Starting phenix.real_space_refine on Fri Dec 27 07:49:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wz4_37946/12_2024/8wz4_37946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wz4_37946/12_2024/8wz4_37946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wz4_37946/12_2024/8wz4_37946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wz4_37946/12_2024/8wz4_37946.map" model { file = "/net/cci-nas-00/data/ceres_data/8wz4_37946/12_2024/8wz4_37946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wz4_37946/12_2024/8wz4_37946.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.014 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 16 5.16 5 C 2198 2.51 5 N 564 2.21 5 O 663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 3441 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1685 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 211} Chain breaks: 1 Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 925 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "L" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Time building chain proxies: 3.77, per 1000 atoms: 1.10 Number of scatterers: 3441 At special positions: 0 Unit cell: (88.692, 82.468, 70.798, 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 16 16.00 O 663 8.00 N 564 7.00 C 2198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.25 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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: 0.83 Conformation dependent library (CDL) restraints added in 424.8 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 27.6% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'C' and resid 73 through 98 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 209 Proline residue: C 205 - end of helix Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.758A pdb=" N ILE C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 262 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 283 Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.004A pdb=" N THR H 91 " --> pdb=" O ASN H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 179 through 180 removed outlier: 10.343A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ARG C 49 " --> pdb=" O GLY C 307 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY C 307 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 301 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL C 300 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N MET C 289 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLN C 302 " --> pdb=" O SER C 287 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER C 287 " --> pdb=" O GLN C 302 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.546A pdb=" N VAL H 18 " --> pdb=" O ILE H 83 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 78 " --> pdb=" O GLU H 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.638A pdb=" N THR H 113 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR H 94 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.638A pdb=" N THR H 113 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR H 110 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR H 94 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG H 98 " --> pdb=" O TYR H 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 46 154 hydrogen bonds defined for protein. 417 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: 0.90 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 564 1.28 - 1.41: 843 1.41 - 1.54: 2069 1.54 - 1.67: 5 1.67 - 1.81: 24 Bond restraints: 3505 Sorted by residual: bond pdb=" C VAL C 164 " pdb=" O VAL C 164 " ideal model delta sigma weight residual 1.237 1.145 0.092 1.19e-02 7.06e+03 5.99e+01 bond pdb=" N VAL C 164 " pdb=" CA VAL C 164 " ideal model delta sigma weight residual 1.460 1.369 0.091 1.21e-02 6.83e+03 5.65e+01 bond pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.30e-02 5.92e+03 4.82e+01 bond pdb=" N LYS C 166 " pdb=" CA LYS C 166 " ideal model delta sigma weight residual 1.459 1.380 0.079 1.20e-02 6.94e+03 4.35e+01 bond pdb=" C ALA C 170 " pdb=" N LEU C 171 " ideal model delta sigma weight residual 1.331 1.416 -0.084 1.32e-02 5.74e+03 4.09e+01 ... (remaining 3500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 4645 2.53 - 5.05: 84 5.05 - 7.58: 10 7.58 - 10.10: 7 10.10 - 12.63: 1 Bond angle restraints: 4747 Sorted by residual: angle pdb=" N VAL C 164 " pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 110.72 103.29 7.43 1.01e+00 9.80e-01 5.41e+01 angle pdb=" N GLU C 163 " pdb=" CA GLU C 163 " pdb=" C GLU C 163 " ideal model delta sigma weight residual 111.28 119.14 -7.86 1.09e+00 8.42e-01 5.19e+01 angle pdb=" CA LYS C 