Starting phenix.real_space_refine on Fri Dec 27 10:35:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnv_27581/12_2024/8dnv_27581.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnv_27581/12_2024/8dnv_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_27581/12_2024/8dnv_27581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnv_27581/12_2024/8dnv_27581.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnv_27581/12_2024/8dnv_27581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnv_27581/12_2024/8dnv_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-5532/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: 3.59, per 1000 atoms: 0.86 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: 1.12 Conformation dependent library (CDL) restraints added in 507.6 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: 0.48 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: 1.19 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 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: 1.080 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.150 Find NCS groups from input model: 0.030 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- 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= 0.243 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 *********************** 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 : 0.427 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: 0.1886 time to fit residues: 12.1270 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 : 0.426 ------------------------------------------------------------------------------- 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: 6.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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= 0.211 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 *********************** 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 : 0.474 Fit side-chains revert: symmetry clash REVERT: B 12 ARG cc_start: 0.7331 (ttm-80) cc_final: 0.6331 (mmp-170) REVERT: A 20 GLN cc_start: 0.7526 (tt0) cc_final: 0.6860 (pt0) REVERT: A 77 MET cc_start: 0.8380 (mmp) cc_final: 0.8167 (mmt) REVERT: A 143 MET cc_start: 0.6861 (mtt) cc_final: 0.6604 (mtt) REVERT: A 208 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7191 (mt-10) REVERT: A 307 MET cc_start: 0.7152 (mtt) cc_final: 0.6920 (mmm) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.1792 time to fit residues: 11.2729 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 : 0.489 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 0.0970 chunk 13 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1140 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= 0.159 Angle : 0.495 9.388 5747 Z= 0.241 Chirality : 0.038 0.133 678 Planarity : 0.004 0.043 704 Dihedral : 3.703 17.308 571 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.89 % Allowed : 6.00 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.42 (0.37), residues: 525 helix: 2.47 (0.26), residues: 386 sheet: -1.69 (1.59), residues: 12 loop : -0.86 (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 0.010 0.001 PHE A 312 TYR 0.005 0.001 TYR A 343 ARG 0.008 0.000 ARG B 24 *********************** 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 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.583 Fit side-chains REVERT: A 20 GLN cc_start: 0.7463 (tt0) cc_final: 0.6868 (pt0) REVERT: A 65 MET cc_start: 0.7617 (mtm) cc_final: 0.7307 (mtp) REVERT: A 208 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7202 (mt-10) REVERT: A 307 MET cc_start: 0.7217 (mtt) cc_final: 0.6975 (mmm) REVERT: A 464 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6151 (mp0) outliers start: 4 outliers final: 2 residues processed: 52 average time/residue: 0.1841 time to fit residues: 12.3122 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 : 0.431 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 241 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1286 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= 0.181 Angle : 0.496 9.048 5747 Z= 0.242 Chirality : 0.038 0.137 678 Planarity : 0.004 0.044 704 Dihedral : 3.685 17.061 571 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.67 % Allowed : 7.56 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.52 (0.26), residues: 386 sheet: -1.63 (1.62), residues: 12 loop : -0.95 (0.50), 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 0.010 0.001 PHE A 312 TYR 0.004 0.001 TYR A 137 ARG 0.009 0.000 ARG B 24 *********************** 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: 3 poor density : 47 time to evaluate : 0.474 Fit side-chains REVERT: A 20 GLN cc_start: 0.7452 (tt0) cc_final: 0.7022 (pt0) REVERT: A 65 MET cc_start: 0.7619 (mtm) cc_final: 0.7316 (mtp) REVERT: A 208 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7216 (mt-10) REVERT: A 307 MET cc_start: 0.7157 (mtt) cc_final: 0.6874 (mmm) REVERT: A 464 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6315 (mp0) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.1918 time to fit residues: 12.0140 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 : 0.422 ------------------------------------------------------------------------------- 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 29 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 26 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.0050 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1432 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= 0.175 Angle : 0.485 8.404 5747 Z= 0.239 Chirality : 0.038 0.136 678 Planarity : 0.004 0.045 704 Dihedral : 3.649 16.899 571 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.67 % Allowed : 8.00 % 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 (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: 2.49 (0.37), residues: 525 helix: 2.56 (0.26), residues: 386 sheet: -1.40 (1.65), residues: 12 loop : -1.02 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 285 ARG 0.010 0.001 ARG B 24 *********************** 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: 3 poor density : 51 time to evaluate : 0.474 Fit side-chains REVERT: A 20 GLN cc_start: 0.7457 (tt0) cc_final: 0.7055 (pt0) REVERT: A 25 LYS cc_start: 0.8266 (tptp) cc_final: 0.7951 (ttpp) REVERT: A 208 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7232 (mt-10) REVERT: A 307 MET cc_start: 0.7176 (mtt) cc_final: 0.6899 (mmm) REVERT: A 464 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6324 (mp0) outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.2626 time to fit residues: 18.4266 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 : 0.605 ------------------------------------------------------------------------------- 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 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1524 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= 0.197 Angle : 0.504 8.704 5747 Z= 0.244 Chirality : 0.038 0.138 678 Planarity : 0.004 0.047 704 Dihedral : 3.693 17.015 571 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.33 % Allowed : 8.22 % 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 (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: 2.47 (0.37), residues: 525 helix: 2.56 (0.26), residues: 386 sheet: -1.32 (1.64), residues: 12 loop : -1.09 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.008 0.001 PHE A 156 TYR 0.006 0.001 TYR A 285 ARG 0.008 0.001 ARG B 24 *********************** 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 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.431 Fit side-chains REVERT: A 20 GLN cc_start: 0.7473 (tt0) cc_final: 0.7085 (pt0) REVERT: A 25 LYS cc_start: 0.8171 (tptp) cc_final: 0.7853 (ttpp) REVERT: A 208 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7237 (mt-10) REVERT: A 464 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6413 (mp0) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 0.1700 time to fit residues: 11.5830 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 : 0.533 ------------------------------------------------------------------------------- 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 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1581 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= 0.202 Angle : 0.508 8.685 5747 Z= 0.247 Chirality : 0.038 0.137 678 Planarity : 0.004 0.047 704 Dihedral : 3.693 17.049 571 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.89 % Allowed : 9.11 % 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: 2.41 (0.36), residues: 525 helix: 2.52 (0.26), residues: 386 sheet: -1.38 (1.61), residues: 12 loop : -1.13 (0.50), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.010 0.001 PHE A 312 TYR 0.006 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 *********************** 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: 4 poor density : 48 time to evaluate : 0.456 Fit side-chains REVERT: A 20 GLN cc_start: 0.7482 (tt0) cc_final: 0.7105 (pt0) REVERT: A 25 LYS cc_start: 0.8226 (tptp) cc_final: 0.7899 (ttpp) REVERT: A 208 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7238 (mt-10) REVERT: A 307 MET cc_start: 0.6699 (mmm) cc_final: 0.6317 (mmm) REVERT: A 464 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6429 (mp0) outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.1871 time to fit residues: 12.0648 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 : 0.440 ------------------------------------------------------------------------------- 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 9 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4246 Z= 0.213 Angle : 0.511 8.888 5747 Z= 0.249 Chirality : 0.038 0.136 678 Planarity : 0.005 0.049 704 Dihedral : 3.704 17.118 571 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 2.39 (0.36), residues: 525 helix: 2.51 (0.26), residues: 386 sheet: -1.43 (1.58), residues: 12 loop : -1.15 (0.50), 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 360 PHE 0.008 0.001 PHE A 156 TYR 0.006 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 *********************** 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 47 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.477 Fit side-chains REVERT: A 20 GLN cc_start: 0.7483 (tt0) cc_final: 0.7110 (pt0) REVERT: A 25 LYS cc_start: 0.8243 (tptp) cc_final: 0.7918 (ttpp) REVERT: A 208 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7242 (mt-10) REVERT: A 307 MET cc_start: 0.6717 (mmm) cc_final: 0.6331 (mmm) REVERT: A 464 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6462 (mp0) outliers start: 3 outliers final: 2 residues processed: 47 average time/residue: 0.1859 time to fit residues: 11.4818 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 : 0.696 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 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 0.040 4246 Z= 0.188 Angle : 0.498 8.389 5747 Z= 0.243 Chirality : 0.038 0.137 678 Planarity : 0.004 0.048 704 Dihedral : 3.673 16.936 571 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 2.55 (0.26), residues: 386 sheet: -1.48 (1.56), 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 0.002 0.001 HIS A 360 PHE 0.010 0.001 PHE A 312 TYR 0.005 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 *********************** 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 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.481 Fit side-chains REVERT: A 20 GLN cc_start: 0.7504 (tt0) cc_final: 0.7144 (pt0) REVERT: A 25 LYS cc_start: 0.8284 (tptp) cc_final: 0.7949 (ttpp) REVERT: A 208 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7233 (mt-10) REVERT: A 307 MET cc_start: 0.6711 (mmm) cc_final: 0.6333 (mmm) REVERT: A 464 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6450 (mp0) outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.2035 time to fit residues: 13.2167 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 : 0.469 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.8980 chunk 48 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 6 optimal weight: 0.0000 overall best weight: 0.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1723 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= 0.159 Angle : 0.487 7.600 5747 Z= 0.238 Chirality : 0.038 0.133 678 Planarity : 0.004 0.046 704 Dihedral : 3.617 16.446 571 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: 2.57 (0.37), residues: 525 helix: 2.63 (0.26), residues: 386 sheet: -1.42 (1.57), residues: 12 loop : -1.04 (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 0.011 0.001 PHE A 156 TYR 0.005 0.001 TYR A 137 ARG 0.010 0.001 ARG B 24 ********************** 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 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.411 Fit side-chains REVERT: A 20 GLN cc_start: 0.7513 (tt0) cc_final: 0.7164 (pt0) REVERT: A 25 LYS cc_start: 0.8292 (tptp) cc_final: 0.7958 (ttpp) REVERT: A 46 CYS cc_start: 0.7482 (p) cc_final: 0.7206 (p) REVERT: A 208 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 307 MET cc_start: 0.6744 (mmm) cc_final: 0.6414 (mmm) REVERT: A 464 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6432 (mp0) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.2026 time to fit residues: 12.6103 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 : 0.477 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.163872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127893 restraints weight = 4771.745| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.04 r_work: 0.3454 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1731 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= 0.184 Angle : 0.495 7.931 5747 Z= 0.241 Chirality : 0.038 0.135 678 Planarity : 0.004 0.046 704 Dihedral : 3.617 16.646 571 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.67 % Allowed : 9.78 % 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: 2.55 (0.37), residues: 525 helix: 2.62 (0.26), residues: 386 sheet: -1.46 (1.56), residues: 12 loop : -1.05 (0.51), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 PHE 0.010 0.001 PHE A 312 TYR 0.005 0.001 TYR A 285 ARG 0.010 0.001 ARG B 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1266.13 seconds wall clock time: 23 minutes 51.45 seconds (1431.45 seconds total)