Starting phenix.real_space_refine on Tue Mar 3 11:24:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wro_32734/03_2026/7wro_32734.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wro_32734/03_2026/7wro_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_2026/7wro_32734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wro_32734/03_2026/7wro_32734.map" model { file = "/net/cci-nas-00/data/ceres_data/7wro_32734/03_2026/7wro_32734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wro_32734/03_2026/7wro_32734.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 0.89, per 1000 atoms: 0.28 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: 0.24 Conformation dependent library (CDL) restraints added in 125.6 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: 0.11 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: 0.44 Time building geometry restraints manager: 0.34 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: 3.580 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: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.840 ------------------------------------------------------------------------------- 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 3261 Z= 0.346 Angle : 1.116 13.264 4430 Z= 0.602 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (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 ARG 0.018 0.002 ARG H 57 TYR 0.018 0.002 TYR R 380 PHE 0.021 0.004 PHE H 87 TRP 0.017 0.003 TRP L 56 HIS 0.001 0.000 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00815 ( 3256) covalent geometry : angle 1.10752 ( 4420) SS BOND : bond 0.00833 ( 5) SS BOND : angle 3.05262 ( 10) hydrogen bonds : bond 0.26392 ( 73) hydrogen bonds : angle 13.04473 ( 168) *********************** 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 : 0.148 Fit side-chains revert: symmetry clash REVERT: H 102 MET cc_start: 0.6642 (tpp) cc_final: 0.6025 (tpp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0605 time to fit residues: 6.5215 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 : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.163388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.139499 restraints weight = 4368.726| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.38 r_work: 0.3549 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3261 Z= 0.202 Angle : 0.711 8.753 4430 Z= 0.367 Chirality : 0.047 0.137 470 Planarity : 0.006 0.064 579 Dihedral : 5.800 25.317 456 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.67 % Favored : 94.09 % Rotamer: Outliers : 1.16 % Allowed : 13.58 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.44), residues: 406 helix: -4.38 (0.51), residues: 32 sheet: -1.53 (0.44), residues: 131 loop : -0.28 (0.44), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 57 TYR 0.012 0.001 TYR R 380 PHE 0.018 0.002 PHE R 486 TRP 0.013 0.002 TRP L 56 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 3256) covalent geometry : angle 0.70216 ( 4420) SS BOND : bond 0.00605 ( 5) SS BOND : angle 2.39077 ( 10) hydrogen bonds : bond 0.04394 ( 73) hydrogen bonds : angle 8.76931 ( 168) *********************** 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 82 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.097 Fit side-chains REVERT: R 417 LYS cc_start: 0.7953 (tppt) cc_final: 0.7142 (ttpt) REVERT: R 443 SER cc_start: 0.7805 (t) cc_final: 0.7473 (p) outliers start: 4 outliers final: 4 residues processed: 79 average time/residue: 0.0618 time to fit residues: 5.9401 Evaluate side-chains 76 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain R residue 487 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3943 r_free = 0.3943 target = 0.161588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137253 restraints weight = 4389.126| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.40 r_work: 0.3498 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3261 Z= 0.232 Angle : 0.716 11.000 4430 Z= 0.364 Chirality : 0.047 0.153 470 Planarity : 0.005 0.064 579 Dihedral : 5.580 24.409 456 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.44), residues: 406 helix: -4.11 (0.57), residues: 32 sheet: -1.76 (0.42), residues: 140 loop : -0.12 (0.46), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 57 TYR 0.017 0.002 TYR R 421 PHE 0.016 0.002 PHE H 87 TRP 0.015 0.002 TRP L 56 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 3256) covalent geometry : angle 0.70655 ( 4420) SS BOND : bond 0.00591 ( 5) SS BOND : angle 2.49536 ( 10) hydrogen bonds : bond 0.03869 ( 73) hydrogen bonds : angle 8.23275 ( 168) *********************** 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 88 