Starting phenix.real_space_refine on Fri Dec 27 09:30:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g9x_51160/12_2024/9g9x_51160.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g9x_51160/12_2024/9g9x_51160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g9x_51160/12_2024/9g9x_51160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g9x_51160/12_2024/9g9x_51160.map" model { file = "/net/cci-nas-00/data/ceres_data/9g9x_51160/12_2024/9g9x_51160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g9x_51160/12_2024/9g9x_51160.cif" } resolution = 3.13 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= 0.001 sd= 0.042 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: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 22 5.16 5 C 2630 2.51 5 N 622 2.21 5 O 678 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: 3955 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1906 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {' K': 3, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: B Time building chain proxies: 3.59, per 1000 atoms: 0.91 Number of scatterers: 3955 At special positions: 0 Unit cell: (60.736, 70.72, 89.856, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 22 16.00 O 678 8.00 N 622 7.00 C 2630 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: 1.15 Conformation dependent library (CDL) restraints added in 470.3 milliseconds 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 908 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 1 through 52 removed outlier: 4.237A pdb=" N ASN A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Proline residue: A 33 - end of helix removed outlier: 3.598A pdb=" N GLN A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 143 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 182 removed outlier: 3.713A pdb=" N LEU A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 removed outlier: 3.539A pdb=" N THR A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 4.113A pdb=" N THR A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'B' and resid 2 through 52 removed outlier: 5.601A pdb=" N GLU B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Proline residue: B 33 - end of helix removed outlier: 3.597A pdb=" N GLN B 46 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 143 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 182 removed outlier: 3.712A pdb=" N LEU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 removed outlier: 3.539A pdb=" N THR B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 removed outlier: 4.115A pdb=" N THR B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 252 314 hydrogen bonds defined for protein. 924 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: 1.17 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 612 1.32 - 1.44: 1146 1.44 - 1.56: 2262 1.56 - 1.68: 0 1.68 - 1.80: 34 Bond restraints: 4054 Sorted by residual: bond pdb=" CBC Y01 B 302 " pdb=" OAW Y01 B 302 " ideal model delta sigma weight residual 1.437 1.467 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CBC Y01 A 302 " pdb=" OAW Y01 A 302 " ideal model delta sigma weight residual 1.437 1.467 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" CB ILE B 200 " pdb=" CG2 ILE B 200 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CB ILE A 200 " pdb=" CG2 ILE A 200 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.60e+00 bond pdb=" CAL Y01 A 302 " pdb=" CAX Y01 A 302 " ideal model delta sigma weight residual 1.540 1.516 0.024 2.00e-02 2.50e+03 1.49e+00 ... (remaining 4049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 4924 1.08 - 2.17: 496 2.17 - 3.25: 86 3.25 - 4.34: 12 4.34 - 5.42: 16 Bond angle restraints: 5534 Sorted by residual: angle pdb=" N ARG A 79 " pdb=" CA ARG A 79 " pdb=" C ARG A 79 " ideal model delta sigma weight residual 108.74 105.16 3.58 1.38e+00 5.25e-01 6.75e+00 angle pdb=" N ARG B 79 " pdb=" CA ARG B 79 " pdb=" C ARG B 79 " ideal model delta sigma weight residual 108.74 105.16 3.58 1.38e+00 5.25e-01 6.74e+00 angle pdb=" N GLY A 117 " pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 113.18 118.60 -5.42 2.37e+00 1.78e-01 5.24e+00 angle pdb=" N GLY B 117 " pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 113.18 118.57 -5.39 2.37e+00 1.78e-01 5.18e+00 angle pdb=" N GLU B 32 " pdb=" CA GLU B 32 " pdb=" C GLU B 32 " ideal model delta sigma weight residual 109.81 114.60 -4.79 2.21e+00 2.05e-01 4.69e+00 ... (remaining 5529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 