 0.015 0.001 TYR R 421 ARG 0.005 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.356 Fit side-chains REVERT: H 32 LYS cc_start: 0.7236 (mmmt) cc_final: 0.7002 (mmmt) REVERT: H 57 ARG cc_start: 0.7832 (ptt90) cc_final: 0.7586 (ptt90) REVERT: R 417 LYS cc_start: 0.7987 (tppt) cc_final: 0.7088 (ttmt) REVERT: R 434 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7756 (pt) REVERT: R 443 SER cc_start: 0.7795 (t) cc_final: 0.7386 (p) outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 0.1667 time to fit residues: 16.9835 Evaluate side-chains 74 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain R residue 434 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.160593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135914 restraints weight = 4301.240| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.40 r_work: 0.3497 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3256 Z= 0.361 Angle : 0.668 7.044 4420 Z= 0.346 Chirality : 0.046 0.140 470 Planarity : 0.005 0.063 579 Dihedral : 5.358 23.765 456 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 4.05 % Allowed : 15.32 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.43), residues: 406 helix: -3.97 (0.63), residues: 32 sheet: -1.94 (0.42), residues: 130 loop : -0.11 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 56 HIS 0.002 0.001 HIS L 55 PHE 0.025 0.002 PHE H 87 TYR 0.018 0.002 TYR R 421 ARG 0.004 0.001 ARG R 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.363 Fit side-chains REVERT: H 102 MET cc_start: 0.7448 (tpp) cc_final: 0.7190 (tpp) REVERT: R 417 LYS cc_start: 0.8157 (tppt) cc_final: 0.7258 (ttmt) REVERT: R 443 SER cc_start: 0.7945 (t) cc_final: 0.7601 (p) outliers start: 14 outliers final: 11 residues processed: 86 average time/residue: 0.1560 time to fit residues: 16.2316 Evaluate side-chains 85 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.164194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140684 restraints weight = 4314.731| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.32 r_work: 0.3561 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3256 Z= 0.239 Angle : 0.606 7.118 4420 Z= 0.313 Chirality : 0.045 0.141 470 Planarity : 0.005 0.057 579 Dihedral : 5.062 22.727 456 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.20 % Allowed : 16.47 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.43), residues: 406 helix: -3.83 (0.68), residues: 32 sheet: -1.87 (0.43), residues: 128 loop : -0.10 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 PHE 0.034 0.002 PHE H 87 TYR 0.014 0.001 TYR R 421 ARG 0.005 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.338 Fit side-chains REVERT: R 417 LYS cc_start: 0.8086 (tppt) cc_final: 0.7234 (ttmt) REVERT: R 442 ASP cc_start: 0.8361 (m-30) cc_final: 0.8115 (m-30) REVERT: R 443 SER cc_start: 0.7910 (t) cc_final: 0.7487 (p) outliers start: 18 outliers final: 14 residues processed: 91 average time/residue: 0.1479 time to fit residues: 16.3714 Evaluate side-chains 90 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 22 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.0170 chunk 16 optimal weight: 2.9990 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.167799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.143923 restraints weight = 4375.276| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.39 r_work: 0.3603 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3256 Z= 0.148 Angle : 0.606 10.708 4420 Z= 0.308 Chirality : 0.045 0.189 470 Planarity : 0.005 0.056 579 Dihedral : 4.820 22.323 456 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.05 % Allowed : 17.63 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.43), residues: 406 helix: -3.87 (0.67), residues: 32 sheet: -1.38 (0.47), residues: 107 loop : -0.36 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 56 HIS 0.001 0.001 HIS L 55 PHE 0.029 0.001 PHE H 87 TYR 0.012 0.001 TYR R 380 ARG 0.006 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.377 Fit side-chains REVERT: R 417 LYS cc_start: 0.8006 (tppt) cc_final: 0.7153 (ttpt) REVERT: R 443 SER cc_start: 0.7699 (t) cc_final: 0.7200 (p) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.1426 time to fit residues: 15.4977 Evaluate side-chains 91 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.0570 chunk 36 optimal weight: 6.9990 chunk 5 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.165204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141759 restraints weight = 4292.833| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.31 r_work: 0.3573 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3256 Z= 0.245 Angle : 0.633 8.061 4420 Z= 0.322 Chirality : 0.045 0.163 470 Planarity : 0.005 0.054 579 Dihedral : 4.895 22.070 456 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.20 % Allowed : 17.05 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.43), residues: 406 helix: -3.75 (0.72), residues: 32 sheet: -1.67 (0.44), residues: 123 loop : -0.14 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 56 HIS 0.001 0.001 HIS H 22 PHE 0.032 0.002 PHE H 87 TYR 0.014 0.001 TYR R 421 ARG 0.007 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.358 Fit side-chains