Starting phenix.real_space_refine on Fri Aug 22 14:31:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnv_27581/08_2025/8dnv_27581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnv_27581/08_2025/8dnv_27581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dnv_27581/08_2025/8dnv_27581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnv_27581/08_2025/8dnv_27581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dnv_27581/08_2025/8dnv_27581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnv_27581/08_2025/8dnv_27581.map" } resolution = 3.03 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= 0.004 sd= 0.045 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 26 5.16 5 C 2747 2.51 5 N 673 2.21 5 O 711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4157 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 486 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 3420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3420 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 1.30, per 1000 atoms: 0.31 Number of scatterers: 4157 At special positions: 0 Unit cell: (92.4, 80.85, 79.8, 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 26 16.00 O 711 8.00 N 673 7.00 C 2747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 161.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 980 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 4 sheets defined 75.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 66 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 69 through 95 Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.542A pdb=" N VAL A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 10 through 15' Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 139 through 144 Processing helix chain 'A' and resid 145 through 172 Processing helix chain 'A' and resid 177 through 197 removed outlier: 3.572A pdb=" N ALA A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.933A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 260 Processing helix chain 'A' and resid 288 through 312 removed outlier: 3.601A pdb=" N ARG A 311 " --> pdb=" O MET A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 322 Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 409 through 439 Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 442 through 468 removed outlier: 3.544A pdb=" N GLY A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 282 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.585A pdb=" N THR A 323 " --> pdb=" O VAL A 338 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 936 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: 0.65 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 633 1.31 - 1.44: 1118 1.44 - 1.56: 2452 1.56 - 1.68: 0 1.68 - 1.81: 43 Bond restraints: 4246 Sorted by residual: bond pdb=" C SER A 443 " pdb=" O SER A 443 " ideal model delta sigma weight residual 1.235 1.187 0.048 1.26e-02 6.30e+03 1.46e+01 bond pdb=" CA GLY A 446 " pdb=" C GLY A 446 " ideal model delta sigma weight residual 1.516 1.483 0.033 1.12e-02 7.97e+03 8.69e+00 bond pdb=" C ARG A 66 " pdb=" O ARG A 66 " ideal model delta sigma weight residual 1.236 1.203 0.033 1.15e-02 7.56e+03 8.09e+00 bond pdb=" CA ALA A 440 " pdb=" C ALA A 440 " ideal model delta sigma weight residual 1.524 1.488 0.035 1.30e-02 5.92e+03 7.40e+00 bond pdb=" CA MET C 86 " pdb=" C MET C 86 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.29e-02 6.01e+03 7.31e+00 ... (remaining 4241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 5674 2.28 - 4.55: 58 4.55 - 6.83: 13 6.83 - 9.11: 1 9.11 - 11.39: 1 Bond angle restraints: 5747 Sorted by residual: angle pdb=" N ILE A 441 " pdb=" CA ILE A 441 " pdb=" C ILE A 441 " ideal model delta sigma weight residual 109.58 104.56 5.02 1.29e+00 6.01e-01 1.51e+01 angle pdb=" N MET A 65 " pdb=" CA MET A 65 " pdb=" C MET A 65 " ideal model delta sigma weight residual 113.38 108.82 4.56 1.23e+00 6.61e-01 1.37e+01 angle pdb=" C VAL A 67 " pdb=" CA VAL A 67 " pdb=" CB VAL A 67 " ideal model delta sigma weight residual 112.14 107.59 4.55 1.35e+00 5.49e-01 1.13e+01 angle pdb=" N LEU A 69 " pdb=" CA LEU A 69 " pdb=" C LEU A 69 " ideal model delta sigma weight residual 113.30 109.06 4.24 1.34e+00 5.57e-01 1.00e+01 angle pdb=" N GLU A 464 " pdb=" CA GLU A 464 " pdb=" CB GLU A 464 " ideal model delta sigma weight residual 110.28 114.86 -4.58 1.55e+00 4.16e-01 8.74e+00 ... (remaining 5742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 2321 17.34 - 34.68: 168 34.68 - 52.02: 16 52.02 - 69.37: 3 69.37 - 86.71: 5 Dihedral angle restraints: 2513 sinusoidal: 985 harmonic: 1528 Sorted by residual: dihedral pdb=" CA LYS A 171 " pdb=" C LYS A 171 " pdb=" N GLY A 172 " pdb=" CA GLY A 172 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ILE A 416 " pdb=" C ILE A 416 " pdb=" N ILE A 417 " pdb=" CA ILE A 417 " ideal model delta harmonic