Starting phenix.real_space_refine on Fri Dec 27 05:23:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3o_44147/12_2024/9b3o_44147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3o_44147/12_2024/9b3o_44147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3o_44147/12_2024/9b3o_44147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3o_44147/12_2024/9b3o_44147.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3o_44147/12_2024/9b3o_44147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3o_44147/12_2024/9b3o_44147.cif" } resolution = 3.18 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= -0.000 sd= 0.038 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 15 5.16 5 C 1770 2.51 5 N 406 2.21 5 O 439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2630 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2630 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 12, 'TRANS': 350} Chain breaks: 3 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Time building chain proxies: 3.07, per 1000 atoms: 1.17 Number of scatterers: 2630 At special positions: 0 Unit cell: (60.225, 69.3, 80.85, 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 15 16.00 O 439 8.00 N 406 7.00 C 1770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 352.3 milliseconds 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 652 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 92.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 4.052A pdb=" N PHE A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY A 20 " --> pdb=" O PHE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 30 removed outlier: 4.217A pdb=" N VAL A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 65 removed outlier: 3.897A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 68 through 88 removed outlier: 3.984A pdb=" N CYS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 119 Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 127 through 152 Proline residue: A 144 - end of helix removed outlier: 3.716A pdb=" N GLU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 175 Processing helix chain 'A' and resid 204 through 233 removed outlier: 3.705A pdb=" N ILE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 266 removed outlier: 6.384A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 288 Processing helix chain 'A' and resid 291 through 302 removed outlier: 3.678A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 321 Proline residue: A 311 - end of helix Processing helix chain 'A' and resid 324 through 354 Proline residue: A 344 - end of helix Processing helix chain 'A' and resid 356 through 390 244 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 784 1.34 - 1.46: 651 1.46 - 1.58: 1230 1.58 - 1.69: 0 1.69 - 1.81: 29 Bond restraints: 2694 Sorted by residual: bond pdb=" CG PRO A 24 " pdb=" CD PRO A 24 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.34e-01 bond pdb=" CG PRO A 311 " pdb=" CD PRO A 311 " ideal model delta sigma weight residual 1.503 1.482 0.021 3.40e-02 8.65e+02 3.96e-01 bond pdb=" CB PRO A 207 " pdb=" CG PRO A 207 " ideal model delta sigma weight residual 1.492 1.462 0.030 5.00e-02 4.00e+02 3.66e-01 bond pdb=" C PHE A 306 " pdb=" O PHE A 306 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.19e-02 7.06e+03 3.63e-01 bond pdb=" CG PRO A 121 " pdb=" CD PRO A 121 " ideal model delta sigma weight residual 1.503 1.483 0.020 3.40e-02 8.65e+02 3.47e-01 ... (remaining 2689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 3607 1.78 - 3.56: 39 3.56 - 5.34: 13 5.34 - 7.13: 3 7.13 - 8.91: 3 Bond angle restraints: 3665 Sorted by residual: angle pdb=" C GLY A 66 " pdb=" N LYS A 67 " pdb=" CA LYS A 67 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.17e+00 angle pdb=" CA LEU A 65 " pdb=" CB LEU A 65 " pdb=" CG LEU A 65 " ideal model delta sigma weight residual 116.30 125.21 -8.91 3.50e+00 8.16e-02 6.48e+00 angle pdb=" CA LEU A 386 " pdb=" CB LEU A 386 " pdb=" CG LEU A 386 " ideal model delta sigma weight residual 116.30 124.56 -8.26 3.50e+00 8.16e-02 5.58e+00 angle pdb=" CB MET A 95 " pdb=" CG MET A 95 " pdb=" SD MET A 95 " ideal model delta sigma weight residual 112.70 119.32 -6.62 3.00e+00 1.11e-01 4.88e+00 angle pdb=" CA LEU A 69 " pdb=" CB LEU A 69 " pdb=" CG LEU A 69 " ideal model delta sigma weight residual 116.30 123.84 -7.54 3.50e+00 8.16e-02 4.64e+00 ... (remaining 3660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.04: 1248 14.04 - 28.07: 177 28.07 - 42.11: 68 42.11 - 56.14: 22 56.14 - 70.18: 5 Dihedral angle restraints: 1520 sinusoidal: 498 harmonic: 1022 Sorted by residual: dihedral pdb=" CA LYS A 67 " pdb=" C LYS A 67 " pdb=" N LYS A 68 " pdb=" CA LYS A 68 " ideal model delta harmonic sigma weight residual 180.00 161.81 18.19 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA LYS A 64 " pdb=" C LYS A 64 " pdb=" N LEU A 65 " pdb=" CA LEU A 65 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " pdb=" CG ARG A 98 " pdb=" CD ARG A 98 " ideal model delta sinusoidal sigma weight residual -60.00 -119.91 59.91 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 269 0.025 - 0.050: 90 0.050 - 0.075: 50 0.075 - 0.100: 27 0.100 - 0.125: 4 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA PRO A 344 " pdb=" N PRO A 344 " pdb=" C PRO A 344 " pdb=" CB PRO A 344 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" CA PRO A 237 " pdb=" N PRO A 237 " pdb=" C PRO A 237 " pdb=" CB PRO A 237 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 2.87e-01 chirality pdb=" CA PRO A 144 " pdb=" N PRO A 144 " pdb=" C PRO A 144 " pdb=" CB PRO A 144 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.65e-01 ... (remaining 437 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 212 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C LEU A 212 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 212 