Starting phenix.real_space_refine on Tue Mar 3 12:35:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ul2_26589/03_2026/7ul2_26589.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ul2_26589/03_2026/7ul2_26589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ul2_26589/03_2026/7ul2_26589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ul2_26589/03_2026/7ul2_26589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ul2_26589/03_2026/7ul2_26589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ul2_26589/03_2026/7ul2_26589.map" } resolution = 2.4 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= -0.001 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1879 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians S 15 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 1724 2.51 5 N 428 2.21 5 O 455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 2624 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2185 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 277} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 6, 'HIS:plan': 3, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 383 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 59} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TRP:plan': 1, 'TYR:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 56 Unusual residues: {' NA': 1, 'Q6Q': 1} Classifications: {'undetermined': 2, 'water': 13} Link IDs: {None: 14} Time building chain proxies: 0.84, per 1000 atoms: 0.32 Number of scatterers: 2624 At special positions: 0 Unit cell: (69.416, 50.3266, 103.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 15 16.00 Na 1 11.00 O 455 8.00 N 428 7.00 C 1724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.23 Conformation dependent library (CDL) restraints added in 103.2 milliseconds 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 73.5% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'R' and resid 60 through 90 removed outlier: 3.575A pdb=" N PHE R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 118 removed outlier: 3.919A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 127 removed outlier: 3.775A pdb=" N VAL R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 removed outlier: 3.598A pdb=" N GLY R 140 " --> pdb=" O PHE R 136 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 removed outlier: 3.784A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 200 Processing helix chain 'R' and resid 200 through 206 removed outlier: 4.015A pdb=" N LEU R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 264 Processing helix chain 'R' and resid 272 through 329 Proline residue: R 318 - end of helix removed outlier: 3.545A pdb=" N PHE R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS R 327 " --> pdb=" O ARG R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 368 removed outlier: 3.505A pdb=" N PHE R 353 " --> pdb=" O THR R 349 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR R 354 " --> pdb=" O ASN R 350 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 379 removed outlier: 3.512A pdb=" N ARG R 372 " --> pdb=" O SER R 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 207 through 212 Processing sheet with id=AA2, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.067A pdb=" N GLU D 100 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET D 36 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN D 98 " --> pdb=" O MET D 36 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 597 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: 0.33 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 605 1.33 - 1.47: 939 1.47 - 1.60: 1106 1.60 - 1.74: 1 1.74 - 1.88: 24 Bond restraints: 2675 Sorted by residual: bond pdb=" C2 Q6Q R 501 " pdb=" O1 Q6Q R 501 " ideal model delta sigma weight residual 1.246 1.196 0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" C2 Q6Q R 501 " pdb=" O2 Q6Q R 501 " ideal model delta sigma weight residual 1.244 1.194 0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 Q6Q R 501 " pdb=" C2 Q6Q R 501 " ideal model delta sigma weight residual 1.573 1.524 0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" CB CYS R 224 " pdb=" SG CYS R 224 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.44e+00 bond pdb=" CB ARG R 303 " pdb=" CG ARG R 303 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.09e+00 ... (remaining 2670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 3504 2.17 - 4.34: 133 4.34 - 6.51: 25 6.51 - 8.68: 2 8.68 - 10.85: 1 Bond angle restraints: 3665 Sorted by residual: angle pdb=" N ILE R 359 " pdb=" CA ILE R 359 " pdb=" C ILE R 359 " ideal model delta sigma weight residual 110.72 114.28 -3.56 