2360 17.21 - 34.41: 132 34.41 - 51.62: 22 51.62 - 68.82: 4 68.82 - 86.02: 2 Dihedral angle restraints: 2520 sinusoidal: 1100 harmonic: 1420 Sorted by residual: dihedral pdb=" CA HIS A 98 " pdb=" C HIS A 98 " pdb=" N ALA A 99 " pdb=" CA ALA A 99 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N ALA B 99 " pdb=" CA ALA B 99 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA ASP A 204 " pdb=" C ASP A 204 " pdb=" N TYR A 205 " pdb=" CA TYR A 205 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 2517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 277 0.032 - 0.063: 231 0.063 - 0.095: 99 0.095 - 0.126: 31 0.126 - 0.158: 12 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA LEU A 208 " pdb=" N LEU A 208 " pdb=" C LEU A 208 " pdb=" CB LEU A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA LEU B 208 " pdb=" N LEU B 208 " pdb=" C LEU B 208 " pdb=" CB LEU B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA THR B 93 " pdb=" N THR B 93 " pdb=" C THR B 93 " pdb=" CB THR B 93 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 647 not shown) Planarity restraints: 668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 173 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.68e+00 pdb=" C ILE A 173 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE A 173 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A 174 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 20 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C LEU B 20 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU B 20 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 21 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 173 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C ILE B 173 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE B 173 " 0.016 2.00e-02 2.50e+03 pdb=" N GLY B 174 " 0.015 2.00e-02 2.50e+03 ... (remaining 665 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.95: 1809 2.95 - 3.50: 4785 3.50 - 4.05: 7006 4.05 - 4.59: 10684 4.59 - 5.14: 14537 Nonbonded interactions: 38821 Sorted by model distance: nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.404 3.040 nonbonded pdb=" O THR B 198 " pdb=" OG1 THR B 199 " model vdw 2.404 3.040 nonbonded pdb=" OH TYR B 96 " pdb=" OG1 THR B 196 " model vdw 2.420 3.040 nonbonded pdb=" OH TYR A 96 " pdb=" OG1 THR A 196 " model vdw 2.421 3.040 nonbonded pdb=" OE2 GLU A 182 " pdb=" OH TYR A 220 " model vdw 2.423 3.040 ... (remaining 38816 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 252 or resid 301 through 302)) selection = chain 'B' } 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: 1.320 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 : 0.007 0.045 4054 Z= 0.461 Angle : 0.749 5.423 5534 Z= 0.442 Chirality : 0.052 0.158 650 Planarity : 0.006 0.026 668 Dihedral : 11.299 86.025 1612 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -1.06 (0.34), residues: 480 helix: -0.43 (0.23), residues: 396 sheet: None (None), residues: 0 loop : -1.24 (0.70), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 78 HIS 0.001 0.001 HIS B 180 PHE 0.019 0.002 PHE A 202 TYR 0.023 0.004 TYR A 85 ARG 0.004 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.407 Fit side-chains REVERT: A 44 ARG cc_start: 0.6659 (ttt90) cc_final: 0.6434 (ttt-90) REVERT: A 130 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6543 (tm-30) REVERT: A 135 LEU cc_start: 0.7284 (tp) cc_final: 0.6593 (mp) REVERT: A 249 MET cc_start: 0.5337 (ttt) cc_final: 0.5109 (ttp) REVERT: B 44 ARG cc_start: 0.6659 (ttt90) cc_final: 0.6435 (ttt-90) REVERT: B 130 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6552 (tm-30) REVERT: B 135 LEU cc_start: 0.7280 (tp) cc_final: 0.6592 (mp) REVERT: B 249 MET cc_start: 0.5342 (ttt) cc_final: 0.5115 (ttp) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2101 time to fit residues: 16.6663 Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN B 126 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.201 Angle : 0.516 4.964 5534 Z= 0.279 Chirality : 0.039 0.157 650 Planarity : 0.003 0.016 668 Dihedral : 5.450 50.527 818 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.55 % Allowed : 4.12 % Favored : 94.33 % 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: 2.46 (0.39), residues: 480 helix: 1.93 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 0.42 (0.79), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 184 HIS 0.001 0.000 HIS B 72 PHE 0.012 0.001 PHE A 109 TYR 0.014 0.001 TYR A 85 ARG 0.004 0.000 