sigma weight residual -180.00 -165.28 -14.72 0 5.00e+00 4.00e-02 8.67e+00 dihedral pdb=" CA THR A 286 " pdb=" C THR A 286 " pdb=" N SER A 287 " pdb=" CA SER A 287 " ideal model delta harmonic sigma weight residual -180.00 -165.79 -14.21 0 5.00e+00 4.00e-02 8.07e+00 ... (remaining 2510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 415 0.030 - 0.060: 182 0.060 - 0.089: 60 0.089 - 0.119: 16 0.119 - 0.149: 5 Chirality restraints: 678 Sorted by residual: chirality pdb=" CA ILE A 441 " pdb=" N ILE A 441 " pdb=" C ILE A 441 " pdb=" CB ILE A 441 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA GLU A 464 " pdb=" N GLU A 464 " pdb=" C GLU A 464 " pdb=" CB GLU A 464 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CB ILE A 380 " pdb=" CA ILE A 380 " pdb=" CG1 ILE A 380 " pdb=" CG2 ILE A 380 " both_signs ideal model delta sigma weight residual False 2.64 2.52 0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 675 not shown) Planarity restraints: 704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 386 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 387 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 417 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 418 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 418 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 418 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 82 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO A 83 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.024 5.00e-02 4.00e+02 ... (remaining 701 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1050 2.80 - 3.33: 4254 3.33 - 3.85: 7033 3.85 - 4.38: 7675 4.38 - 4.90: 13988 Nonbonded interactions: 34000 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OG SER A 346 " model vdw 2.276 3.040 nonbonded pdb=" OG SER A 197 " pdb=" OE1 GLU A 210 " model vdw 2.285 3.040 nonbonded pdb=" O PRO A 17 " pdb=" NZ LYS A 117 " model vdw 2.304 3.120 nonbonded pdb=" O ILE A 460 " pdb=" OE1 GLU A 464 " model vdw 2.362 3.040 nonbonded pdb=" NH2 ARG A 236 " pdb=" O PRO A 240 " model vdw 2.376 3.120 ... (remaining 33995 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: 1.520 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.650 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.004 0.048 4246 Z= 0.235 Angle : 0.593 11.387 5747 Z= 0.317 Chirality : 0.039 0.149 678 Planarity : 0.005 0.045 704 Dihedral : 11.811 86.707 1533 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 aren not related in a simple way. whole: 1.82 (0.37), residues: 525 helix: 1.93 (0.26), residues: 389 sheet: -1.99 (1.47), residues: 12 loop : -0.79 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.004 0.001 TYR A 285 PHE 0.014 0.001 PHE A 252 TRP 0.006 0.001 TRP A 64 HIS 0.003 0.002 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4246) covalent geometry : angle 0.59266 ( 5747) hydrogen bonds : bond 0.11955 ( 314) hydrogen bonds : angle 5.06847 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.101 Fit side-chains REVERT: A 18 GLU cc_start: 0.7361 (pm20) cc_final: 0.7159 (pm20) REVERT: A 20 GLN cc_start: 0.7493 (tt0) cc_final: 0.6930 (pt0) REVERT: A 77 MET cc_start: 0.8344 (mmp) cc_final: 0.8140 (mmt) REVERT: A 154 GLN cc_start: 0.7879 (mt0) cc_final: 0.7461 (mt0) REVERT: A 208 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7329 (mt-10) REVERT: A 307 MET cc_start: 0.7183 (mtt) cc_final: 0.6846 (mmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0780 time to fit residues: 4.8947 Evaluate side-chains 39 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127105 restraints weight = 4774.549| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.04 r_work: 0.3440 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4246 Z= 0.144 Angle : 0.542 11.294 5747 Z= 0.264 Chirality : 0.039 0.139 678 Planarity : 0.005 0.043 704 Dihedral : 3.815 17.768 571 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.67 % Allowed : 4.22 % Favored : 95.11 % 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 aren not related in a simple way. whole: 2.18 (0.37), residues: 525 helix: 2.31 (0.26), residues: 385 sheet: -1.87 (1.54), residues: 12 loop : -0.95 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 24 TYR 0.007 0.001 TYR A 263 PHE 0.007 0.001 PHE A 252 TRP 0.004 0.001 TRP A 379 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4246) covalent geometry : angle 0.54203 ( 5747) hydrogen bonds : bond 0.04123 ( 314) hydrogen bonds : angle 4.21863 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.096 Fit side-chains REVERT: B 12 ARG cc_start: 0.7515 (ttm-80) cc_final: 0.6366 (mmp-170) REVERT: A 20 GLN cc_start: 0.7714 (tt0) cc_final: 0.7052 (pt0) REVERT: A 65 MET cc_start: 0.8111 (mtm) cc_final: 0.7892 (mtp) REVERT: A 208 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8255 (mt-10) REVERT: A 307 MET cc_start: 0.7464 (mtt) cc_final: 