Starting phenix.real_space_refine on Fri Dec 27 06:47:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnn_34917/12_2024/8hnn_34917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnn_34917/12_2024/8hnn_34917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnn_34917/12_2024/8hnn_34917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnn_34917/12_2024/8hnn_34917.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnn_34917/12_2024/8hnn_34917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnn_34917/12_2024/8hnn_34917.cif" } resolution = 3.6 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= 0.080 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 S 17 5.16 5 Cl 2 4.86 5 C 1993 2.51 5 N 527 2.21 5 O 524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3063 Number of models: 1 Model: "" Number of chains: 3 Chain: "N" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 852 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2150 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'43I': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.97, per 1000 atoms: 0.97 Number of scatterers: 3063 At special positions: 0 Unit cell: (71.4, 52.7, 123.25, 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) Cl 2 17.00 S 17 16.00 O 524 8.00 N 527 7.00 C 1993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " distance=2.03 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: 0.86 Conformation dependent library (CDL) restraints added in 367.9 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 4 sheets defined 56.6% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 55 through 80 Processing helix chain 'R' and resid 86 through 105 removed outlier: 3.851A pdb=" N ASP R 99 " --> pdb=" O LEU R 95 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU R 101 " --> pdb=" O VAL R 97 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 115 removed outlier: 3.909A pdb=" N TRP R 109 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 154 removed outlier: 4.064A pdb=" N PHE R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR R 136 " --> pdb=" O ASN R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 189 Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 211 through 244 Proline residue: R 227 - end of helix removed outlier: 3.889A pdb=" N SER R 244 " --> pdb=" O ALA R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 291 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 300 through 329 removed outlier: 4.207A pdb=" N CYS R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix removed outlier: 3.675A pdb=" N VAL R 329 " --> pdb=" O LEU R 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 4 through 9 Processing sheet with id=AA2, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.842A pdb=" N TRP N 38 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER N 52 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET N 36 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU N 33 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG N 102 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP N 35 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.842A pdb=" N TRP N 38 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER N 52 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET N 36 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU N 33 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG N 102 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP N 35 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 190 through 191 removed outlier: 4.145A pdb=" N SER R 191 " --> pdb=" O GLN R 204 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN R 204 " --> pdb=" O SER R 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 205 hydrogen bonds defined for protein. 591 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: 0.88 Time building geometry restraints manager: 0.93 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: 972 1.34 - 1.46: 711 1.46 - 1.58: 1424 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3131 Sorted by residual: bond pdb=" C19 43I R 401 " pdb=" C22 43I R 401 " ideal model delta sigma weight residual 1.437 1.379 0.058 2.00e-02 2.50e+03 8.44e+00 bond pdb=" C10 43I R 401 " pdb=" C11 43I R 401 " ideal model delta sigma weight residual 1.524 1.488 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C22 43I R 401 " pdb="CL2 43I R 401 " ideal model delta sigma weight residual 1.763 1.730 0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C23 43I R 401 " pdb=" N6 43I R 401 " ideal model delta sigma weight residual 1.347 1.318 0.029 2.00e-02 2.50e+03 2.08e+00 bond pdb=" C14 43I R 401 " pdb=" C15 43I R 401 " ideal model delta sigma weight residual 1.388 1.359 0.029 2.00e-02 2.50e+03 2.07e+00 ... (remaining 3126 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4138 1.61 - 3.21: 