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.423 Fit side-chains REVERT: A 135 LEU cc_start: 0.7177 (tp) cc_final: 0.6523 (mp) REVERT: B 135 LEU cc_start: 0.7183 (tp) cc_final: 0.6535 (mp) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.2083 time to fit residues: 13.6555 Evaluate side-chains 46 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.0470 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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: 0.7327 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4054 Z= 0.233 Angle : 0.504 5.071 5534 Z= 0.270 Chirality : 0.040 0.153 650 Planarity : 0.003 0.018 668 Dihedral : 5.460 49.247 818 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.55 % Allowed : 6.19 % Favored : 92.27 % 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: 3.31 (0.40), residues: 480 helix: 2.44 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 1.17 (0.85), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 78 HIS 0.001 0.000 HIS A 98 PHE 0.010 0.001 PHE A 109 TYR 0.012 0.001 TYR B 85 ARG 0.002 0.000 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.506 Fit side-chains REVERT: A 135 LEU cc_start: 0.7284 (tp) cc_final: 0.6628 (mp) REVERT: B 135 LEU cc_start: 0.7276 (tp) cc_final: 0.6624 (mp) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.1994 time to fit residues: 14.0667 Evaluate side-chains 46 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7360 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4054 Z= 0.284 Angle : 0.519 5.135 5534 Z= 0.278 Chirality : 0.041 0.148 650 Planarity : 0.003 0.017 668 Dihedral : 5.571 48.237 818 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.03 % Allowed : 7.22 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.40 (0.40), residues: 480 helix: 2.47 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 1.36 (0.87), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 78 HIS 0.001 0.000 HIS A 98 PHE 0.010 0.001 PHE B 16 TYR 0.011 0.001 TYR A 85 ARG 0.004 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.393 Fit side-chains REVERT: A 135 LEU cc_start: 0.7250 (tp) cc_final: 0.6596 (mp) REVERT: B 135 LEU cc_start: 0.7244 (tp) cc_final: 0.6593 (mp) outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.2069 time to fit residues: 12.6070 Evaluate side-chains 50 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 133 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.195 Angle : 0.471 5.063 5534 Z= 0.250 Chirality : 0.038 0.144 650 Planarity : 0.003 0.017 668 Dihedral : 5.385 46.527 818 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.29 % Allowed : 7.99 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.72 (0.40), residues: 480 helix: 2.77 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.11 (0.83), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.001 0.000 HIS B 98 PHE 0.010 0.001 PHE A 109 TYR 0.009 0.001 TYR B 85 ARG 0.004 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.334 Fit side-chains REVERT: A 135 LEU cc_start: 0.7264 (tp) cc_final: 0.6663 (mp) REVERT: B 135 LEU cc_start: 0.7259 (tp) cc_final: 0.6662 (mp) outliers start: 5 outliers final: 4 residues processed: 55 average time/residue: 0.2058 time to fit residues: 13.7711 Evaluate side-chains 49 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7334 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4054 Z= 0.214 Angle : 0.481 5.116 5534 Z= 0.256 Chirality : 0.039 0.144 650 Planarity : 0.003 0.027 668 Dihedral : 5.371 45.247 818 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.06 % Allowed : 6.96 % Favored : 90.98 % 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: 3.87 (0.40), residues: 480 helix: 2.88 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.12 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 PHE 0.009 0.001 PHE A 109 TYR 0.009 0.001 TYR B 113 ARG 0.007 0.001 ARG A 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.312 Fit side-chains REVERT: A 135 LEU cc_start: 0.7264 (tp) cc_final: 0.6622 (mp) REVERT: B 135 LEU cc_start: 0.7274 (tp) cc_final: 0.6640 (mp) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.2004 time to fit residues: 12.4573 Evaluate side-chains 52 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7330 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.204 Angle : 0.482 5.107 5534 Z= 0.255 Chirality : 0.038 0.141 650 Planarity : 0.003 0.025 668 Dihedral : 5.281 42.522 818 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.55 % Allowed : 7.99 % Favored : 90.46 % 