1.01e+00 9.80e-01 1.24e+01 angle pdb=" N ASN R 360 " pdb=" CA ASN R 360 " pdb=" C ASN R 360 " ideal model delta sigma weight residual 109.81 117.53 -7.72 2.21e+00 2.05e-01 1.22e+01 angle pdb=" CA LEU R 258 " pdb=" CB LEU R 258 " pdb=" CG LEU R 258 " ideal model delta sigma weight residual 116.30 105.45 10.85 3.50e+00 8.16e-02 9.61e+00 angle pdb=" N TYR R 328 " pdb=" CA TYR R 328 " pdb=" C TYR R 328 " ideal model delta sigma weight residual 113.30 117.38 -4.08 1.34e+00 5.57e-01 9.28e+00 angle pdb=" CA TYR R 256 " pdb=" CB TYR R 256 " pdb=" CG TYR R 256 " ideal model delta sigma weight residual 113.90 108.43 5.47 1.80e+00 3.09e-01 9.25e+00 ... (remaining 3660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 1460 17.86 - 35.72: 60 35.72 - 53.58: 22 53.58 - 71.45: 3 71.45 - 89.31: 2 Dihedral angle restraints: 1547 sinusoidal: 530 harmonic: 1017 Sorted by residual: dihedral pdb=" N ASN R 126 " pdb=" CA ASN R 126 " pdb=" CB ASN R 126 " pdb=" CG ASN R 126 " ideal model delta sinusoidal sigma weight residual -180.00 -120.54 -59.46 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG R 323 " pdb=" CB ARG R 323 " pdb=" CG ARG R 323 " pdb=" CD ARG R 323 " ideal model delta sinusoidal sigma weight residual -60.00 -113.69 53.69 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ARG D 32 " pdb=" CB ARG D 32 " pdb=" CG ARG D 32 " pdb=" CD ARG D 32 " ideal model delta sinusoidal sigma weight residual -60.00 -111.39 51.39 3 1.50e+01 4.44e-03 9.01e+00 ... (remaining 1544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 280 0.052 - 0.103: 125 0.103 - 0.155: 28 0.155 - 0.207: 9 0.207 - 0.258: 1 Chirality restraints: 443 Sorted by residual: chirality pdb=" CA ASN R 360 " pdb=" N ASN R 360 " pdb=" C ASN R 360 " pdb=" CB ASN R 360 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA TYR R 145 " pdb=" N TYR R 145 " pdb=" C TYR R 145 " pdb=" CB TYR R 145 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA PHE R 127 " pdb=" N PHE R 127 " pdb=" C PHE R 127 " pdb=" CB PHE R 127 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 440 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C Q6Q R 501 " -0.015 2.00e-02 2.50e+03 2.26e-02 1.03e+01 pdb=" C12 Q6Q R 501 " 0.036 2.00e-02 2.50e+03 pdb=" C13 Q6Q R 501 " 0.006 2.00e-02 2.50e+03 pdb=" C14 Q6Q R 501 " -0.011 2.00e-02 2.50e+03 pdb=" C22 Q6Q R 501 " 0.009 2.00e-02 2.50e+03 pdb=" C23 Q6Q R 501 " 0.027 2.00e-02 2.50e+03 pdb=" N1 Q6Q R 501 " -0.014 2.00e-02 2.50e+03 pdb=" N2 Q6Q R 501 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 Q6Q R 501 " -0.046 2.00e-02 2.50e+03 1.77e-02 9.37e+00 pdb=" C24 Q6Q R 501 " 0.003 2.00e-02 2.50e+03 pdb=" C25 Q6Q R 501 " -0.010 2.00e-02 2.50e+03 pdb=" C26 Q6Q R 501 " -0.005 2.00e-02 2.50e+03 pdb=" C27 Q6Q R 501 " 0.008 2.00e-02 2.50e+03 pdb=" C28 Q6Q R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C29 Q6Q R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C30 Q6Q R 501 " 0.008 2.00e-02 2.50e+03 pdb=" C31 Q6Q R 501 " -0.001 2.00e-02 2.50e+03 pdb=" N2 Q6Q R 501 " 0.037 2.00e-02 2.50e+03 pdb=" N3 Q6Q R 501 " 0.000 2.00e-02 2.50e+03 pdb="CL Q6Q R 501 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 334 " 0.019 2.00e-02 2.50e+03 1.28e-02 4.11e+00 pdb=" CG TRP R 334 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP R 334 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 334 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 334 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 334 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP R 334 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 334 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 334 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 334 " 0.004 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 743 2.82 - 3.34: 2497 3.34 - 3.86: 4251 3.86 - 4.38: 4846 4.38 - 4.90: 8051 Nonbonded interactions: 20388 Sorted by model distance: nonbonded pdb=" N TYR D 39 " pdb=" O TYR D 96 " model vdw 2.306 3.120 nonbonded pdb=" O TYR D 39 " pdb=" N TYR D 96 " model vdw 2.371 3.120 nonbonded pdb=" O PHE R 74 " pdb=" OG1 THR R 78 " model vdw 2.379 3.040 nonbonded pdb=" OD1 ASP R 112 " pdb="NA NA R 502 " model vdw 2.385 2.470 nonbonded pdb=" O LYS R 63 " pdb=" OG1 THR R 67 " model vdw 2.428 3.040 ... (remaining 20383 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 4.890 Find NCS groups from input model: 0.010 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:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 0.070 2676 Z= 0.351 Angle : 1.024 10.850 3667 Z= 0.563 Chirality : 0.061 0.258 443 Planarity : 0.006 0.040 440 Dihedral : 12.544 89.306 884 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.84 % Allowed : 