101 3.21 - 4.82: 17 4.82 - 6.42: 14 6.42 - 8.03: 2 Bond angle restraints: 4272 Sorted by residual: angle pdb=" C8 43I R 401 " pdb=" C7 43I R 401 " pdb=" N2 43I R 401 " ideal model delta sigma weight residual 115.50 123.35 -7.85 3.00e+00 1.11e-01 6.84e+00 angle pdb=" C LEU R 225 " pdb=" N LEU R 226 " pdb=" CA LEU R 226 " ideal model delta sigma weight residual 121.80 115.59 6.21 2.44e+00 1.68e-01 6.47e+00 angle pdb=" C HIS R 94 " pdb=" N LEU R 95 " pdb=" CA LEU R 95 " ideal model delta sigma weight residual 121.58 117.00 4.58 1.95e+00 2.63e-01 5.52e+00 angle pdb=" CA LEU R 95 " pdb=" CB LEU R 95 " pdb=" CG LEU R 95 " ideal model delta sigma weight residual 116.30 124.33 -8.03 3.50e+00 8.16e-02 5.26e+00 angle pdb=" C19 43I R 401 " pdb=" N1 43I R 401 " pdb=" C5 43I R 401 " ideal model delta sigma weight residual 118.45 124.82 -6.37 3.00e+00 1.11e-01 4.50e+00 ... (remaining 4267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.68: 1847 32.68 - 65.37: 34 65.37 - 98.05: 4 98.05 - 130.74: 6 130.74 - 163.42: 2 Dihedral angle restraints: 1893 sinusoidal: 765 harmonic: 1128 Sorted by residual: dihedral pdb=" CB CYS R 124 " pdb=" SG CYS R 124 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual 93.00 -178.02 -88.98 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" C11 43I R 401 " pdb=" C7 43I R 401 " pdb=" N2 43I R 401 " pdb=" C3 43I R 401 " ideal model delta sinusoidal sigma weight residual 198.38 34.96 163.42 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C11 43I R 401 " pdb=" C7 43I R 401 " pdb=" N2 43I R 401 " pdb=" C6 43I R 401 " ideal model delta sinusoidal sigma weight residual 63.87 -94.22 158.09 1 3.00e+01 1.11e-03 2.06e+01 ... (remaining 1890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.818: 507 0.818 - 1.635: 0 1.635 - 2.453: 0 2.453 - 3.271: 0 3.271 - 4.089: 1 Chirality restraints: 508 Sorted by residual: chirality pdb=" C7 43I R 401 " pdb=" C11 43I R 401 " pdb=" C8 43I R 401 " pdb=" N2 43I R 401 " both_signs ideal model delta sigma weight residual False 2.33 -1.76 4.09 2.00e-01 2.50e+01 4.18e+02 chirality pdb=" CG LEU R 321 " pdb=" CB LEU R 321 " pdb=" CD1 LEU R 321 " pdb=" CD2 LEU R 321 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LEU R 106 " pdb=" N LEU R 106 " pdb=" C LEU R 106 " pdb=" CB LEU R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 505 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 222 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ALA R 222 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA R 222 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY R 223 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 196 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C GLU R 196 " 0.022 2.00e-02 2.50e+03 pdb=" O GLU R 196 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG R 197 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 135 " 0.010 2.00e-02 2.50e+03 7.74e-03 1.05e+00 pdb=" CG PHE R 135 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE R 135 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 135 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 135 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 135 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 135 " 0.004 2.00e-02 2.50e+03 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 318 2.74 - 3.28: 2951 3.28 - 3.82: 4849 3.82 - 4.36: 5235 4.36 - 4.90: 9449 Nonbonded interactions: 22802 Sorted by model distance: nonbonded pdb=" O ALA R 273 " pdb=" OG1 THR R 277 " model vdw 2.206 3.040 nonbonded pdb=" NZ LYS R 125 " pdb=" O LEU R 190 " model vdw 2.272 3.120 nonbonded pdb=" OG SER N 9 " pdb=" OG SER N 23 " model vdw 2.287 3.040 nonbonded pdb=" O GLN R 158 " pdb=" NH1 ARG R 162 " model vdw 2.317 3.120 nonbonded pdb=" O GLU R 253 " pdb=" ND2 ASN R 257 " model vdw 2.351 3.120 ... (remaining 22797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.830 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3131 Z= 0.251 Angle : 0.688 8.025 4272 Z= 0.338 Chirality : 0.186 4.089 508 Planarity : 0.003 0.021 521 Dihedral : 17.325 163.420 1165 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.62 (0.44), residues: 386 helix: 1.05 (0.35), residues: 217 sheet: 2.72 (0.80), residues: 44 loop : -1.64 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.010 0.001 TYR R 233 ARG 0.002 0.000 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 101 TYR cc_start: 0.8965 (p90) cc_final: 0.8449 (p90) REVERT: N 113 TRP cc_start: 0.8339 (m100) cc_final: 0.7985 (m-90) REVERT: R 254 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7233 (ttpt) REVERT: R 274 LEU cc_start: 0.8379 (tt) cc_final: 0.8176 (tp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1220 time to fit residues: 9.3935 Evaluate side-chains 56 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.0270 chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN R 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3131 Z= 0.185 Angle : 0.627 8.419 4272 Z= 0.298 Chirality : 0.039 0.119 508 Planarity : 0.003 0.021 521 Dihedral : 13.061 139.782 538 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.88 % Allowed : 8.97 % Favored : 88.14 % 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: 0.96 (0.44), residues: 386 helix: 1.29 (0.36), residues: 217 sheet: 2.21 (0.77), residues: 49 loop : -1.28 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.020 0.002 PHE R 328 TYR 0.009 0.001 TYR R 233 ARG 0.002 0.000 ARG R 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 36 MET cc_start: 0.7856 (mtt) cc_final: 0.7571 (mmm) REVERT: N 113 TRP cc_start: 0.8307 (m100) cc_final: 0.7930 (m-90) REVERT: R 189 PHE cc_start: 0.8019 (m-10) cc_final: 0.7770 (m-10) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.1193 time to fit residues: 9.0643 Evaluate side-chains 60 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 243 LYS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3131 Z= 0.212 Angle : 0.628 9.318 4272 Z= 0.303 Chirality : 0.039 0.124 508 Planarity : 0.003 0.021 521 Dihedral : 12.607 139.925 538 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.21 % Allowed : 15.06 % Favored : 81.73 % 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: 1.00 (0.44), residues: 386 helix: 1.35 (0.37), residues: 217 sheet: 2.16 (0.77), residues: 49 loop : -1.29 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 106 HIS 0.005 0.001 HIS R 318 PHE 0.019 0.002 PHE R 187 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 36 MET cc_start: 0.7823 (mtt) cc_final: 0.7597 (mmm) REVERT: N 113 TRP cc_start: 0.8322 (m100) cc_final: 0.7904 (m-90) REVERT: R 189 PHE cc_start: 0.8078 (m-10) cc_final: 0.7757 (m-10) outliers start: 10 outliers final: 7 residues processed: 58 average time/residue: 0.1100 time to fit residues: 8.3723 Evaluate side-chains 62 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.0570 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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: 0.7411 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3131 Z= 0.200 Angle : 0.608 9.279 4272 Z= 0.294 Chirality : 0.038 0.122 508 Planarity : 0.003 0.020 521 Dihedral : 12.418 140.588 538 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.49 % Allowed : 16.99 % Favored : 78.53 % 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: 1.13 (0.44), residues: 386 helix: 1.43 (0.37), residues: 217 sheet: 2.35 (0.76), residues: 49 loop : -1.26 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.016 0.001 PHE R 135 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8346 (m100) cc_final: 0.7937 (m-90) REVERT: R 187 PHE cc_start: 0.8166 (m-80) cc_final: 0.7776 (m-80) REVERT: R 189 PHE cc_start: 0.8054 (m-10) cc_final: 0.7711 (m-10) outliers start: 14 outliers final: 9 residues processed: 61 average time/residue: 0.1070 time to fit residues: 8.5599 Evaluate side-chains 65 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 0.1980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 75 ASN R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3131 Z= 0.279 Angle : 0.683 9.330 4272 Z= 0.329 Chirality : 0.040 0.135 508 Planarity : 0.003 0.019 521 Dihedral : 12.298 141.605 538 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.53 % Allowed : 18.91 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.44), residues: 386 helix: 1.21 (0.36), residues: 218 sheet: 2.20 (0.75), residues: 49 loop : -1.29 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.018 0.002 PHE R 135 TYR 0.013 0.001 TYR R 235 ARG 0.002 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8320 (m100) cc_final: 0.7913 (m-90) REVERT: R 189 PHE cc_start: 0.8124 (m-10) cc_final: 0.7776 (m-10) outliers start: 11 outliers final: 11 residues processed: 60 average time/residue: 0.1186 time to fit residues: 9.4431 Evaluate side-chains 64 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3131 Z= 0.214 Angle : 0.634 9.414 4272 Z= 0.304 Chirality : 0.039 0.123 508 Planarity : 0.003 0.020 521 Dihedral : 12.129 146.031 538 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.45 % Allowed : 18.27 % Favored : 76.28 % 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: 1.00 (0.44), residues: 386 helix: 1.33 (0.36), residues: 218 sheet: 2.15 (0.74), residues: 49 loop : -1.25 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.016 0.001 PHE R 135 TYR 0.013 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8305 (m100) cc_final: 0.7910 (m-90) REVERT: R 189 PHE cc_start: 0.8084 (m-10) cc_final: 0.7732 (m-10) outliers start: 17 outliers final: 13 residues processed: 61 average time/residue: 0.1101 time to fit residues: 8.7476 Evaluate side-chains 65 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3131 Z= 0.200 Angle : 0.624 