0.7162 (mmm) REVERT: A 464 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.6130 (mp0) REVERT: A 465 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7240 (mm-40) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.0811 time to fit residues: 5.0444 Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.164545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128128 restraints weight = 4840.922| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.07 r_work: 0.3442 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4246 Z= 0.135 Angle : 0.516 10.440 5747 Z= 0.251 Chirality : 0.038 0.136 678 Planarity : 0.005 0.042 704 Dihedral : 3.760 17.993 571 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 6.00 % Favored : 93.33 % 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 aren not related in a simple way. whole: 2.27 (0.36), residues: 525 helix: 2.37 (0.26), residues: 386 sheet: -1.80 (1.56), residues: 12 loop : -0.95 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 24 TYR 0.006 0.001 TYR A 364 PHE 0.010 0.001 PHE A 312 TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4246) covalent geometry : angle 0.51581 ( 5747) hydrogen bonds : bond 0.03892 ( 314) hydrogen bonds : angle 4.06074 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.107 Fit side-chains REVERT: A 20 GLN cc_start: 0.7619 (tt0) cc_final: 0.7073 (pt0) REVERT: A 77 MET cc_start: 0.8922 (mmp) cc_final: 0.8655 (mmt) REVERT: A 205 ARG cc_start: 0.7756 (mtt90) cc_final: 0.7506 (mmt180) REVERT: A 208 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 307 MET cc_start: 0.7559 (mtt) cc_final: 0.7240 (mmm) REVERT: A 464 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: A 465 GLN cc_start: 0.7510 (mm-40) cc_final: 0.7298 (mm-40) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.0659 time to fit residues: 4.1376 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.160695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.124506 restraints weight = 4780.073| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.03 r_work: 0.3414 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4246 Z= 0.167 Angle : 0.530 10.396 5747 Z= 0.260 Chirality : 0.039 0.138 678 Planarity : 0.005 0.041 704 Dihedral : 3.815 18.287 571 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.89 % Allowed : 6.89 % Favored : 92.22 % 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 aren not related in a simple way. whole: 2.15 (0.36), residues: 525 helix: 2.31 (0.26), residues: 386 sheet: -1.78 (1.57), residues: 12 loop : -1.09 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 24 TYR 0.006 0.001 TYR A 285 PHE 0.009 0.001 PHE A 261 TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 4246) covalent geometry : angle 0.52999 ( 5747) hydrogen bonds : bond 0.03984 ( 314) hydrogen bonds : angle 4.08077 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.172 Fit side-chains REVERT: A 20 GLN cc_start: 0.7619 (tt0) cc_final: 0.7152 (pt0) REVERT: A 65 MET cc_start: 0.8198 (mtm) cc_final: 0.7893 (mtp) REVERT: A 77 MET cc_start: 0.8966 (mmp) cc_final: 0.8721 (mmt) REVERT: A 205 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7517 (mmt180) REVERT: A 208 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8261 (mt-10) REVERT: A 464 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: A 465 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7266 (mm-40) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.0801 time to fit residues: 4.8638 Evaluate side-chains 47 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.163415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.126838 restraints weight = 4859.385| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.07 r_work: 0.3426 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4246 Z= 0.130 Angle : 0.496 9.176 5747 Z= 0.244 Chirality : 0.038 0.138 678 Planarity : 0.004 0.045 704 Dihedral : 3.747 17.786 571 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.11 % Allowed : 7.56 % Favored : 91.33 % 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 aren not related in a simple way. whole: 2.26 (0.37), residues: 525 helix: 2.39 (0.26), residues: 386 sheet: -1.46 (1.62), residues: 12 loop : -1.09 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 24 TYR 0.005 0.001 TYR A 285 PHE 0.009 0.001 PHE A 312 TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4246) covalent geometry : angle 0.49646 ( 5747) hydrogen bonds : bond 0.03744 ( 314) hydrogen bonds : angle 3.99315 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.168 Fit side-chains REVERT: A 20 GLN cc_start: 0.7632 (tt0) cc_final: 0.7240 (pt0) REVERT: A 65 MET cc_start: 0.8105 (mtm) cc_final: 0.7806 (mtp) REVERT: A 77 MET cc_start: 0.8978 (mmp) cc_final: 0.8731 (mmt) REVERT: A 205 ARG cc_start: 0.7922 (mtt90) cc_final: 0.7538 (mmt180) REVERT: A 208 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8300 (mt-10) REVERT: A 307 MET cc_start: 0.7143 (mmm) cc_final: 0.6740 (mmm) REVERT: A 464 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6301 (mp0) REVERT: A 465 GLN cc_start: 0.7379 (mm-40) cc_final: 0.7143 (mm-40) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 0.0763 time to fit residues: 5.0842 Evaluate side-chains 51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.162964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.126296 restraints weight = 4954.804| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.09 r_work: 0.3427 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4246 Z= 0.145 Angle : 0.505 9.116 5747 Z= 0.249 Chirality : 0.038 0.136 678 Planarity : 0.005 0.045 704 Dihedral : 3.746 17.869 571 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.89 % Allowed : 8.67 % Favored : 90.44 % 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 aren not related in a simple way. whole: 2.23 (0.37), residues: 525 helix: 2.37 (0.26), residues: 386 sheet: -1.24 (1.66), residues: 12 loop : -1.15 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 24 TYR 0.006 0.001 TYR A 285 PHE 0.008 0.001 PHE A 312 TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4246) covalent geometry : angle 0.50474 ( 5747) hydrogen bonds : bond 0.03799 ( 314) hydrogen bonds : angle 4.00326 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.153 Fit side-chains REVERT: A 20 GLN cc_start: 0.7637 (tt0) cc_final: 0.7281 (pt0) REVERT: A 77 MET cc_start: 0.8939 (mmp) cc_final: 0.8682 (mmt) REVERT: A 205 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7522 (mmt180) REVERT: A 208 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8281 (mt-10) REVERT: A 464 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6407 (mp0) REVERT: A 465 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7194 (mm-40) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.0784 time to fit residues: 5.0802 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.162407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125671 restraints weight = 4931.992| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.07 r_work: 0.3420 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4246 Z= 0.153 Angle : 0.513 9.314 5747 Z= 0.252 Chirality : 0.039 0.136 678 Planarity : 0.005 0.051 704 Dihedral : 3.762 17.786 571 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.67 % Allowed : 9.11 % Favored : 90.22 % 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 aren not related in a simple way. whole: 2.21 (0.37), residues: 525 helix: 2.36 (0.26), residues: 386 sheet: -1.03 (1.72), residues: 12 loop : -1.18 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 24 TYR 0.006 0.001 TYR A 285 PHE 0.008 0.001 PHE A 261 TRP 0.006 0.001 TRP A 64 HIS 0.003 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4246) covalent geometry : angle 0.51344 ( 5747) hydrogen bonds : bond 0.03828 ( 314) hydrogen bonds : angle 4.01459 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.100 Fit side-chains REVERT: A 20 GLN cc_start: 0.7646 (tt0) cc_final: 0.7298 (pt0) REVERT: A 77 MET cc_start: 0.8943 (mmp) cc_final: 0.8693 (mmt) REVERT: A 208 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8298 (mt-10) REVERT: A 307 MET cc_start: 0.7262 (mmm) cc_final: 0.6873 (mmm) REVERT: A 464 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: A 465 GLN cc_start: 0.7387 (mm-40) cc_final: 0.7165 (mm-40) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.0689 time to fit residues: 4.4664 Evaluate side-chains 51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 47 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.164442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.128083 restraints weight = 4852.701| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.06 r_work: 0.3448 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4246 Z= 0.121 Angle : 0.488 8.330 5747 Z= 0.240 Chirality : 0.038 0.137 678 Planarity : 0.004 0.047 704 Dihedral : 3.686 17.278 571 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.89 % Allowed : 8.89 % Favored : 90.22 % 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 aren not related in a simple way. whole: 2.35 (0.37), residues: 525 helix: 2.47 (0.26), residues: 386 sheet: -0.98 (1.72), residues: 12 loop : -1.15 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 24 TYR 0.005 0.001 TYR A 137 PHE 0.009 0.001 PHE A 156 TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4246) covalent geometry : angle 0.48848 ( 5747) hydrogen bonds : bond 0.03604 ( 314) hydrogen bonds : angle 3.93378 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.099 Fit side-chains REVERT: A 20 GLN cc_start: 0.7603 (tt0) cc_final: 0.7276 (pt0) REVERT: A 77 MET cc_start: 0.8966 (mmp) cc_final: 0.8694 (mmt) REVERT: A 208 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 464 