166 " pdb=" C LYS C 166 " pdb=" N ILE C 167 " ideal model delta sigma weight residual 117.17 124.76 -7.59 1.18e+00 7.18e-01 4.14e+01 angle pdb=" N LEU C 171 " pdb=" CA LEU C 171 " pdb=" C LEU C 171 " ideal model delta sigma weight residual 112.72 105.07 7.65 1.36e+00 5.41e-01 3.16e+01 angle pdb=" CA VAL C 164 " pdb=" C VAL C 164 " pdb=" N ASN C 165 " ideal model delta sigma weight residual 117.28 123.60 -6.32 1.16e+00 7.43e-01 2.97e+01 ... (remaining 4742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.95: 1806 13.95 - 27.91: 222 27.91 - 41.86: 57 41.86 - 55.81: 19 55.81 - 69.77: 5 Dihedral angle restraints: 2109 sinusoidal: 835 harmonic: 1274 Sorted by residual: dihedral pdb=" CB CYS C 155 " pdb=" SG CYS C 155 " pdb=" SG CYS C 290 " pdb=" CB CYS C 290 " ideal model delta sinusoidal sigma weight residual -86.00 -155.77 69.77 1 1.00e+01 1.00e-02 6.28e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual -86.00 -121.03 35.03 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CA ILE C 291 " pdb=" C ILE C 291 " pdb=" N ILE C 292 " pdb=" CA ILE C 292 " ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 2106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 529 0.120 - 0.240: 17 0.240 - 0.359: 2 0.359 - 0.479: 1 0.479 - 0.599: 1 Chirality restraints: 550 Sorted by residual: chirality pdb=" CA GLU C 163 " pdb=" N GLU C 163 " pdb=" C GLU C 163 " pdb=" CB GLU C 163 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CA LYS C 166 " pdb=" N LYS C 166 " pdb=" C LYS C 166 " pdb=" CB LYS C 166 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA VAL C 164 " pdb=" N VAL C 164 " pdb=" C VAL C 164 " pdb=" CB VAL C 164 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 547 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 170 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C ALA C 170 " 0.073 2.00e-02 2.50e+03 pdb=" O ALA C 170 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU C 171 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 168 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C LYS C 168 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS C 168 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 169 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 167 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C ILE C 167 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE C 167 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS C 168 " -0.016 2.00e-02 2.50e+03 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 84 2.67 - 3.23: 3256 3.23 - 3.79: 5006 3.79 - 4.34: 6907 4.34 - 4.90: 12143 Nonbonded interactions: 27396 Sorted by model distance: nonbonded pdb=" OH TYR H 99 " pdb=" OH TYR L 96 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.253 3.040 nonbonded pdb=" OH TYR L 49 " pdb=" OD1 ASP L 56 " model vdw 2.302 3.040 nonbonded pdb=" O LEU C 252 " pdb=" NH1 ARG C 282 " model vdw 2.363 3.120 nonbonded pdb=" O THR H 110 " pdb=" OG1 THR H 110 " model vdw 2.369 3.040 ... (remaining 27391 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.980 Find NCS groups from input model: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.010 0.092 3505 Z= 0.638 Angle : 0.895 12.627 4747 Z= 0.540 Chirality : 0.062 0.599 550 Planarity : 0.005 0.042 593 Dihedral : 13.979 69.590 1279 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.26 % Allowed : 9.28 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.33), residues: 431 helix: -1.06 (0.42), residues: 116 sheet: -2.97 (0.36), residues: 141 loop : -3.46 (0.35), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 50 HIS 0.004 0.002 HIS L 90 PHE 0.016 0.002 PHE L 91 TYR 0.018 0.002 TYR H 80 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.416 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.1714 time to fit residues: 23.5792 Evaluate side-chains 72 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN L 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3505 Z= 0.205 Angle : 0.590 7.836 4747 Z= 0.312 Chirality : 0.044 0.207 550 Planarity : 0.004 0.033 593 Dihedral : 5.313 48.479 466 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.32 % Allowed : 14.43 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -2.31 (0.38), residues: 431 helix: 1.02 (0.49), residues: 116 sheet: -2.36 (0.38), residues: 139 loop : -2.52 (0.40), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.003 0.001 HIS C 159 PHE 0.019 0.002 PHE H 70 TYR 0.012 0.002 TYR H 80 ARG 0.007 0.001 ARG C 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.413 Fit side-chains REVERT: C 77 LYS cc_start: 0.7433 (tptm) cc_final: 0.7188 (ttpt) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.1809 time to