7.56 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.60 (0.41), residues: 329 helix: 1.95 (0.30), residues: 224 sheet: 1.57 (1.66), residues: 9 loop : -1.17 (0.52), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG R 299 TYR 0.031 0.004 TYR R 256 PHE 0.026 0.004 PHE R 337 TRP 0.032 0.004 TRP R 334 HIS 0.004 0.002 HIS R 172 Details of bonding type rmsd covalent geometry : bond 0.00754 ( 2675) covalent geometry : angle 1.01588 ( 3665) SS BOND : bond 0.01850 ( 1) SS BOND : angle 5.44670 ( 2) hydrogen bonds : bond 0.26394 ( 203) hydrogen bonds : angle 6.47504 ( 597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.093 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.5174 time to fit residues: 26.4764 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.149545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129284 restraints weight = 2962.491| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.38 r_work: 0.3394 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2676 Z= 0.172 Angle : 0.578 8.836 3667 Z= 0.325 Chirality : 0.041 0.174 443 Planarity : 0.004 0.028 440 Dihedral : 5.775 50.054 430 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.10 % Allowed : 7.56 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 3.01 (0.44), residues: 329 helix: 3.32 (0.31), residues: 225 sheet: 1.56 (1.71), residues: 9 loop : -1.47 (0.50), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 102 TYR 0.014 0.002 TYR R 256 PHE 0.015 0.002 PHE R 375 TRP 0.009 0.001 TRP R 316 HIS 0.002 0.001 HIS R 229 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2675) covalent geometry : angle 0.57370 ( 3665) SS BOND : bond 0.00663 ( 1) SS BOND : angle 3.22649 ( 2) hydrogen bonds : bond 0.08124 ( 203) hydrogen bonds : angle 4.05941 ( 597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.108 Fit side-chains REVERT: R 65 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7294 (tt) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 0.4726 time to fit residues: 20.4457 Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125764 restraints weight = 2942.414| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.39 r_work: 0.3354 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2676 Z= 0.177 Angle : 0.574 8.239 3667 Z= 0.320 Chirality : 0.040 0.152 443 Planarity : 0.004 0.032 440 Dihedral : 5.012 44.554 428 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.36 % Allowed : 6.72 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.92 (0.44), residues: 329 helix: 3.21 (0.31), residues: 229 sheet: 1.37 (2.02), residues: 9 loop : -1.63 (0.51), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 102 TYR 0.016 0.002 TYR R 256 PHE 0.016 0.002 PHE R 375 TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2675) covalent geometry : angle 0.56802 ( 3665) SS BOND : bond 0.00920 ( 1) SS BOND : angle 3.56596 ( 2) hydrogen bonds : bond 0.08503 ( 203) hydrogen bonds : angle 3.96863 ( 597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.071 Fit side-chains REVERT: R 65 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7253 (tt) REVERT: R 123 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: D 36 MET cc_start: 0.8615 (mtp) cc_final: 0.8348 (mtp) outliers start: 8 outliers final: 2 residues processed: 42 average time/residue: 0.4116 time to fit residues: 17.7828 Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.0020 chunk 17 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.2966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.153740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133248 restraints weight = 2936.431| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.39 r_work: 0.3448 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2676 Z= 0.129 Angle : 0.468 7.889 3667 Z= 0.263 Chirality : 0.037 0.140 443 Planarity : 0.004 0.031 440 Dihedral : 4.864 42.294 428 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.52 % Allowed : 8.82 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 3.29 (0.45), residues: 329 helix: 3.53 (0.31), residues: 229 sheet: 1.60 (1.97), residues: 9 loop : -1.63 (0.50), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 322 TYR 0.013 0.001 TYR R 144 PHE 0.012 0.001 PHE R 375 TRP 0.006 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 2675) covalent geometry : angle 0.46454 ( 3665) SS BOND : bond 0.00471 ( 1) SS BOND : angle 2.39777 ( 2) hydrogen bonds : bond 0.06115 ( 203) hydrogen bonds : angle 3.71342 ( 597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.086 Fit side-chains REVERT: R 123 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7815 (tt0) outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 0.4589 