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL A 213 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 343 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO A 344 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 211 " -0.007 2.00e-02 2.50e+03 1.39e-02 1.95e+00 pdb=" C THR A 211 " 0.024 2.00e-02 2.50e+03 pdb=" O THR A 211 " -0.009 2.00e-02 2.50e+03 pdb=" N LEU A 212 " -0.008 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 810 2.82 - 3.34: 2787 3.34 - 3.86: 4536 3.86 - 4.38: 4895 4.38 - 4.90: 8587 Nonbonded interactions: 21615 Sorted by model distance: nonbonded pdb=" O LEU A 30 " pdb=" N LEU A 35 " model vdw 2.295 3.120 nonbonded pdb=" OD1 ASN A 137 " pdb=" NE ARG A 310 " model vdw 2.306 3.120 nonbonded pdb=" O GLY A 101 " pdb=" OG SER A 104 " model vdw 2.314 3.040 nonbonded pdb=" O ILE A 295 " pdb=" OG SER A 299 " model vdw 2.359 3.040 nonbonded pdb=" O ALA A 321 " pdb=" NE2 GLN A 325 " model vdw 2.368 3.120 ... (remaining 21610 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.360 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.550 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 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 : 0.003 0.030 2694 Z= 0.224 Angle : 0.604 8.907 3665 Z= 0.299 Chirality : 0.038 0.125 440 Planarity : 0.004 0.038 448 Dihedral : 16.770 70.178 868 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 34.14 % Favored : 65.86 % 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: 2.11 (0.46), residues: 355 helix: 1.93 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -3.86 (0.78), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 PHE 0.014 0.001 PHE A 47 TYR 0.007 0.001 TYR A 292 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.225 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1153 time to fit residues: 8.1872 Evaluate side-chains 56 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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: 0.8372 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2694 Z= 0.264 Angle : 0.572 8.121 3665 Z= 0.287 Chirality : 0.038 0.130 440 Planarity : 0.004 0.039 448 Dihedral : 3.793 17.530 374 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.41 % Allowed : 32.13 % Favored : 65.46 % 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: 2.42 (0.46), residues: 355 helix: 2.05 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.70 (0.93), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 201 HIS 0.002 0.001 HIS A 379 PHE 0.014 0.002 PHE A 47 TYR 0.009 0.001 TYR A 278 ARG 0.002 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.288 Fit side-chains REVERT: A 324 ARG cc_start: 0.6960 (mmt180) cc_final: 0.6721 (mtp85) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.1035 time to fit residues: 8.5913 Evaluate side-chains 61 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.0870 chunk 27 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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: 0.8355 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2694 Z= 0.221 Angle : 0.546 8.054 3665 Z= 0.269 Chirality : 0.038 0.126 440 Planarity : 0.004 0.037 448 Dihedral : 3.783 17.644 374 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.42 % Allowed : 29.72 % Favored : 65.86 % 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: 2.56 (0.46), residues: 355 helix: 2.14 (0.29), residues: 325 sheet: None (None), residues: 0 loop : -3.56 (0.95), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 PHE 0.012 0.001 PHE A 47 TYR 0.013 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.289 Fit side-chains REVERT: A 8 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8343 (mp) REVERT: A 324 ARG cc_start: 0.7001 (mmt180) cc_final: 0.6749 (mtp85) outliers start: 11 outliers final: 4 residues processed: 67 average time/residue: 0.1023 time to fit residues: 8.8077 Evaluate side-chains 64 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8365 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2694 Z= 0.240 Angle : 0.561 8.050 3665 Z= 0.276 Chirality : 0.038 0.138 440 Planarity : 0.004 0.037 448 Dihedral : 3.775 17.310 374 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.02 % Allowed : 32.53 % Favored : 63.45 % 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: 2.56 (0.46), residues: 355 helix: 2.13 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.67 (1.00), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.013 0.001 PHE A 47 TYR 0.010 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.292 Fit side-chains REVERT: A 8 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 65 LEU cc_start: 0.6355 (mp) cc_final: 0.6081 (tt) REVERT: A 324 ARG cc_start: 0.7069 (mmt180) cc_final: 0.6808 (mtp85) outliers start: 10 outliers final: 8 residues processed: 66 average time/residue: 0.1096 time to fit residues: 9.2308 Evaluate side-chains 67 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 17 optimal weight: 0.0570 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.0000 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.3102 ------------------------------------------------------------------------------- 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: 0.8329 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2694 Z= 0.184 Angle : 0.539 7.708 3665 Z= 0.263 Chirality : 0.037 0.149 440 Planarity : 0.004 0.035 448 Dihedral : 3.685 16.994 374 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.42 % Allowed : 32.13 % Favored : 63.45 % 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: 2.75 (0.46), residues: 355 helix: 2.25 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.55 (1.02), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.014 0.001 PHE A 327 TYR 0.012 0.001 TYR A 228 ARG 0.001 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.287 Fit side-chains REVERT: A 8 