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.112 Fit side-chains REVERT: R 417 LYS cc_start: 0.8057 (tppt) cc_final: 0.7214 (ttpt) REVERT: R 443 SER cc_start: 0.7896 (t) cc_final: 0.7587 (p) outliers start: 8 outliers final: 6 residues processed: 84 average time/residue: 0.0707 time to fit residues: 7.0868 Evaluate side-chains 79 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.083 ------------------------------------------------------------------------------- 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 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.0980 chunk 32 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.164793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.140932 restraints weight = 4280.049| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.37 r_work: 0.3550 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3261 Z= 0.138 Angle : 0.621 7.027 4430 Z= 0.321 Chirality : 0.045 0.138 470 Planarity : 0.005 0.061 579 Dihedral : 5.146 22.880 456 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.76 % Allowed : 16.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.43), residues: 406 helix: -4.06 (0.59), residues: 32 sheet: -1.78 (0.43), residues: 126 loop : -0.12 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 57 TYR 0.013 0.001 TYR R 421 PHE 0.019 0.001 PHE H 87 TRP 0.011 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3256) covalent geometry : angle 0.61354 ( 4420) SS BOND : bond 0.00557 ( 5) SS BOND : angle 2.05349 ( 10) hydrogen bonds : bond 0.03405 ( 73) hydrogen bonds : angle 7.66034 ( 168) *********************** 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: 13 poor density : 79 time to evaluate : 0.141 Fit side-chains REVERT: H 32 LYS cc_start: 0.7228 (mmmt) cc_final: 0.6936 (mmmt) REVERT: R 417 LYS cc_start: 0.8007 (tppt) cc_final: 0.7158 (ttpt) REVERT: R 434 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7761 (pt) REVERT: R 443 SER cc_start: 0.7789 (t) cc_final: 0.7399 (p) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.0658 time to fit residues: 7.1144 Evaluate side-chains 85 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 81 ASP 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 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 19 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.162493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138335 restraints weight = 4361.260| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.38 r_work: 0.3509 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3261 Z= 0.185 Angle : 0.650 8.705 4430 Z= 0.331 Chirality : 0.046 0.202 470 Planarity : 0.005 0.062 579 Dihedral : 5.070 22.352 456 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.76 % Allowed : 17.63 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.44), residues: 406 helix: -3.79 (0.71), residues: 32 sheet: -1.72 (0.43), residues: 135 loop : -0.14 (0.45), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 57 TYR 0.015 0.001 TYR R 421 PHE 0.032 0.002 PHE H 87 TRP 0.013 0.002 TRP L 56 HIS 0.001 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 3256) covalent geometry : angle 0.64236 ( 4420) SS BOND : bond 0.00527 ( 5) SS BOND : angle 2.19043 ( 10) hydrogen bonds : bond 0.03282 ( 73) hydrogen bonds : angle 7.54134 ( 168) *********************** 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 92 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.096 Fit side-chains REVERT: R 417 LYS cc_start: 0.8073 (tppt) cc_final: 0.7184 (ttmt) REVERT: R 442 ASP cc_start: 0.8339 (m-30) cc_final: 0.8078 (m-30) REVERT: R 443 SER cc_start: 0.7833 (t) cc_final: 0.7433 (p) outliers start: 13 outliers final: 11 residues processed: 87 average time/residue: 0.0663 time to fit residues: 6.9858 Evaluate side-chains 86 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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 116 LEU 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 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 35 GLN R 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.163271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.139565 restraints weight = 4298.783| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.34 r_work: 0.3549 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3261 Z= 0.165 Angle : 0.635 9.499 4430 Z= 0.325 Chirality : 0.046 0.202 470 Planarity : 0.005 0.057 579 Dihedral : 5.046 22.661 456 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.43), residues: 406 helix: -3.80 (0.70), residues: 32 sheet: -1.78 (0.44), residues: 122 loop : -0.24 (0.43), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 57 TYR 0.014 0.001 TYR R 421 PHE 0.031 