Starting phenix.real_space_refine on Mon Feb 10 22:48:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wro_32734/02_2025/7wro_32734.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wro_32734/02_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_32734/02_2025/7wro_32734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wro_32734/02_2025/7wro_32734.map" model { file = "/net/cci-nas-00/data/ceres_data/7wro_32734/02_2025/7wro_32734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wro_32734/02_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-5592/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: 3.91, per 1000 atoms: 1.23 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: 0.70 Conformation dependent library (CDL) restraints added in 385.6 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: 0.41 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: 0.80 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: 2.720 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.800 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.700 ------------------------------------------------------------------------------- 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 : 0.377 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: 0.1500 time to fit residues: 15.8929 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 : 0.368 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.163551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.139630 restraints weight = 4351.094| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.39 r_work: 0.3561 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 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 8.945 4420 Z= 0.364 Chirality : 0.047 0.138 470 Planarity : 0.006 0.064 579 Dihedral : 5.834 25.279 456 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 : 0.340 Fit side-chains REVERT: R 417 LYS cc_start: 0.7958 (tppt) cc_final: 0.7172 (ttpt) REVERT: R 443 SER cc_start: 0.7852 (t) cc_final: 0.7506 (p) outliers start: 3 outliers final: 3 residues processed: 80 average time/residue: 0.1515 time to fit residues: 14.7477 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 : 0.375 ------------------------------------------------------------------------------- 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: 0.3980 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3971 r_free = 0.3971 target = 0.164097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.140161 restraints weight = 4236.237| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.36 r_work: 0.3537 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1624 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 : 0.662 11.379 4420 Z= 0.335 Chirality : 0.045 0.140 470 Planarity : 0.005 0.062 579 Dihedral : 5.363 24.859 456 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.31 % Allowed : 16.47 % 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: -1.63 (0.43), residues: 406 helix: -4.10 (0.58), residues: 32 sheet: -1.77 (0.43), residues: 126 loop : -0.12 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 56 HIS 0.002 0.001 HIS L 55 PHE 0.016 0.001 PHE H 87 TYR 0.016 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: 8 poor density : 78 time to evaluate : 0.341 Fit side-chains REVERT: H 57 ARG cc_start: 0.7854 (ptt90) cc_final: 0.7604 (ptt90) REVERT: R 417 LYS cc_start: 0.8005 (tppt) cc_final: 0.7134 (ttpt) REVERT: R 434 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7759 (pt) REVERT: R 442 ASP cc_start: 0.8287 (m-30) cc_final: 0.8082 (m-30) REVERT: R 443 SER cc_start: 0.7777 (t) cc_final: 0.7466 (p) outliers start: 8 outliers final: 5 residues processed: 83 average time/residue: 0.1555 time to fit residues: 15.6033 Evaluate side-chains 76 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 385 THR 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: 0.5980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 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 = 0.3956 r_free = 0.3956 target = 0.162772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138655 restraints weight = 4277.592| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.36 r_work: 0.3525 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3256 Z= 0.278 Angle : 0.634 7.047 4420 Z= 0.327 Chirality : 0.045 0.169 470 Planarity : 0.005 0.061 579 Dihedral : 5.180 22.570 456 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.62 % Allowed : 15.32 % Favored : 80.06 % 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 (0.43), residues: 406 helix: -3.96 (0.63), residues: 32 sheet: -1.83 (0.43), residues: 124 loop : -0.21 (0.43), residues: 250 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 0.042 0.002 PHE H 87 TYR 0.015 0.001 TYR R 421 ARG 0.004 0.001 ARG H 57 *********************** 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 93 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.363 Fit side-chains REVERT: R 417 LYS cc_start: 