REVERT: R 417 LYS cc_start: 0.8079 (tppt) cc_final: 0.7296 (ttpt) REVERT: R 434 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7722 (pt) REVERT: R 443 SER cc_start: 0.7790 (t) cc_final: 0.7352 (p) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.1543 time to fit residues: 17.5509 Evaluate side-chains 97 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.0570 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.170030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.147472 restraints weight = 4253.990| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.22 r_work: 0.3635 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3256 Z= 0.168 Angle : 0.604 8.073 4420 Z= 0.309 Chirality : 0.044 0.161 470 Planarity : 0.004 0.055 579 Dihedral : 4.675 22.162 456 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.91 % Allowed : 17.34 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.43), residues: 406 helix: -3.88 (0.65), residues: 32 sheet: -1.34 (0.46), residues: 113 loop : -0.24 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 PHE 0.024 0.001 PHE H 87 TYR 0.011 0.001 TYR R 421 ARG 0.007 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.342 Fit side-chains REVERT: H 81 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7491 (t0) REVERT: R 417 LYS cc_start: 0.8046 (tppt) cc_final: 0.7164 (ttpt) REVERT: R 443 SER cc_start: 0.7677 (t) cc_final: 0.7157 (p) outliers start: 17 outliers final: 14 residues processed: 97 average time/residue: 0.1418 time to fit residues: 16.7563 Evaluate side-chains 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.162706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139532 restraints weight = 4304.513| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.26 r_work: 0.3535 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 : 0.006 0.055 3256 Z= 0.379 Angle : 0.716 8.716 4420 Z= 0.368 Chirality : 0.047 0.185 470 Planarity : 0.005 0.053 579 Dihedral : 5.126 22.112 456 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.62 % Allowed : 19.08 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.43), residues: 406 helix: -3.91 (0.80), residues: 26 sheet: -1.84 (0.43), residues: 127 loop : -0.11 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 56 HIS 0.002 0.001 HIS L 55 PHE 0.036 0.002 PHE H 87 TYR 0.019 0.002 TYR R 421 ARG 0.010 0.001 ARG H 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.371 Fit side-chains REVERT: R 417 LYS cc_start: 0.8174 (tppt) cc_final: 0.7283 (ttmt) REVERT: R 443 SER cc_start: 0.7904 (t) cc_final: 0.7491 (p) outliers start: 16 outliers final: 14 residues processed: 91 average time/residue: 0.1686 time to fit residues: 18.4523 Evaluate side-chains 93 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.0970 chunk 29 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.168025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145447 restraints weight = 4272.378| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.25 r_work: 0.3605 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3256 Z= 0.191 Angle : 0.639 8.233 4420 Z= 0.331 Chirality : 0.046 0.188 470 Planarity : 0.005 0.055 579 Dihedral : 4.854 22.302 456 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.76 % Allowed : 19.65 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.43), residues: 406 helix: -4.06 (0.72), residues: 26 sheet: -1.70 (0.44), residues: 126 loop : -0.07 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 56 HIS 0.000 0.000 HIS L 55 PHE 0.026 0.002 PHE H 87 TYR 0.013 0.001 TYR R 421 ARG 0.009 0.001 ARG H 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.388 Fit side-chains REVERT: H 102 MET cc_start: 0.7447 (tpp) cc_final: 0.7174 (tpt) REVERT: R 417 LYS cc_start: 0.8051 (tppt) cc_final: 0.7145 (ttmt) REVERT: R 434 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7653 (pt) REVERT: R 443 SER cc_start: 0.7673 (t) cc_final: 0.7209 (p) outliers start: 13 outliers final: 12 residues processed: 91 average time/residue: 0.1358 time to fit residues: 15.1640 Evaluate side-chains 95 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain R residue 402 ILE Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.0000 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 15 optimal weight: 0.0070 overall best weight: 0.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.171216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149154 restraints weight = 4272.607| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.22 r_work: 0.3654 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3256 Z= 0.154 Angle : 0.611 8.329 4420 Z= 0.316 Chirality : 0.045 0.167 470 Planarity : 0.005 0.055 579 Dihedral : 4.564 21.902 456 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.76 % Allowed : 20.52 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.43), residues: 406 helix: -4.12 (0.67), residues: 27 sheet: -1.26 (0.47), residues: 114 loop : -0.08 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 56 HIS 0.002 0.001 HIS H 22 PHE 0.022 0.001 PHE H 87 TYR 0.010 0.001 TYR R 421 ARG 0.010 0.001 ARG H 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.51 seconds wall clock time: 35 minutes 0.47 seconds (2100.47 seconds total)