0.001 PHE H 87 TRP 0.012 0.002 TRP L 56 HIS 0.001 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 3256) covalent geometry : angle 0.62537 ( 4420) SS BOND : bond 0.00526 ( 5) SS BOND : angle 2.37204 ( 10) hydrogen bonds : bond 0.03139 ( 73) hydrogen bonds : angle 7.36215 ( 168) *********************** 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: 17 poor density : 82 time to evaluate : 0.116 Fit side-chains REVERT: R 417 LYS cc_start: 0.8096 (tppt) cc_final: 0.7223 (ttmt) REVERT: R 443 SER cc_start: 0.7887 (t) cc_final: 0.7411 (p) outliers start: 17 outliers final: 13 residues processed: 92 average time/residue: 0.0608 time to fit residues: 6.9136 Evaluate side-chains 90 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.116 ------------------------------------------------------------------------------- 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 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 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 21 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.0980 chunk 34 optimal weight: 0.7980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.168034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.145300 restraints weight = 4338.320| |-----------------------------------------------------------------------------| r_work (start): 0.3755 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: 0.7592 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3261 Z= 0.125 Angle : 0.614 7.439 4430 Z= 0.314 Chirality : 0.045 0.154 470 Planarity : 0.005 0.056 579 Dihedral : 4.808 22.330 456 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 : 4.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.43), residues: 406 helix: -3.83 (0.68), residues: 32 sheet: -1.70 (0.43), residues: 123 loop : -0.16 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 57 TYR 0.012 0.001 TYR R 421 PHE 0.026 0.001 PHE H 87 TRP 0.009 0.001 TRP L 56 HIS 0.001 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3256) covalent geometry : angle 0.60606 ( 4420) SS BOND : bond 0.00497 ( 5) SS BOND : angle 2.12132 ( 10) hydrogen bonds : bond 0.03197 ( 73) hydrogen bonds : angle 7.21957 ( 168) *********************** 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 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.087 Fit side-chains REVERT: H 57 ARG cc_start: 0.7682 (ptt90) cc_final: 0.7459 (ptt90) REVERT: R 417 LYS cc_start: 0.8078 (tppt) cc_final: 0.7242 (ttpt) REVERT: R 434 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7712 (pt) REVERT: R 443 SER cc_start: 0.7779 (t) cc_final: 0.7318 (p) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 0.0618 time to fit residues: 6.8724 Evaluate side-chains 89 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 97 THR 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 Chi-restraints excluded: chain R residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.0060 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.0970 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.167970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.145067 restraints weight = 4386.242| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.28 r_work: 0.3610 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3261 Z= 0.123 Angle : 0.614 7.985 4430 Z= 0.312 Chirality : 0.045 0.167 470 Planarity : 0.004 0.055 579 Dihedral : 4.733 22.453 456 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.20 % Allowed : 17.92 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.43), residues: 406 helix: -3.86 (0.67), residues: 32 sheet: -1.57 (0.44), residues: 123 loop : -0.12 (0.43), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 57 TYR 0.012 0.001 TYR R 421 PHE 0.025 0.001 PHE H 87 TRP 0.010 0.001 TRP L 56 HIS 0.002 0.001 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3256) covalent geometry : angle 0.60730 ( 4420) SS BOND : bond 0.00493 ( 5) SS BOND : angle 1.98143 ( 10) hydrogen bonds : bond 0.03060 ( 73) hydrogen bonds : angle 7.06965 ( 168) *********************** 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 103 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.128 Fit side-chains REVERT: R 417 LYS cc_start: 0.8091 (tppt) cc_final: 0.7234 (ttpt) REVERT: R 443 SER cc_start: 0.7765 (t) cc_final: 0.7273 (p) outliers start: 18 outliers final: 16 residues processed: 95 average time/residue: 0.0652 time to fit residues: 7.5843 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 : 0.114 ------------------------------------------------------------------------------- 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 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 11 optimal weight: 0.0060 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.166637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143334 restraints weight = 4310.825| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.26 r_work: 0.3595 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.004 0.036 3261 Z= 0.171 Angle : 0.653 8.133 4430 Z= 0.334 Chirality : 0.045 0.171 470 Planarity : 0.005 0.054 579 Dihedral : 4.844 22.100 456 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.20 % Allowed : 17.