time to fit residues: 17.4879 Evaluate side-chains 35 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.127947 restraints weight = 2932.258| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.43 r_work: 0.3383 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2676 Z= 0.153 Angle : 0.524 7.994 3667 Z= 0.291 Chirality : 0.038 0.142 443 Planarity : 0.004 0.041 440 Dihedral : 4.857 43.518 428 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.10 % Allowed : 10.08 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 3.14 (0.45), residues: 329 helix: 3.42 (0.31), residues: 229 sheet: 1.25 (1.93), residues: 9 loop : -1.67 (0.51), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 322 TYR 0.014 0.001 TYR R 256 PHE 0.013 0.002 PHE R 375 TRP 0.008 0.001 TRP R 316 HIS 0.004 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2675) covalent geometry : angle 0.51988 ( 3665) SS BOND : bond 0.00763 ( 1) SS BOND : angle 2.98387 ( 2) hydrogen bonds : bond 0.07450 ( 203) hydrogen bonds : angle 3.79333 ( 597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.064 Fit side-chains REVERT: R 65 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7113 (mt) REVERT: R 123 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7886 (tt0) outliers start: 5 outliers final: 2 residues processed: 37 average time/residue: 0.4888 time to fit residues: 18.5457 Evaluate side-chains 38 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 31 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.147653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126789 restraints weight = 2934.370| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.40 r_work: 0.3364 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2676 Z= 0.163 Angle : 0.544 8.110 3667 Z= 0.301 Chirality : 0.039 0.144 443 Planarity : 0.004 0.042 440 Dihedral : 4.931 44.002 428 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.10 % Allowed : 12.18 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.96 (0.45), residues: 329 helix: 3.22 (0.31), residues: 235 sheet: 0.60 (1.74), residues: 9 loop : -1.83 (0.53), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.015 0.002 TYR R 256 PHE 0.013 0.002 PHE R 375 TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2675) covalent geometry : angle 0.53927 ( 3665) SS BOND : bond 0.00886 ( 1) SS BOND : angle 3.21232 ( 2) hydrogen bonds : bond 0.07896 ( 203) hydrogen bonds : angle 3.85764 ( 597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.093 Fit side-chains REVERT: R 65 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7171 (mt) REVERT: R 123 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7867 (tt0) outliers start: 5 outliers final: 2 residues processed: 38 average time/residue: 0.4806 time to fit residues: 18.7432 Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.127878 restraints weight = 2975.519| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.42 r_work: 0.3377 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2676 Z= 0.155 Angle : 0.528 8.094 3667 Z= 0.293 Chirality : 0.038 0.145 443 Planarity : 0.004 0.044 440 Dihedral : 4.892 43.662 428 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.52 % Allowed : 11.34 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.99 (0.45), residues: 329 helix: 3.26 (0.32), residues: 235 sheet: 0.44 (1.70), residues: 9 loop : -1.83 (0.53), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.014 0.001 TYR R 256 PHE 0.013 0.002 PHE R 375 TRP 0.007 0.001 TRP R 316 HIS 0.004 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2675) covalent geometry : angle 0.52299 ( 3665) SS BOND : bond 0.00784 ( 1) SS BOND : angle 3.05448 ( 2) hydrogen bonds : bond 0.07511 ( 203) hydrogen bonds : angle 3.80845 ( 597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.106 Fit side-chains REVERT: R 65 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7139 (mt) REVERT: R 123 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7880 (tt0) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.5022 time to fit residues: 20.1365 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 31 optimal weight: 0.0570 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129026 restraints weight = 2975.482| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.41 r_work: 0.3393 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2676 Z= 0.147 Angle : 0.509 8.011 3667 Z= 0.283 Chirality : 0.038 0.142 443 Planarity : 0.004 0.044 440 Dihedral : 4.847 43.174 428 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.52 % Allowed : 11.34 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 3.07 (0.45), residues: 329 helix: 3.32 (0.32), residues: 235 sheet: 