Starting phenix.real_space_refine on Mon Jun 24 13:41:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbg_38217/06_2024/8xbg_38217_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbg_38217/06_2024/8xbg_38217.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbg_38217/06_2024/8xbg_38217_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbg_38217/06_2024/8xbg_38217_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbg_38217/06_2024/8xbg_38217_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbg_38217/06_2024/8xbg_38217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbg_38217/06_2024/8xbg_38217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbg_38217/06_2024/8xbg_38217_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xbg_38217/06_2024/8xbg_38217_updated.pdb" } resolution = 3.43 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 ------------------------------------------------------------------------------- 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= -0.024 sd= 0.464 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 P 1 5.49 5 S 22 5.16 5 C 1637 2.51 5 N 399 2.21 5 O 402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 2461 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2424 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'KW0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.01, per 1000 atoms: 0.82 Number of scatterers: 2461 At special positions: 0 Unit cell: (75.956, 64.786, 70.371, 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) S 22 16.00 P 1 15.00 O 402 8.00 N 399 7.00 C 1637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 299 " distance=2.06 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 204 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 0.85 Conformation dependent library (CDL) restraints added in 445.2 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 9 helices and 0 sheets defined 79.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 51 through 80 Processing helix chain 'A' and resid 88 through 116 Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 124 through 156 removed outlier: 4.157A pdb=" N TYR A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 194 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 214 through 251 Processing helix chain 'A' and resid 260 through 294 removed outlier: 3.543A pdb=" N PHE A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Proline residue: A 281 - end of helix removed outlier: 4.395A pdb=" N PHE A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 330 removed outlier: 3.596A pdb=" N ILE A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 332 through 341 189 hydrogen bonds defined for protein. 567 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: 0.67 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 397 1.31 - 1.44: 653 1.44 - 1.57: 1423 1.57 - 1.70: 7 1.70 - 1.83: 34 Bond restraints: 2514 Sorted by residual: bond pdb=" CA SER A 268 " pdb=" CB SER A 268 " ideal model delta sigma weight residual 1.529 1.430 0.099 1.55e-02 4.16e+03 4.05e+01 bond pdb=" C TYR A 135 " pdb=" O TYR A 135 " ideal model delta sigma weight residual 1.237 1.299 -0.063 1.19e-02 7.06e+03 2.79e+01 bond pdb=" C SER A 141 " pdb=" N ILE A 142 " ideal model delta sigma weight residual 1.334 1.277 0.057 1.26e-02 6.30e+03 2.08e+01 bond pdb=" C ARG A 152 " pdb=" O ARG A 152 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.17e-02 7.31e+03 1.98e+01 bond pdb=" C LEU A 145 " pdb=" O LEU A 145 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.17e-02 7.31e+03 1.83e+01 ... (remaining 2509 not shown) Histogram of bond angle deviations from ideal: 96.35 - 104.04: 23 104.04 - 111.74: 1069 111.74 - 119.44: 1222 119.44 - 127.13: 1050 127.13 - 134.83: 26 Bond angle restraints: 3390 Sorted by residual: angle pdb=" C10 KW0 A 401 " pdb=" C9 KW0 A 401 " pdb=" C8 KW0 A 401 " ideal model delta sigma weight residual 152.63 128.76 23.87 3.00e+00 1.11e-01 6.33e+01 angle pdb=" C11 KW0 A 401 " pdb=" C10 KW0 A 401 " pdb=" C9 KW0 A 401 " ideal model delta sigma weight residual 112.23 128.98 -16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" NE ARG A 152 " pdb=" CZ ARG A 152 " pdb=" NH1 ARG A 152 " ideal model delta sigma weight residual 121.50 116.50 5.00 1.00e+00 1.00e+00 2.50e+01 angle pdb=" N ILE A 290 " pdb=" CA ILE A 290 " pdb=" C ILE A 290 " ideal model delta sigma weight residual 110.72 106.30 4.42 1.01e+00 9.80e-01 1.91e+01 angle pdb=" C PRO A 281 " pdb=" CA PRO A 281 " pdb=" CB PRO A 281 " ideal model delta sigma weight residual 113.20 105.86 7.34 1.69e+00 3.50e-01 1.89e+01 ... (remaining 3385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 1423 25.88 - 51.75: 64 51.75 - 77.63: 8 77.63 - 103.50: 1 103.50 - 129.38: 2 Dihedral angle restraints: 1498 sinusoidal: 616 harmonic: 882 Sorted by residual: dihedral pdb=" CB CYS A 46 " pdb=" SG CYS A 46 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual -86.00 -5.52 -80.48 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" C15 KW0 A 401 " pdb=" C16 KW0 A 401 " pdb=" C17 KW0 A 401 " pdb=" C18 KW0 A 401 " ideal model delta sinusoidal sigma weight residual 196.90 67.52 129.38 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C3 KW0 A 401 " pdb=" C4 KW0 A 401 " pdb=" C5 KW0 A 401 " pdb=" C6 KW0 A 401 " ideal model delta sinusoidal sigma weight residual 174.55 58.53 116.02 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 1495 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.106: 329 0.106 - 0.211: 67 0.211 - 0.316: 4 0.316 - 0.422: 0 0.422 - 0.527: 1 Chirality restraints: 401 Sorted by residual: chirality pdb=" CB ILE A 142 " pdb=" CA ILE A 142 " pdb=" CG1 ILE A 142 " pdb=" CG2 ILE A 142 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.94e+00 chirality pdb=" CB ILE A 290 " pdb=" CA ILE A 290 " pdb=" CG1 ILE A 290 " pdb=" CG2 ILE A 290 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB ILE A 239 " pdb=" CA ILE A 239 " pdb=" CG1 ILE A 239 " pdb=" CG2 ILE A 239 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 398 not shown) Planarity restraints: 397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 KW0 A 401 " 0.121 2.00e-02 2.50e+03 9.19e-02 8.44e+01 pdb=" C11 KW0 A 401 " -0.047 2.00e-02 2.50e+03 pdb=" C8 KW0 A 401 " 0.047 2.00e-02 2.50e+03 pdb=" C9 KW0 A 401 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 269 " 0.057 2.00e-02 2.50e+03 3.96e-02 2.75e+01 pdb=" CG PHE A 269 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 269 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE A 269 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 269 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 PHE A 269 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 269 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 92 " 0.045 2.00e-02 2.50e+03 3.53e-02 2.49e+01 pdb=" CG TYR A 92 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR A 92 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR A 92 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 92 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 92 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR A 92 " -0.014 2.00e-02 2.50e+03 ... (remaining 394 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 172 2.74 - 3.28: 2749 3.28 - 3.82: 3924 3.82 - 4.36: 4881 4.36 - 4.90: 8084 Nonbonded interactions: 19810 Sorted by model distance: nonbonded pdb=" OG SER A 54 " pdb=" O HIS A 114 " model vdw 2.198 2.440 nonbonded pdb=" O LYS A 254 " pdb=" OG SER A 258 " model vdw 2.213 2.440 nonbonded pdb=" OD1 ASN A 244 " pdb=" NH2 ARG A 247 " model vdw 2.233 2.520 nonbonded pdb=" O MET A 203 " pdb=" NH2 ARG A 208 " model vdw 2.257 2.520 nonbonded pdb=" O LYS A 155 " pdb=" OG SER A 159 " model vdw 2.294 2.440 ... (remaining 19805 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.240 Find NCS groups from input model: 0.050 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 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 : 0.016 0.099 2514 Z= 1.012 Angle : 1.578 23.866 3390 Z= 1.034 Chirality : 0.086 0.527 401 Planarity : 0.011 0.092 397 Dihedral : 15.245 129.375 922 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.36 % Allowed : 2.91 % Favored : 96.73 % 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: 0.00 (0.43), residues: 296 helix: 0.67 (0.29), residues: 237 sheet: None (None), residues: 0 loop : -2.57 (0.62), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.009 TRP A 179 HIS 0.013 0.004 HIS A 306 PHE 0.058 0.013 PHE A 269 TYR 0.081 0.013 TYR A 92 ARG 0.028 0.003 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.205 Fit side-chains REVERT: A 250 LYS cc_start: 0.7426 (tptm) cc_final: 0.7032 (ptmt) REVERT: A 260 LYS cc_start: 0.7126 (pttm) cc_final: 0.6168 (tttp) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.1774 time to fit residues: 9.6657 Evaluate side-chains 43 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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: 0.6584 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2514 Z= 0.205 Angle : 0.554 5.453 3390 Z= 0.294 Chirality : 0.039 0.132 401 Planarity : 0.004 0.044 397 Dihedral : 10.987 108.682 347 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.55 % Allowed : 11.64 % Favored : 85.82 % 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: 1.30 (0.45), residues: 296 helix: 1.66 (0.31), residues: 237 sheet: None (None), residues: 0 loop : -2.53 (0.63), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.003 0.001 HIS A 306 PHE 0.011 0.002 PHE A 186 TYR 0.010 0.001 TYR A 289 ARG 0.003 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.276 Fit side-chains REVERT: A 250 LYS cc_start: 0.7432 (tptm) cc_final: 0.6995 (ptmt) REVERT: A 260 LYS cc_start: 0.7140 (pttm) cc_final: 0.6133 (tttp) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.2132 time to fit residues: 11.1597 Evaluate side-chains 50 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 308 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.6553 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2514 Z= 0.177 Angle : 0.512 7.536 3390 Z= 0.270 Chirality : 0.038 0.138 401 Planarity : 0.003 0.041 397 Dihedral : 10.165 101.936 347 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.55 % Allowed : 14.18 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.47), residues: 296 helix: 1.97 (0.31), residues: 240 sheet: None (None), residues: 0 loop : -2.61 (0.66), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.002 0.001 HIS A 306 PHE 0.009 0.002 PHE A 231 TYR 0.008 0.001 TYR A 92 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.273 Fit side-chains REVERT: A 250 LYS cc_start: 0.7407 (tptm) cc_final: 0.6981 (ptmt) REVERT: A 260 LYS cc_start: 0.7114 (pttm) cc_final: 0.6099 (tttp) outliers start: 7 outliers final: 7 residues processed: 47 average time/residue: 0.2012 time to fit residues: 10.8831 Evaluate side-chains 51 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 308 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 0.0270 chunk 17 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- 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: 0.6513 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 2514 Z= 0.157 Angle : 0.485 6.701 3390 Z= 0.256 Chirality : 0.037 0.136 401 Planarity : 0.003 0.036 397 Dihedral : 9.343 100.158 347 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.82 % Allowed : 17.82 % Favored : 80.36 % 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: 2.21 (0.48), residues: 296 helix: 2.31 (0.32), residues: 240 sheet: None (None), residues: 0 loop : -2.53 (0.69), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 301 HIS 0.001 0.000 HIS A 199 PHE 0.007 0.001 PHE A 134 TYR 0.008 0.001 TYR A 139 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.235 Fit side-chains REVERT: A 172 ILE cc_start: 0.6816 (mm) cc_final: 0.6547 (mm) REVERT: A 201 SER cc_start: 0.8324 (m) cc_final: 0.8030 (t) REVERT: A 250 LYS cc_start: 0.7407 (tptm) cc_final: 0.7050 (tttm) REVERT: A 260 LYS cc_start: 0.6995 (pttm) cc_final: 0.6001 (tttp) REVERT: A 266 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6569 (ptp-170) REVERT: A 312 MET cc_start: 0.7895 (mmt) cc_final: 0.7648 (mmt) outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.2305 time to fit residues: 11.7870 