Starting phenix.real_space_refine on Wed Jul 23 19:45:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnv_27581/07_2025/8dnv_27581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnv_27581/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dnv_27581/07_2025/8dnv_27581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnv_27581/07_2025/8dnv_27581.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnv_27581/07_2025/8dnv_27581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnv_27581/07_2025/8dnv_27581.cif" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.34, per 1000 atoms: 0.80 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: 1.04 Conformation dependent library (CDL) restraints added in 504.2 milliseconds 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: 0.46 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: 1.16 Time building geometry restraints manager: 1.23 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: 1.000 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.860 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (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 TRP 0.006 0.001 TRP A 64 HIS 0.003 0.002 HIS A 360 PHE 0.014 0.001 PHE A 252 TYR 0.004 0.001 TYR A 285 ARG 0.004 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.11955 ( 314) hydrogen bonds : angle 5.06847 ( 936) covalent geometry : bond 0.00382 ( 4246) covalent geometry : angle 0.59266 ( 5747) *********************** 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 : 0.491 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: 0.1924 time to fit residues: 12.3814 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 : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4015 r_free = 0.4015 target = 0.163613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.127405 restraints weight = 4746.558| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.04 r_work: 0.3441 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.0874 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= 0.143 Angle : 0.541 11.181 5747 Z= 0.264 Chirality : 0.039 0.140 678 Planarity : 0.005 0.043 704 Dihedral : 3.801 17.738 571 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 4.00 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.37), residues: 525 helix: 2.31 (0.26), residues: 385 sheet: -1.83 (1.55), residues: 12 loop : -0.93 (0.51), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.008 0.001 PHE A 252 TYR 0.007 0.001 TYR A 263 ARG 0.006 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 314) hydrogen bonds : angle 4.25617 ( 936) covalent geometry : bond 0.00331 ( 4246) covalent geometry : angle 0.54116 ( 5747) *********************** 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 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: B 12 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.6373 (mmp-170) REVERT: A 20 GLN cc_start: 0.7702 (tt0) cc_final: 0.7034 (pt0) REVERT: A 143 MET cc_start: 0.7044 (mtt) cc_final: 0.6781 (mtt) REVERT: A 208 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8224 (mt-10) REVERT: A 307 MET cc_start: 0.7469 (mtt) cc_final: 0.7171 (mmm) REVERT: A 465 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7249 (mm-40) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.1806 time to fit residues: 11.4367 Evaluate side-chains 46 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.163894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.127493 restraints weight = 4819.450| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.06 r_work: 0.3425 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4246 Z= 0.147 Angle : 0.527 10.552 5747 Z= 0.257 Chirality : 0.038 0.138 678 Planarity : 0.005 0.043 704 Dihedral : 3.789 18.021 571 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.67 % Allowed : 6.44 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.37), residues: 525 helix: 2.32 (0.26), residues: 386 sheet: -1.92 (1.56), residues: 12 loop : -0.95 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 218 PHE 0.010 0.001 PHE A 312 TYR 0.006 0.001 TYR A 285 ARG 0.009 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 314) hydrogen bonds : angle 4.10812 ( 936) covalent geometry : bond 0.00347 ( 4246) covalent geometry : angle 0.52722 ( 5747) *********************** 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 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.475 Fit side-chains REVERT: A 20 GLN cc_start: 0.7619 (tt0) cc_final: 0.7032 (pt0) REVERT: A 65 MET cc_start: 0.8118 (mtm) cc_final: 0.7816 (mtp) REVERT: A 208 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8320 (mt-10) REVERT: A 307 MET cc_start: 0.7481 (mtt) cc_final: 0.7150 (mmm) REVERT: A 464 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: A 465 GLN cc_start: 0.7466 (mm-40) cc_final: 0.7238 (mm-40) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.2594 time to fit residues: 16.5644 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 : 0.625 ------------------------------------------------------------------------------- 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 48 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 44 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 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 27 GLN A 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.163289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127407 restraints weight = 4808.412| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.03 r_work: 0.3443 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1285 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= 0.121 Angle : 0.490 8.988 5747 Z= 0.240 Chirality : 0.038 0.136 678 Planarity : 0.004 0.043 704 Dihedral : 3.721 17.672 571 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.89 % Allowed : 6.67 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.37), residues: 525 helix: 2.44 (0.26), residues: 386 sheet: -1.78 (1.55), residues: 12 loop : -0.98 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.009 0.001 PHE A 312 TYR 0.005 0.001 TYR A 364 ARG 0.010 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 314) hydrogen bonds : angle 3.98074 ( 936) covalent geometry : bond 0.00281 ( 4246) covalent geometry : angle 0.48974 ( 5747) *********************** 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 : 1.086 Fit side-chains