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: 4.00 (0.39), residues: 480 helix: 2.98 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 1.08 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS B 98 PHE 0.009 0.001 PHE A 109 TYR 0.009 0.001 TYR A 113 ARG 0.006 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.389 Fit side-chains REVERT: A 135 LEU cc_start: 0.7248 (tp) cc_final: 0.6633 (mp) REVERT: B 135 LEU cc_start: 0.7246 (tp) cc_final: 0.6632 (mp) outliers start: 6 outliers final: 6 residues processed: 51 average time/residue: 0.2120 time to fit residues: 13.2558 Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7326 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.196 Angle : 0.474 5.100 5534 Z= 0.250 Chirality : 0.038 0.139 650 Planarity : 0.003 0.024 668 Dihedral : 5.140 38.778 818 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.55 % Allowed : 7.73 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.07 (0.39), residues: 480 helix: 3.06 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.99 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.001 0.000 HIS B 180 PHE 0.009 0.001 PHE B 109 TYR 0.009 0.001 TYR A 113 ARG 0.006 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.373 Fit side-chains REVERT: A 135 LEU cc_start: 0.7222 (tp) cc_final: 0.6580 (mp) REVERT: B 135 LEU cc_start: 0.7244 (tp) cc_final: 0.6625 (mp) outliers start: 6 outliers final: 6 residues processed: 51 average time/residue: 0.2138 time to fit residues: 13.3050 Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 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: 0.7325 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.192 Angle : 0.475 5.091 5534 Z= 0.250 Chirality : 0.038 0.138 650 Planarity : 0.003 0.024 668 Dihedral : 5.049 37.887 818 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.80 % Allowed : 7.73 % Favored : 90.46 % 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: 4.11 (0.39), residues: 480 helix: 3.10 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.92 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS A 98 PHE 0.009 0.001 PHE A 109 TYR 0.009 0.001 TYR A 113 ARG 0.005 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.390 Fit side-chains REVERT: A 135 LEU cc_start: 0.7234 (tp) cc_final: 0.6612 (mp) REVERT: B 135 LEU cc_start: 0.7229 (tp) cc_final: 0.6607 (mp) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 0.2073 time to fit residues: 13.3819 Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7333 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4054 Z= 0.212 Angle : 0.484 5.125 5534 Z= 0.256 Chirality : 0.038 0.136 650 Planarity : 0.003 0.022 668 Dihedral : 5.071 37.479 818 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.55 % Allowed : 8.25 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.09 (0.39), residues: 480 helix: 3.09 (0.25), residues: 390 sheet: None (None), residues: 0 loop : 0.89 (0.79), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.001 0.000 HIS A 98 PHE 0.009 0.001 PHE A 109 TYR 0.009 0.001 TYR B 113 ARG 0.005 0.001 ARG A 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 960 Ramachandran restraints generated. 480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.366 Fit side-chains REVERT: A 135 LEU cc_start: 0.7250 (tp) cc_final: 0.6631 (mp) REVERT: B 135 LEU cc_start: 0.7247 (tp) cc_final: 0.6629 (mp) outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 0.1983 time to fit residues: 12.8598 Evaluate side-chains 54 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 247 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.0770 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.180178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119078 restraints weight = 3834.202| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.32 r_work: 0.3177 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4054 Z= 0.136 Angle : 0.493 9.941 5534 Z= 0.242 Chirality : 0.036 0.140 650 Planarity : 0.003 0.022 668 Dihedral : 4.786 35.784 818 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.03 % Allowed : 8.76 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.24 (0.39), residues: 480 helix: 3.23 (0.26), residues: 390 sheet: None (None), residues: 0 loop : 0.78 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 184 HIS 0.000 0.000 HIS B 72 PHE 0.009 0.001 PHE A 109 TYR 0.007 0.001 TYR B 113 ARG 0.005 0.001 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1139.85 seconds wall clock time: 22 minutes 14.38 seconds (1334.38 seconds total)