0.17 (1.65), residues: 9 loop : -1.80 (0.54), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.013 0.001 TYR R 256 PHE 0.013 0.001 PHE R 375 TRP 0.007 0.001 TRP R 129 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 2675) covalent geometry : angle 0.50450 ( 3665) SS BOND : bond 0.00729 ( 1) SS BOND : angle 2.89769 ( 2) hydrogen bonds : bond 0.07141 ( 203) hydrogen bonds : angle 3.76388 ( 597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.094 Fit side-chains REVERT: R 65 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7097 (mt) REVERT: R 123 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7863 (tt0) outliers start: 6 outliers final: 3 residues processed: 38 average time/residue: 0.5090 time to fit residues: 19.8657 Evaluate side-chains 39 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.0020 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.0980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.131379 restraints weight = 3020.031| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.41 r_work: 0.3425 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2676 Z= 0.135 Angle : 0.482 7.935 3667 Z= 0.268 Chirality : 0.037 0.141 443 Planarity : 0.004 0.044 440 Dihedral : 4.771 42.703 428 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.52 % Allowed : 11.76 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 3.24 (0.45), residues: 329 helix: 3.56 (0.32), residues: 229 sheet: 0.10 (1.64), residues: 9 loop : -1.67 (0.53), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 322 TYR 0.012 0.001 TYR R 144 PHE 0.012 0.001 PHE R 375 TRP 0.006 0.001 TRP R 129 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 2675) covalent geometry : angle 0.47787 ( 3665) SS BOND : bond 0.00598 ( 1) SS BOND : angle 2.58235 ( 2) hydrogen bonds : bond 0.06446 ( 203) hydrogen bonds : angle 3.69326 ( 597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.092 Fit side-chains REVERT: R 65 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7009 (mt) REVERT: R 123 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7849 (tt0) outliers start: 6 outliers final: 3 residues processed: 39 average time/residue: 0.5040 time to fit residues: 20.2167 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.147130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.126225 restraints weight = 3028.453| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.40 r_work: 0.3355 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2676 Z= 0.176 Angle : 0.572 8.293 3667 Z= 0.313 Chirality : 0.040 0.149 443 Planarity : 0.005 0.046 440 Dihedral : 4.931 44.554 428 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.94 % Allowed : 10.92 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.87 (0.45), residues: 329 helix: 3.19 (0.31), residues: 235 sheet: -0.18 (1.56), residues: 9 loop : -1.88 (0.54), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.016 0.002 TYR R 256 PHE 0.014 0.002 PHE R 375 TRP 0.010 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 2675) covalent geometry : angle 0.56709 ( 3665) SS BOND : bond 0.00997 ( 1) SS BOND : angle 3.30449 ( 2) hydrogen bonds : bond 0.08234 ( 203) hydrogen bonds : angle 3.86332 ( 597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.060 Fit side-chains REVERT: R 65 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7180 (mt) REVERT: R 123 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7873 (tt0) outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 0.4998 time to fit residues: 20.5718 Evaluate side-chains 40 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN R 229 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.128085 restraints weight = 2981.924| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.40 r_work: 0.3383 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2676 Z= 0.155 Angle : 0.536 8.172 3667 Z= 0.294 Chirality : 0.038 0.148 443 Planarity : 0.004 0.047 440 Dihedral : 4.886 43.658 428 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.94 % Allowed : 10.92 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.94 (0.45), residues: 329 helix: 3.25 (0.32), residues: 235 sheet: -0.24 (1.56), residues: 9 loop : -1.87 (0.54), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 32 TYR 0.013 0.001 TYR R 256 PHE 0.013 0.001 PHE R 375 TRP 0.007 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 2675) covalent geometry : angle 0.53126 ( 3665) SS BOND : bond 0.00780 ( 1) SS BOND : angle 3.01246 ( 2) hydrogen bonds : bond 0.07465 ( 203) hydrogen bonds : angle 3.78952 ( 597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1195.93 seconds wall clock time: 21 minutes 1.86 seconds (1261.86 seconds total)