REVERT: A 20 GLN cc_start: 0.7614 (tt0) cc_final: 0.7191 (pt0) REVERT: A 25 LYS cc_start: 0.8288 (tptt) cc_final: 0.8005 (ttpp) REVERT: A 65 MET cc_start: 0.8098 (mtm) cc_final: 0.7781 (mtp) REVERT: A 77 MET cc_start: 0.8779 (mmp) cc_final: 0.8519 (mmt) REVERT: A 205 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7532 (mmt180) REVERT: A 208 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8274 (mt-10) REVERT: A 307 MET cc_start: 0.7574 (mtt) cc_final: 0.7353 (mmm) REVERT: A 464 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: A 465 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7196 (mm-40) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.3157 time to fit residues: 20.3597 Evaluate side-chains 48 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 2 optimal weight: 0.0270 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 0.0010 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.163593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.127666 restraints weight = 4882.057| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.05 r_work: 0.3459 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1378 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= 0.117 Angle : 0.478 8.224 5747 Z= 0.237 Chirality : 0.037 0.134 678 Planarity : 0.004 0.045 704 Dihedral : 3.671 17.438 571 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.89 % Allowed : 7.56 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.37), residues: 525 helix: 2.55 (0.26), residues: 386 sheet: -1.54 (1.58), residues: 12 loop : -1.00 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.009 0.001 PHE A 312 TYR 0.005 0.001 TYR A 364 ARG 0.010 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 314) hydrogen bonds : angle 3.92322 ( 936) covalent geometry : bond 0.00271 ( 4246) covalent geometry : angle 0.47794 ( 5747) *********************** 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 55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 1.908 Fit side-chains REVERT: A 20 GLN cc_start: 0.7605 (tt0) cc_final: 0.7257 (pt0) REVERT: A 25 LYS cc_start: 0.8250 (tptt) cc_final: 0.7966 (ttpp) REVERT: A 77 MET cc_start: 0.8889 (mmp) cc_final: 0.8533 (mmt) REVERT: A 91 MET cc_start: 0.7086 (mmp) cc_final: 0.6832 (mmm) REVERT: A 205 ARG cc_start: 0.7804 (mtt90) cc_final: 0.7518 (mmt180) REVERT: A 208 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8229 (mt-10) REVERT: A 464 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: A 465 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7173 (mm-40) outliers start: 4 outliers final: 2 residues processed: 55 average time/residue: 0.3618 time to fit residues: 24.1775 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 : 0.727 ------------------------------------------------------------------------------- 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 44 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.162676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126672 restraints weight = 4782.432| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.02 r_work: 0.3444 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4246 Z= 0.135 Angle : 0.487 8.184 5747 Z= 0.242 Chirality : 0.038 0.135 678 Planarity : 0.004 0.047 704 Dihedral : 3.719 17.425 571 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.37), residues: 525 helix: 2.51 (0.26), residues: 386 sheet: -1.58 (1.54), residues: 12 loop : -1.06 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.008 0.001 PHE A 156 TYR 0.005 0.001 TYR A 285 ARG 0.009 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 314) hydrogen bonds : angle 3.93084 ( 936) covalent geometry : bond 0.00321 ( 4246) covalent geometry : angle 0.48733 ( 5747) *********************** 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 53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.484 Fit side-chains REVERT: A 20 GLN cc_start: 0.7650 (tt0) cc_final: 0.7295 (pt0) REVERT: A 25 LYS cc_start: 0.8301 (tptt) cc_final: 0.8003 (ttpp) REVERT: A 205 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7518 (mmt180) REVERT: A 208 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8231 (mt-10) REVERT: A 307 MET cc_start: 0.7147 (mmm) cc_final: 0.6788 (mmm) REVERT: A 464 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: A 465 GLN cc_start: 0.7363 (mm-40) cc_final: 0.7137 (mm-40) outliers start: 4 outliers final: 2 residues processed: 53 average time/residue: 0.2163 time to fit residues: 14.7603 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 : 0.475 ------------------------------------------------------------------------------- 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 39 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.163485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.126984 restraints weight = 4817.607| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.06 r_work: 0.3437 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4246 Z= 0.146 Angle : 0.504 8.495 5747 Z= 0.248 Chirality : 0.038 0.136 678 Planarity : 0.004 0.048 704 Dihedral : 3.737 17.582 571 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 8.67 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.37), residues: 525 helix: 2.48 (0.26), residues: 386 sheet: -1.47 (1.56), residues: 12 loop : -1.08 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.009 0.001 PHE A 312 TYR 0.006 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 314) hydrogen bonds : angle 3.95049 ( 936) covalent geometry : bond 0.00352 ( 4246) covalent geometry : angle 0.50413 ( 5747) *********************** 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 53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.486 Fit side-chains REVERT: A 20 GLN cc_start: 0.7660 (tt0) cc_final: 0.7321 (pt0) REVERT: A 25 LYS cc_start: 0.8342 (tptt) cc_final: 0.8086 (ttpp) REVERT: A 208 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8280 (mt-10) REVERT: A 307 MET cc_start: 0.7179 (mmm) cc_final: 0.6784 (mmm) REVERT: A 464 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: A 465 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7149 (mm-40) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.1946 time to fit residues: 12.9011 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 : 0.489 ------------------------------------------------------------------------------- 