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 157 MET cc_start: 0.7915 (tpt) cc_final: 0.7532 (tpp) REVERT: A 324 ARG cc_start: 0.7006 (mmt180) cc_final: 0.6730 (mtp85) outliers start: 11 outliers final: 5 residues processed: 69 average time/residue: 0.1094 time to fit residues: 9.4980 Evaluate side-chains 65 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.8339 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2694 Z= 0.205 Angle : 0.539 7.364 3665 Z= 0.265 Chirality : 0.038 0.157 440 Planarity : 0.004 0.035 448 Dihedral : 3.675 16.837 374 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.21 % Allowed : 32.53 % Favored : 64.26 % 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: 2.74 (0.46), residues: 355 helix: 2.26 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.70 (0.93), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.011 0.001 PHE A 47 TYR 0.011 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.268 Fit side-chains REVERT: A 8 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8382 (mp) REVERT: A 157 MET cc_start: 0.7897 (tpt) cc_final: 0.7501 (tpp) REVERT: A 324 ARG cc_start: 0.6986 (mmt180) cc_final: 0.6711 (mtp85) outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.1080 time to fit residues: 8.9839 Evaluate side-chains 62 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.8331 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2694 Z= 0.201 Angle : 0.545 7.567 3665 Z= 0.265 Chirality : 0.038 0.153 440 Planarity : 0.004 0.034 448 Dihedral : 3.655 16.320 374 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.42 % Allowed : 30.92 % Favored : 64.66 % 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: 2.81 (0.46), residues: 355 helix: 2.30 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.65 (0.96), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.012 0.001 PHE A 47 TYR 0.013 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.278 Fit side-chains REVERT: A 8 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 324 ARG cc_start: 0.6984 (mmt180) cc_final: 0.6712 (mtp85) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 0.1044 time to fit residues: 8.9124 Evaluate side-chains 64 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8354 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2694 Z= 0.232 Angle : 0.583 10.315 3665 Z= 0.280 Chirality : 0.039 0.150 440 Planarity : 0.004 0.035 448 Dihedral : 3.715 16.380 374 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.21 % Allowed : 32.53 % Favored : 64.26 % 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: 2.71 (0.46), residues: 355 helix: 2.24 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.79 (0.91), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 PHE 0.020 0.001 PHE A 266 TYR 0.014 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.245 Fit side-chains REVERT: A 324 ARG cc_start: 0.7010 (mmt180) cc_final: 0.6780 (mtp85) outliers start: 8 outliers final: 6 residues processed: 64 average time/residue: 0.0998 time to fit residues: 8.1918 Evaluate side-chains 61 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8350 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2694 Z= 0.235 Angle : 0.591 9.944 3665 Z= 0.281 Chirality : 0.039 0.149 440 Planarity : 0.004 0.035 448 Dihedral : 3.734 16.272 374 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.41 % Allowed : 32.13 % Favored : 65.46 % 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: 2.71 (0.46), residues: 355 helix: 2.23 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.73 (0.94), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.026 0.002 PHE A 327 TYR 0.014 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.390 Fit side-chains REVERT: A 324 ARG cc_start: 0.7044 (mmt180) cc_final: 0.6787 (mtp85) outliers start: 6 outliers final: 6 residues processed: 61 average time/residue: 0.1086 time to fit residues: 8.4783 Evaluate side-chains 62 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 235 TYR Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 2694 Z= 0.254 Angle : 0.593 10.009 3665 Z= 0.286 Chirality : 0.039 0.150 440 Planarity : 0.004 0.035 448 Dihedral : 3.782 16.795 374 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.81 % Allowed : 31.73 % Favored : 65.46 % 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: 2.66 (0.46), residues: 355 helix: 2.21 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.79 (0.92), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 201 HIS 0.002 0.000 HIS A 379 PHE 0.024 0.002 PHE A 327 TYR 0.017 0.001 TYR A 228 ARG 0.001 0.000 ARG A 324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.224 Fit side-chains REVERT: A 324 ARG cc_start: 0.7058 (mmt180) cc_final: 0.6801 (mtp85) outliers start: 7 outliers final: 6 residues processed: 61 average time/residue: 0.1092 time to fit residues: 8.4910 Evaluate side-chains 60 residues out of total 295 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.139433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115085 restraints weight = 3953.782| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.79 r_work: 0.3262 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2694 Z= 0.244 Angle : 0.592 9.876 3665 Z= 0.284 Chirality : 0.039 0.150 440 Planarity : 0.004 0.035 448 Dihedral : 3.779 16.970 374 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.81 % Allowed : 32.93 % Favored : 64.26 % 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: 2.69 (0.46), residues: 355 helix: 2.23 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -3.81 (0.92), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 201 HIS 0.001 0.000 HIS A 379 PHE 0.024 0.002 PHE A 327 TYR 0.037 0.002 TYR A 228 ARG 0.001 0.000 ARG A 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1037.24 seconds wall clock time: 19 minutes 23.50 seconds (1163.50 seconds total)