fit residues: 16.6932 Evaluate side-chains 70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3505 Z= 0.293 Angle : 0.639 8.231 4747 Z= 0.336 Chirality : 0.044 0.157 550 Planarity : 0.003 0.027 593 Dihedral : 5.485 44.381 466 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.12 % Allowed : 15.98 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.60 (0.40), residues: 431 helix: 1.64 (0.49), residues: 116 sheet: -1.90 (0.37), residues: 159 loop : -2.10 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.004 0.002 HIS L 90 PHE 0.014 0.002 PHE H 70 TYR 0.012 0.002 TYR C 299 ARG 0.004 0.001 ARG C 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: C 222 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7400 (mt-10) REVERT: C 289 MET cc_start: 0.8928 (tpt) cc_final: 0.8192 (tpt) REVERT: H 32 TYR cc_start: 0.8538 (m-80) cc_final: 0.8230 (m-80) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 0.1653 time to fit residues: 16.2875 Evaluate side-chains 70 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.0020 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 GLN L 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3505 Z= 0.253 Angle : 0.584 7.436 4747 Z= 0.306 Chirality : 0.043 0.150 550 Planarity : 0.003 0.025 593 Dihedral : 5.208 39.034 466 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.38 % Allowed : 18.30 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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 (0.41), residues: 431 helix: 1.95 (0.49), residues: 116 sheet: -1.41 (0.39), residues: 153 loop : -2.00 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.012 0.002 PHE H 70 TYR 0.012 0.002 TYR C 299 ARG 0.003 0.000 ARG C 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: C 222 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7405 (mt-10) REVERT: C 289 MET cc_start: 0.8966 (tpt) cc_final: 0.8208 (tpt) REVERT: H 32 TYR cc_start: 0.8511 (m-80) cc_final: 0.8143 (m-80) outliers start: 17 outliers final: 13 residues processed: 74 average time/residue: 0.1475 time to fit residues: 13.6022 Evaluate side-chains 72 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7919 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3505 Z= 0.311 Angle : 0.625 7.707 4747 Z= 0.325 Chirality : 0.044 0.184 550 Planarity : 0.003 0.027 593 Dihedral : 5.282 35.437 466 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.90 % Allowed : 19.07 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.12 (0.41), residues: 431 helix: 1.91 (0.49), residues: 116 sheet: -1.37 (0.39), residues: 157 loop : -2.02 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.004 0.002 HIS L 90 PHE 0.013 0.002 PHE L 91 TYR 0.016 0.002 TYR H 80 ARG 0.003 0.000 ARG C 282 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.396 Fit side-chains REVERT: C 222 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7454 (mt-10) REVERT: C 289 MET cc_start: 0.8999 (tpt) cc_final: 0.8205 (tpt) REVERT: H 73 GLU cc_start: 0.6836 (mp0) cc_final: 0.6136 (mp0) outliers start: 19 outliers final: 18 residues processed: 73 average time/residue: 0.1522 time to fit residues: 13.9172 Evaluate side-chains 74 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3505 Z= 0.302 Angle : 0.604 7.550 4747 Z= 0.318 Chirality : 0.043 0.148 550 Planarity : 0.003 0.025 593 Dihedral : 5.197 29.660 466 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.70 % Allowed : 20.10 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.04 (0.41), residues: 431 helix: 1.90 (0.49), residues: 116 sheet: -1.25 (0.39), residues: 155 loop : -2.00 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.004 0.001 HIS L 90 PHE 0.012 0.002 PHE L 91 TYR 0.016 0.002 TYR H 80 ARG 0.002 0.001 ARG C 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.379 Fit side-chains REVERT: C 222 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7472 (mt-10) REVERT: C 289 MET cc_start: 0.9017 (tpt) cc_final: 0.8134 (tpt) REVERT: L 81 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7313 (pm20) outliers start: 26 outliers final: 20 residues processed: 78 average time/residue: 0.1467 time to fit residues: 14.4728 Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 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: 0.7906 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3505 Z= 0.262 Angle : 0.571 7.124 4747 Z= 0.302 Chirality : 0.042 0.152 550 Planarity : 0.003 0.025 593 Dihedral : 5.013 26.010 466 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.93 % Allowed : 20.62 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.86 (0.42), residues: 431 helix: 1.98 (0.49), residues: 116 sheet: -1.13 (0.41), residues: 155 loop : -1.86 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.011 0.002 PHE L 91 TYR 0.017 0.002 TYR H 80 ARG 0.002 0.000 ARG C 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.412 Fit side-chains REVERT: C 289 MET cc_start: 0.9051 (tpt) cc_final: 0.8071 (tpt) REVERT: L 81 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7300 (pm20) outliers start: 23 outliers final: 20 residues processed: 77 average time/residue: 0.1530 time to fit residues: 14.9683 Evaluate side-chains 81 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.0370 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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: 0.7868 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3505 Z= 0.202 Angle : 0.531 6.418 4747 Z= 0.282 Chirality : 0.041 0.153 550 Planarity : 0.003 0.027 593 Dihedral : 4.742 23.573 466 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.67 % Allowed : 21.65 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.67 (0.42), residues: 431 helix: 2.24 (0.49), residues: 116 sheet: -1.01 (0.41), residues: 155 loop : -1.83 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.009 0.001 PHE L 91 TYR 0.015 0.001 TYR H 80 ARG 0.002 0.000 ARG C 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.400 Fit side-chains REVERT: C 289 MET cc_start: 0.9035 (tpt) cc_final: 0.8017 (tpt) REVERT: H 32 TYR cc_start: 0.8498 (m-80) cc_final: 0.8051 (m-80) REVERT: L 81 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7317 (pm20) outliers start: 22 outliers final: 20 residues processed: 77 average time/residue: 0.1464 time to fit residues: 14.0176 Evaluate side-chains 79 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.0050 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 ASN L 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3505 Z= 0.235 Angle : 0.563 6.778 4747 Z= 0.299 Chirality : 0.042 0.152 550 Planarity : 0.003 0.027 593 Dihedral : 4.772 23.614 466 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.93 % Allowed : 20.88 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.61 (0.42), residues: 431 helix: 2.30 (0.49), residues: 116 sheet: -0.95 (0.41), residues: 155 loop : -1.84 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.010 0.001 PHE L 91 TYR 0.015 0.002 TYR H 80 ARG 0.002 0.000 ARG C 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.384 Fit side-chains REVERT: C 289 MET cc_start: 0.9043 (tpt) cc_final: 0.8082 (tpt) REVERT: H 32 TYR cc_start: 0.8510 (m-80) cc_final: 0.8039 (m-80) REVERT: L 81 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7381 (pt0) outliers start: 23 outliers final: 21 residues processed: 72 average time/residue: 0.1385 time to fit residues: 12.6350 Evaluate side-chains 78 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 42 LYS Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3505 Z= 0.294 Angle : 0.602 7.242 4747 Z= 0.319 Chirality : 0.043 0.152 550 Planarity : 0.003 0.027 593 Dihedral : 4.947 24.310 466 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.93 % Allowed : 21.39 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.66 (0.42), residues: 431 helix: 2.12 (0.49), residues: 116 sheet: -0.85 (0.42), residues: 155 loop : -1.91 (0.48), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.004 0.001 HIS L 90 PHE 0.013 0.002 PHE L 91 TYR 0.018 0.002 TYR H 80 ARG 0.002 0.001 ARG H 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.390 Fit side-chains REVERT: C 289 MET cc_start: 0.9060 (tpt) cc_final: 0.8087 (tpt) REVERT: L 81 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7350 (pt0) outliers start: 23 outliers final: 21 residues processed: 81 average time/residue: 0.1426 time to fit residues: 14.6860 Evaluate side-chains 82 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 52 LYS Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 ASN L 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118360 restraints weight = 4689.777| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.06 r_work: 0.3319 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3505 Z= 0.204 Angle : 0.541 6.283 4747 Z= 0.288 Chirality : 0.041 0.152 550 Planarity : 0.003 0.027 593 Dihedral : 4.653 23.697 466 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.93 % Allowed : 21.39 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.48 (0.42), residues: 431 helix: 2.29 (0.49), residues: 116 sheet: -0.70 (0.43), residues: 153 loop : -1.88 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.009 0.001 PHE L 91 TYR 0.015 0.001 TYR H 80 ARG 0.002 0.000 ARG C 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1393.39 seconds wall clock time: 26 minutes 38.72 seconds (1598.72 seconds total)