Evaluate side-chains 46 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.0370 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- 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: 0.6594 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 2514 Z= 0.233 Angle : 0.532 6.343 3390 Z= 0.283 Chirality : 0.039 0.166 401 Planarity : 0.003 0.038 397 Dihedral : 9.627 100.039 347 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.27 % Allowed : 20.00 % Favored : 76.73 % 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: 1.77 (0.47), residues: 296 helix: 1.99 (0.31), residues: 240 sheet: None (None), residues: 0 loop : -2.62 (0.72), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 228 HIS 0.002 0.001 HIS A 306 PHE 0.013 0.002 PHE A 186 TYR 0.009 0.001 TYR A 92 ARG 0.004 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.273 Fit side-chains REVERT: A 250 LYS cc_start: 0.7487 (tptm) cc_final: 0.7067 (ptmt) REVERT: A 260 LYS cc_start: 0.7177 (pttm) cc_final: 0.6157 (tttp) outliers start: 9 outliers final: 8 residues processed: 44 average time/residue: 0.1946 time to fit residues: 9.9489 Evaluate side-chains 50 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 333 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.6594 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 2514 Z= 0.225 Angle : 0.535 6.042 3390 Z= 0.286 Chirality : 0.039 0.157 401 Planarity : 0.003 0.036 397 Dihedral : 9.774 101.261 347 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.73 % Allowed : 18.55 % Favored : 76.73 % 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: 1.67 (0.47), residues: 296 helix: 1.91 (0.31), residues: 240 sheet: None (None), residues: 0 loop : -2.60 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 228 HIS 0.002 0.001 HIS A 306 PHE 0.012 0.002 PHE A 186 TYR 0.008 0.001 TYR A 92 ARG 0.005 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.244 Fit side-chains REVERT: A 111 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.7236 (pt) REVERT: A 250 LYS cc_start: 0.7538 (tptm) cc_final: 0.7093 (ptmt) REVERT: A 260 LYS cc_start: 0.7203 (pttm) cc_final: 0.6149 (tttp) REVERT: A 266 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6673 (ptp-170) outliers start: 13 outliers final: 8 residues processed: 48 average time/residue: 0.2058 time to fit residues: 11.2380 Evaluate side-chains 51 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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: 0.6588 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 2514 Z= 0.214 Angle : 0.527 5.932 3390 Z= 0.284 Chirality : 0.039 0.174 401 Planarity : 0.003 0.034 397 Dihedral : 9.725 101.338 347 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.36 % Allowed : 20.73 % Favored : 74.91 % 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: 1.76 (0.48), residues: 296 helix: 1.98 (0.32), residues: 240 sheet: None (None), residues: 0 loop : -2.61 (0.74), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 228 HIS 0.002 0.001 HIS A 306 PHE 0.011 0.002 PHE A 186 TYR 0.008 0.001 TYR A 92 ARG 0.006 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 0.276 Fit side-chains REVERT: A 250 LYS cc_start: 0.7547 (tptm) cc_final: 0.7102 (ptmt) REVERT: A 260 LYS cc_start: 0.7199 (pttm) cc_final: 0.6142 (tttp) REVERT: A 266 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6667 (ptp-170) outliers start: 12 outliers final: 9 residues processed: 47 average time/residue: 0.2231 time to fit residues: 11.8560 Evaluate side-chains 52 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 333 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.6571 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2514 Z= 0.191 Angle : 0.513 5.905 3390 Z= 0.276 Chirality : 0.038 0.176 401 Planarity : 0.003 0.032 397 Dihedral : 9.601 101.526 347 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.73 % Allowed : 21.09 % Favored : 74.18 % 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: 1.98 (0.48), residues: 296 helix: 2.14 (0.32), residues: 240 sheet: None (None), residues: 0 loop : -2.54 (0.75), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 