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.43), residues: 406 helix: -3.79 (0.69), residues: 32 sheet: -1.70 (0.43), residues: 127 loop : -0.05 (0.43), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 57 TYR 0.015 0.001 TYR R 421 PHE 0.028 0.001 PHE H 87 TRP 0.011 0.002 TRP L 56 HIS 0.001 0.001 HIS H 22 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 3256) covalent geometry : angle 0.64533 ( 4420) SS BOND : bond 0.00485 ( 5) SS BOND : angle 2.22450 ( 10) hydrogen bonds : bond 0.03092 ( 73) hydrogen bonds : angle 7.08677 ( 168) *********************** 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 104 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.092 Fit side-chains REVERT: R 417 LYS cc_start: 0.8050 (tppt) cc_final: 0.7186 (ttmt) REVERT: R 443 SER cc_start: 0.7790 (t) cc_final: 0.7378 (p) outliers start: 18 outliers final: 17 residues processed: 95 average time/residue: 0.0624 time to fit residues: 7.2829 Evaluate side-chains 101 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 L residue 97 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 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 23 optimal weight: 0.0070 chunk 34 optimal weight: 0.0170 chunk 30 optimal weight: 0.8980 overall best weight: 0.3236 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.170062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.147291 restraints weight = 4302.554| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.25 r_work: 0.3627 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3261 Z= 0.124 Angle : 0.632 8.300 4430 Z= 0.326 Chirality : 0.045 0.166 470 Planarity : 0.005 0.055 579 Dihedral : 4.675 22.385 456 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.43), residues: 406 helix: -3.81 (0.68), residues: 32 sheet: -1.45 (0.44), residues: 123 loop : -0.08 (0.42), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 57 TYR 0.012 0.001 TYR R 421 PHE 0.022 0.001 PHE H 87 TRP 0.013 0.001 TRP H 128 HIS 0.001 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 3256) covalent geometry : angle 0.62635 ( 4420) SS BOND : bond 0.00489 ( 5) SS BOND : angle 1.95469 ( 10) hydrogen bonds : bond 0.03037 ( 73) hydrogen bonds : angle 6.94354 ( 168) ********************** 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 99 residues out of total 346 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.103 Fit side-chains REVERT: R 417 LYS cc_start: 0.7983 (tppt) cc_final: 0.7131 (ttpt) REVERT: R 434 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7690 (pt) REVERT: R 443 SER cc_start: 0.7651 (t) cc_final: 0.7155 (p) outliers start: 13 outliers final: 12 residues processed: 94 average time/residue: 0.0670 time to fit residues: 7.5245 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 : 0.067 ------------------------------------------------------------------------------- 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 81 ASP Chi-restraints excluded: chain H residue 87 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 = 0.4031 r_free = 0.4031 target = 0.169448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146477 restraints weight = 4322.593| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.27 r_work: 0.3616 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3261 Z= 0.131 Angle : 0.632 8.334 4430 Z= 0.326 Chirality : 0.045 0.168 470 Planarity : 0.005 0.055 579 Dihedral : 4.635 21.963 456 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.05 % Allowed : 20.52 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.43), residues: 406 helix: -4.05 (0.70), residues: 26 sheet: -1.48 (0.44), residues: 125 loop : -0.02 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 57 TYR 0.012 0.001 TYR R 421 PHE 0.024 0.001 PHE H 87 TRP 0.010 0.001 TRP H 128 HIS 0.001 0.000 HIS L 55 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3256) covalent geometry : angle 0.62533 ( 4420) SS BOND : bond 0.00469 ( 5) SS BOND : angle 1.98415 ( 10) hydrogen bonds : bond 0.02998 ( 73) hydrogen bonds : angle 6.82887 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 966.20 seconds wall clock time: 17 minutes 14.12 seconds (1034.12 seconds total)