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 7 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.163564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.127032 restraints weight = 4811.033| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.06 r_work: 0.3434 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1600 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= 0.144 Angle : 0.501 8.464 5747 Z= 0.247 Chirality : 0.038 0.136 678 Planarity : 0.004 0.048 704 Dihedral : 3.732 17.573 571 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.18 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.37), residues: 525 helix: 2.47 (0.26), residues: 386 sheet: -1.37 (1.59), residues: 12 loop : -1.09 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.007 0.001 PHE A 261 TYR 0.006 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 314) hydrogen bonds : angle 3.95168 ( 936) covalent geometry : bond 0.00347 ( 4246) covalent geometry : angle 0.50149 ( 5747) *********************** 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 53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.416 Fit side-chains REVERT: A 20 GLN cc_start: 0.7649 (tt0) cc_final: 0.7314 (pt0) REVERT: A 25 LYS cc_start: 0.8341 (tptt) cc_final: 0.8090 (ttpp) REVERT: A 205 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7519 (mmt180) REVERT: A 208 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8261 (mt-10) REVERT: A 464 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: A 465 GLN cc_start: 0.7365 (mm-40) cc_final: 0.7127 (mm-40) outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.1823 time to fit residues: 12.2072 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 : 0.458 ------------------------------------------------------------------------------- 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 1 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.162867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.126252 restraints weight = 4844.987| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.06 r_work: 0.3415 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1638 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= 0.161 Angle : 0.517 8.957 5747 Z= 0.255 Chirality : 0.039 0.136 678 Planarity : 0.005 0.049 704 Dihedral : 3.766 17.868 571 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.67 % Allowed : 9.33 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.37), residues: 525 helix: 2.45 (0.26), residues: 381 sheet: -1.11 (1.67), residues: 12 loop : -1.19 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.011 0.001 PHE A 312 TYR 0.008 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 314) hydrogen bonds : angle 3.99026 ( 936) covalent geometry : bond 0.00389 ( 4246) covalent geometry : angle 0.51687 ( 5747) *********************** 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 : 0.546 Fit side-chains REVERT: A 20 GLN cc_start: 0.7679 (tt0) cc_final: 0.7349 (pt0) REVERT: A 25 LYS cc_start: 0.8359 (tptt) cc_final: 0.8110 (ttpp) REVERT: A 205 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7523 (mmt180) REVERT: A 208 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 307 MET cc_start: 0.7267 (mmm) cc_final: 0.6890 (mmm) REVERT: A 464 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6427 (mp0) REVERT: A 465 GLN cc_start: 0.7376 (mm-40) cc_final: 0.7141 (mm-40) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.2305 time to fit residues: 14.9569 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 : 0.653 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 6 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.0050 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.163677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127761 restraints weight = 4788.134| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.03 r_work: 0.3453 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1650 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= 0.115 Angle : 0.483 7.525 5747 Z= 0.238 Chirality : 0.038 0.137 678 Planarity : 0.004 0.047 704 Dihedral : 3.676 17.155 571 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.67 % Allowed : 9.33 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.37), residues: 525 helix: 2.60 (0.26), residues: 381 sheet: -1.16 (1.66), residues: 12 loop : -1.12 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.001 0.001 HIS A 360 PHE 0.009 0.001 PHE A 156 TYR 0.005 0.001 TYR A 137 ARG 0.010 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 314) hydrogen bonds : angle 3.89057 ( 936) covalent geometry : bond 0.00267 ( 4246) covalent geometry : angle 0.48297 ( 5747) ********************** 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 51 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.567 Fit side-chains REVERT: A 20 GLN cc_start: 0.7663 (tt0) cc_final: 0.7318 (pt0) REVERT: A 25 LYS cc_start: 0.8329 (tptt) cc_final: 0.8067 (ttpp) REVERT: A 208 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 307 MET cc_start: 0.7110 (mmm) cc_final: 0.6726 (mmm) REVERT: A 464 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: A 465 GLN cc_start: 0.7278 (mm-40) cc_final: 0.7013 (mm-40) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.2195 time to fit residues: 15.0292 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 : 0.553 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.161853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125197 restraints weight = 4836.164| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.06 r_work: 0.3404 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4246 Z= 0.182 Angle : 0.535 9.196 5747 Z= 0.265 Chirality : 0.040 0.138 678 Planarity : 0.005 0.049 704 Dihedral : 3.776 17.689 571 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.89 % Allowed : 9.56 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.37), residues: 525 helix: 2.40 (0.26), residues: 381 sheet: -1.13 (1.67), residues: 12 loop : -1.22 (0.51), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.004 0.002 HIS A 218 PHE 0.010 0.001 PHE A 252 TYR 0.009 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 314) hydrogen bonds : angle 4.02073 ( 936) covalent geometry : bond 0.00446 ( 4246) covalent geometry : angle 0.53487 ( 5747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.59 seconds wall clock time: 57 minutes 5.40 seconds (3425.40 seconds total)