9.505 4272 Z= 0.300 Chirality : 0.038 0.121 508 Planarity : 0.003 0.021 521 Dihedral : 12.238 151.787 538 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.49 % Allowed : 19.87 % Favored : 75.64 % 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: 1.05 (0.44), residues: 386 helix: 1.39 (0.37), residues: 218 sheet: 2.22 (0.74), residues: 49 loop : -1.30 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.016 0.001 PHE R 135 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8319 (m100) cc_final: 0.7921 (m-90) REVERT: R 189 PHE cc_start: 0.8041 (m-10) cc_final: 0.7680 (m-10) outliers start: 14 outliers final: 12 residues processed: 60 average time/residue: 0.1204 time to fit residues: 9.3694 Evaluate side-chains 65 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7434 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3131 Z= 0.184 Angle : 0.646 12.719 4272 Z= 0.301 Chirality : 0.038 0.116 508 Planarity : 0.003 0.021 521 Dihedral : 12.325 154.974 538 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.49 % Allowed : 20.83 % Favored : 74.68 % 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: 1.11 (0.44), residues: 386 helix: 1.45 (0.37), residues: 218 sheet: 2.30 (0.75), residues: 49 loop : -1.31 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.022 0.002 PHE R 187 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8306 (m100) cc_final: 0.7914 (m-90) REVERT: R 189 PHE cc_start: 0.8020 (m-10) cc_final: 0.7654 (m-10) outliers start: 14 outliers final: 13 residues processed: 60 average time/residue: 0.1134 time to fit residues: 8.8549 Evaluate side-chains 66 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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: 0.7410 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3131 Z= 0.166 Angle : 0.638 12.098 4272 Z= 0.294 Chirality : 0.037 0.112 508 Planarity : 0.003 0.021 521 Dihedral : 12.388 158.187 538 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.81 % Allowed : 20.83 % Favored : 74.36 % 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: 1.13 (0.44), residues: 386 helix: 1.51 (0.37), residues: 217 sheet: 2.34 (0.75), residues: 49 loop : -1.40 (0.55), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.015 0.001 PHE R 135 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8288 (m100) cc_final: 0.7916 (m-90) REVERT: R 187 PHE cc_start: 0.7991 (m-80) cc_final: 0.7625 (m-80) REVERT: R 189 PHE cc_start: 0.7979 (m-10) cc_final: 0.7619 (m-10) outliers start: 15 outliers final: 12 residues processed: 63 average time/residue: 0.1119 time to fit residues: 9.1921 Evaluate side-chains 67 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.1980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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: 0.7477 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3131 Z= 0.227 Angle : 0.668 12.175 4272 Z= 0.313 Chirality : 0.039 0.124 508 Planarity : 0.003 0.021 521 Dihedral : 12.660 162.154 538 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.85 % Allowed : 22.12 % Favored : 74.04 % 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: 1.02 (0.44), residues: 386 helix: 1.39 (0.37), residues: 218 sheet: 2.54 (0.72), residues: 48 loop : -1.50 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.004 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.010 0.001 TYR N 39 ARG 0.002 0.000 ARG R 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8305 (m100) cc_final: 0.7915 (m-90) REVERT: R 187 PHE cc_start: 0.8171 (m-80) cc_final: 0.7783 (m-80) REVERT: R 189 PHE cc_start: 0.8037 (m-10) cc_final: 0.7658 (m-10) outliers start: 12 outliers final: 12 residues processed: 59 average time/residue: 0.1116 time to fit residues: 8.5571 Evaluate side-chains 65 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 291 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.190045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.121360 restraints weight = 2945.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125515 restraints weight = 1934.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127764 restraints weight = 1559.959| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3131 Z= 0.218 Angle : 0.660 12.095 4272 Z= 0.309 Chirality : 0.039 0.121 508 Planarity : 0.003 0.020 521 Dihedral : 13.056 170.383 538 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.85 % Allowed : 22.12 % Favored : 74.04 % 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: 1.00 (0.44), residues: 386 helix: 1.37 (0.37), residues: 218 sheet: 2.58 (0.73), residues: 48 loop : -1.53 (0.54), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.016 0.001 PHE R 135 TYR 0.010 0.001 TYR N 101 ARG 0.001 0.000 ARG R 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 981.77 seconds wall clock time: 18 minutes 58.52 seconds (1138.52 seconds total)