228 HIS 0.002 0.000 HIS A 306 PHE 0.010 0.001 PHE A 65 TYR 0.007 0.001 TYR A 92 ARG 0.006 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.263 Fit side-chains REVERT: A 111 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7306 (pt) REVERT: A 250 LYS cc_start: 0.7550 (tptm) cc_final: 0.7107 (ptmt) REVERT: A 260 LYS cc_start: 0.7171 (pttm) cc_final: 0.6139 (tttp) REVERT: A 266 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6638 (ptp-170) outliers start: 13 outliers final: 9 residues processed: 45 average time/residue: 0.2173 time to fit residues: 11.1095 Evaluate side-chains 49 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 333 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 2514 Z= 0.174 Angle : 0.498 5.757 3390 Z= 0.268 Chirality : 0.038 0.174 401 Planarity : 0.003 0.031 397 Dihedral : 9.208 100.562 347 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.27 % Allowed : 22.91 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.49), residues: 296 helix: 2.39 (0.33), residues: 240 sheet: None (None), residues: 0 loop : -2.55 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 228 HIS 0.002 0.000 HIS A 306 PHE 0.010 0.001 PHE A 65 TYR 0.007 0.001 TYR A 327 ARG 0.006 0.001 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.254 Fit side-chains REVERT: A 201 SER cc_start: 0.8103 (m) cc_final: 0.7890 (t) REVERT: A 250 LYS cc_start: 0.7579 (tptm) cc_final: 0.7138 (ptmt) REVERT: A 260 LYS cc_start: 0.7142 (pttm) cc_final: 0.6154 (tttm) REVERT: A 266 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6716 (ptp-170) REVERT: A 312 MET cc_start: 0.7983 (mmt) cc_final: 0.7567 (mmt) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.2274 time to fit residues: 12.1562 Evaluate side-chains 47 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 333 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 2514 Z= 0.178 Angle : 0.509 5.465 3390 Z= 0.276 Chirality : 0.038 0.182 401 Planarity : 0.003 0.030 397 Dihedral : 9.124 100.265 347 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.55 % Allowed : 23.64 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.50), residues: 296 helix: 2.46 (0.33), residues: 240 sheet: None (None), residues: 0 loop : -2.56 (0.76), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 228 HIS 0.001 0.000 HIS A 306 PHE 0.009 0.001 PHE A 65 TYR 0.007 0.001 TYR A 327 ARG 0.006 0.001 ARG A 251 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.265 Fit side-chains REVERT: A 250 LYS cc_start: 0.7579 (tptm) cc_final: 0.7139 (ptmt) REVERT: A 260 LYS cc_start: 0.7145 (pttm) cc_final: 0.6155 (tttm) REVERT: A 266 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6723 (ttp-170) REVERT: A 312 MET cc_start: 0.8015 (mmt) cc_final: 0.7582 (mmt) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.2325 time to fit residues: 11.8231 Evaluate side-chains 47 residues out of total 275 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 200 ASN Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain A residue 333 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 0.0470 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.207147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.169563 restraints weight = 2587.773| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.17 r_work: 0.3786 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 2514 Z= 0.173 Angle : 0.502 5.567 3390 Z= 0.272 Chirality : 0.038 0.175 401 Planarity : 0.003 0.030 397 Dihedral : 8.989 99.865 347 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.55 % Allowed : 23.64 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.50), residues: 296 helix: 2.53 (0.33), residues: 240 sheet: None (None), residues: 0 loop : -2.64 (0.73), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 228 HIS 0.001 0.000 HIS A 306 PHE 0.010 0.001 PHE A 65 TYR 0.009 0.001 TYR A 327 ARG 0.006 0.001 ARG A 251 =============================================================================== Job complete usr+sys time: 884.77 seconds wall clock time: 17 minutes 0.09 seconds (1020.09 seconds total)