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: A 465 GLN cc_start: 0.7355 (mm-40) cc_final: 0.7117 (mm-40) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.0619 time to fit residues: 4.0654 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 28 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 41 optimal weight: 0.0060 chunk 45 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.163444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127619 restraints weight = 4893.400| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.06 r_work: 0.3458 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4246 Z= 0.112 Angle : 0.483 7.515 5747 Z= 0.238 Chirality : 0.038 0.136 678 Planarity : 0.005 0.048 704 Dihedral : 3.636 16.613 571 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 9.56 % Favored : 89.78 % 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 aren not related in a simple way. whole: 2.45 (0.37), residues: 525 helix: 2.54 (0.26), residues: 386 sheet: -1.25 (1.63), residues: 12 loop : -1.12 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 24 TYR 0.005 0.001 TYR A 137 PHE 0.011 0.001 PHE A 156 TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4246) covalent geometry : angle 0.48327 ( 5747) hydrogen bonds : bond 0.03491 ( 314) hydrogen bonds : angle 3.88377 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.096 Fit side-chains REVERT: A 20 GLN cc_start: 0.7632 (tt0) cc_final: 0.7315 (pt0) REVERT: A 77 MET cc_start: 0.8889 (mmp) cc_final: 0.8527 (mmt) REVERT: A 208 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8230 (mt-10) REVERT: A 307 MET cc_start: 0.7158 (mmm) cc_final: 0.6808 (mmm) REVERT: A 464 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: A 465 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7066 (mm-40) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.0700 time to fit residues: 4.5557 Evaluate side-chains 47 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 0.0770 chunk 28 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 0.1980 chunk 50 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.163820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128184 restraints weight = 4766.960| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.02 r_work: 0.3457 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4246 Z= 0.110 Angle : 0.488 7.015 5747 Z= 0.238 Chirality : 0.038 0.136 678 Planarity : 0.004 0.045 704 Dihedral : 3.638 16.650 571 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.44 % Allowed : 10.22 % Favored : 89.33 % 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 aren not related in a simple way. whole: 2.54 (0.37), residues: 525 helix: 2.61 (0.26), residues: 386 sheet: -1.37 (1.59), residues: 12 loop : -1.04 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 24 TYR 0.006 0.001 TYR A 137 PHE 0.011 0.001 PHE A 156 TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 4246) covalent geometry : angle 0.48819 ( 5747) hydrogen bonds : bond 0.03455 ( 314) hydrogen bonds : angle 3.86874 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.102 Fit side-chains REVERT: A 20 GLN cc_start: 0.7633 (tt0) cc_final: 0.7295 (pt0) REVERT: A 77 MET cc_start: 0.8855 (mmp) cc_final: 0.8596 (mmt) REVERT: A 208 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 307 MET cc_start: 0.7076 (mmm) cc_final: 0.6714 (mmm) REVERT: A 464 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: A 465 GLN cc_start: 0.7264 (mm-40) cc_final: 0.6988 (mm-40) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.0577 time to fit residues: 3.5049 Evaluate side-chains 46 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 464 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 0.0270 chunk 50 optimal weight: 3.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.162847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126898 restraints weight = 4813.867| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.04 r_work: 0.3446 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4246 Z= 0.126 Angle : 0.502 7.633 5747 Z= 0.244 Chirality : 0.038 0.136 678 Planarity : 0.004 0.048 704 Dihedral : 3.647 16.679 571 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.89 % Allowed : 10.00 % Favored : 89.11 % 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 aren not related in a simple way. whole: 2.48 (0.37), residues: 525 helix: 2.63 (0.26), residues: 381 sheet: -1.36 (1.59), residues: 12 loop : -1.15 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 24 TYR 0.006 0.001 TYR A 285 PHE 0.010 0.001 PHE A 312 TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4246) covalent geometry : angle 0.50179 ( 5747) hydrogen bonds : bond 0.03566 ( 314) hydrogen bonds : angle 3.87932 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1109.58 seconds wall clock time: 19 minutes 44.27 seconds (1184.27 seconds total)