0.8053 (tppt) cc_final: 0.7215 (ttpt) REVERT: R 443 SER cc_start: 0.7850 (t) cc_final: 0.7508 (p) outliers start: 16 outliers final: 13 residues processed: 85 average time/residue: 0.1633 time to fit residues: 16.7556 Evaluate side-chains 87 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 chunk 29 optimal weight: 0.2980 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.166606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142515 restraints weight = 4257.388| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.37 r_work: 0.3567 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3256 Z= 0.175 Angle : 0.610 7.494 4420 Z= 0.312 Chirality : 0.044 0.160 470 Planarity : 0.005 0.061 579 Dihedral : 4.853 22.691 456 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.47 % Allowed : 17.05 % Favored : 79.48 % 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: -1.58 (0.43), residues: 406 helix: -3.95 (0.64), residues: 32 sheet: -1.68 (0.44), residues: 124 loop : -0.16 (0.43), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 PHE 0.032 0.001 PHE H 87 TYR 0.012 0.001 TYR R 421 ARG 0.006 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 95 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.344 Fit side-chains REVERT: H 102 MET cc_start: 0.7548 (tpp) cc_final: 0.7158 (tpt) REVERT: R 417 LYS cc_start: 0.7997 (tppt) cc_final: 0.7115 (ttmt) REVERT: R 442 ASP cc_start: 0.8252 (m-30) cc_final: 0.8006 (m-30) REVERT: R 443 SER cc_start: 0.7759 (t) cc_final: 0.7289 (p) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.1575 time to fit residues: 17.2017 Evaluate side-chains 87 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 L residue 36 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain R residue 380 TYR Chi-restraints excluded: chain R residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.166046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142684 restraints weight = 4415.989| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.35 r_work: 0.3563 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3256 Z= 0.221 Angle : 0.627 8.673 4420 Z= 0.317 Chirality : 0.045 0.158 470 Planarity : 0.005 0.061 579 Dihedral : 4.831 22.162 456 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.62 % Allowed : 16.47 % Favored : 78.90 % 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: -3.91 (0.65), residues: 32 sheet: -1.71 (0.43), residues: 123 loop : -0.18 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 PHE 0.031 0.002 PHE H 87 TYR 0.013 0.001 TYR R 421 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 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.370 Fit side-chains REVERT: H 102 MET cc_start: 0.7402 (tpp) cc_final: 0.7108 (tpt) REVERT: R 417 LYS cc_start: 0.8053 (tppt) cc_final: 0.7201 (ttpt) REVERT: R 443 SER cc_start: 0.7865 (t) cc_final: 0.7412 (p) outliers start: 16 outliers final: 15 residues processed: 91 average time/residue: 0.1537 time to fit residues: 17.2022 Evaluate side-chains 93 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 116 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 0.0670 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.167663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.144436 restraints weight = 4278.322| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.32 r_work: 0.3602 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2219 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= 0.191 Angle : 0.596 7.150 4420 Z= 0.310 Chirality : 0.045 0.162 470 Planarity : 0.005 0.058 579 Dihedral : 4.707 22.432 456 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.62 % Allowed : 17.34 % Favored : 78.03 % 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 (0.57), residues: 39 sheet: -1.64 (0.43), residues: 129 loop : 0.04 (0.44), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 56 HIS 0.001 0.001 HIS L 55 PHE 0.026 0.001 PHE H 87 TYR 0.010 0.001 TYR R 380 ARG 0.006 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 103 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.330 Fit side-chains REVERT: H 81 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7488 (t0) REVERT: H 102 MET cc_start: 0.7261 (tpp) cc_final: 0.6947 (tpt) REVERT: R 417 LYS cc_start: 0.7935 (tppt) cc_final: 0.7543 (tptt) REVERT: R 443 SER cc_start: 0.7745 (t) cc_final: 0.7289 (p) outliers start: 16 outliers final: 13 residues processed: 94 average time/residue: 0.1492 time to fit residues: 16.9949 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 : 0.400 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.165759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.142054 restraints weight = 4313.248| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.36 r_work: 0.3562 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3256 Z= 0.250 Angle : 0.628 7.169 4420 Z= 0.324 Chirality : 0.045 0.167 470 Planarity : 0.005 0.055 579 Dihedral : 4.810 22.006 456 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.62 % Allowed : 18.21 % Favored : 77.17 % 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: -1.58 (0.43), residues: 406 helix: -3.88 (0.57), residues: 40 sheet: -1.70 (0.43), residues: 129 loop : 0.04 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 56 HIS 0.002 0.001 HIS H 22 PHE 0.027 0.002 PHE H 87 TYR 0.016 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 98 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.370 Fit side-chains REVERT: H 81 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7654 (t0) REVERT: R 417 LYS cc_start: 0.7966 (tppt) cc_final: 0.7073 (ttmt) REVERT: R 443 SER cc_start: 0.7781 (t) cc_final: 0.7349 (p) outliers start: 16 outliers final: 14 residues processed: 91 average time/residue: 0.1412 time to fit residues: 15.8365 Evaluate side-chains 94 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- 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: 0.8980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.165160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.141901 restraints weight = 4302.787| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.29 r_work: 0.3559 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2371 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= 0.283 Angle : 0.664 7.700 4420 Z= 0.344 Chirality : 0.046 0.182 470 Planarity : 0.005 0.054 579 Dihedral : 4.964 22.352 456 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.91 % Allowed : 18.79 % 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: -1.69 (0.43), residues: 406 helix: -3.81 (0.61), residues: 40 sheet: -1.57 (0.43), residues: 129 loop : -0.19 (0.44), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 56 HIS 0.001 0.001 HIS L 55 PHE 0.032 0.002 PHE H 87 TYR 0.015 0.001 TYR R 421 ARG 0.007 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 98 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.348 Fit side-chains REVERT: H 81 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7782 (t0) REVERT: R 417 LYS cc_start: 0.8026 (tppt) cc_final: 0.7181 (ttmt) REVERT: R 443 SER cc_start: 0.7828 (t) cc_final: 0.7404 (p) outliers start: 17 outliers final: 16 residues processed: 90 average time/residue: 0.1506 time to fit residues: 16.4433 Evaluate side-chains 96 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 340 GLU 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: 0.6980 chunk 29 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.168265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.145582 restraints weight = 4275.573| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.25 r_work: 0.3608 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2507 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= 0.193 Angle : 0.626 8.274 4420 Z= 0.324 Chirality : 0.045 0.175 470 Planarity : 0.005 0.055 579 Dihedral : 4.708 22.216 456 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.49 % Allowed : 18.50 % Favored : 76.01 % 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: -3.82 (0.59), residues: 40 sheet: -1.34 (0.47), residues: 112 loop : -0.16 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 128 HIS 0.000 0.000 HIS L 55 PHE 0.025 0.001 PHE H 87 TYR 0.011 0.001 TYR R 421 ARG 0.007 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 105 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.322 Fit side-chains REVERT: H 81 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7732 (t0) REVERT: R 417 LYS cc_start: 0.7908 (tppt) cc_final: 0.7066 (ttmt) REVERT: R 443 SER cc_start: 0.7763 (t) cc_final: 0.7301 (p) outliers start: 19 outliers final: 17 residues processed: 94 average time/residue: 0.1563 time to fit residues: 17.8047 Evaluate side-chains 100 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 22 MET Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain R residue 376 THR 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: 0.3980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 15 optimal weight: 0.8980 overall best weight: 0.3516 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.169200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.146923 restraints weight = 4285.656| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.23 r_work: 0.3625 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 0.038 3256 Z= 0.184 Angle : 0.620 8.408 4420 Z= 0.321 Chirality : 0.045 0.168 470 Planarity : 0.005 0.055 579 Dihedral : 4.611 22.206 456 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.91 % Allowed : 19.36 % 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: -1.35 (0.43), residues: 406 helix: -3.99 (0.62), residues: 34 sheet: -1.32 (0.46), residues: 114 loop : -0.12 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 128 HIS 0.001 0.000 HIS L 55 PHE 0.023 0.001 PHE H 87 TYR 0.010 0.001 TYR R 380 ARG 0.007 0.001 ARG H 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1943.70 seconds wall clock time: 35 minutes 12.21 seconds (2112.21 seconds total)