Starting phenix.real_space_refine on Fri Aug 2 13:23:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/08_2024/8k5b_36900.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/08_2024/8k5b_36900.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/08_2024/8k5b_36900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/08_2024/8k5b_36900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/08_2024/8k5b_36900.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/08_2024/8k5b_36900.cif" } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 17 5.16 5 C 1587 2.51 5 N 399 2.21 5 O 371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 273": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 2374 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2365 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NIO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.07, per 1000 atoms: 0.87 Number of scatterers: 2374 At special positions: 0 Unit cell: (59.76, 72.21, 73.455, 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 17 16.00 O 371 8.00 N 399 7.00 C 1587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 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: 0.87 Conformation dependent library (CDL) restraints added in 392.6 milliseconds 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 558 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 74.6% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.099A pdb=" N ILE A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 89 removed outlier: 4.013A pdb=" N ARG A 63 " --> pdb=" O TRP A 59 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 131 Processing helix chain 'A' and resid 140 through 158 removed outlier: 3.567A pdb=" N LEU A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.604A pdb=" N LYS A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 165' Processing helix chain 'A' and resid 187 through 218 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 225 through 261 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 265 through 268 removed outlier: 4.202A pdb=" N VAL A 268 " --> pdb=" O ASN A 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 269 through 295 removed outlier: 4.060A pdb=" N PHE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 161 hydrogen bonds defined for protein. 477 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: 0.55 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 713 1.34 - 1.46: 611 1.46 - 1.58: 1096 1.58 - 1.70: 0 1.70 - 1.81: 24 Bond restraints: 2444 Sorted by residual: bond pdb=" C2 NIO A 401 " pdb=" C3 NIO A 401 " ideal model delta sigma weight residual 1.390 1.351 0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" C3 NIO A 401 " pdb=" C4 NIO A 401 " ideal model delta sigma weight residual 1.386 1.353 0.033 2.00e-02 2.50e+03 2.74e+00 bond pdb=" C ILE A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.335 1.357 -0.021 1.36e-02 5.41e+03 2.41e+00 bond pdb=" N NIO A 401 " pdb=" C1 NIO A 401 " ideal model delta sigma weight residual 1.329 1.350 -0.021 2.00e-02 2.50e+03 1.14e+00 bond pdb=" N NIO A 401 " pdb=" C5 NIO A 401 " ideal model delta sigma weight residual 1.329 1.349 -0.020 2.00e-02 2.50e+03 1.04e+00 ... (remaining 2439 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.78: 64 106.78 - 113.58: 1340 113.58 - 120.38: 955 120.38 - 127.18: 922 127.18 - 133.99: 36 Bond angle restraints: 3317 Sorted by residual: angle pdb=" C ASP A 97 " pdb=" N ILE A 98 " pdb=" CA ILE A 98 " ideal model delta sigma weight residual 120.24 122.59 -2.35 6.30e-01 2.52e+00 1.39e+01 angle pdb=" C ILE A 98 " pdb=" CA ILE A 98 " pdb=" CB ILE A 98 " ideal model delta sigma weight residual 114.35 110.93 3.42 1.06e+00 8.90e-01 1.04e+01 angle pdb=" CA TRP A 256 " pdb=" CB TRP A 256 " pdb=" CG TRP A 256 " ideal model delta sigma weight residual 113.60 119.65 -6.05 1.90e+00 2.77e-01 1.01e+01 angle pdb=" CA LEU A 195 " pdb=" CB LEU A 195 " pdb=" CG LEU A 195 " ideal model delta sigma weight residual 116.30 126.03 -9.73 3.50e+00 8.16e-02 7.72e+00 angle pdb=" C ASN A 171 " pdb=" CA ASN A 171 " pdb=" CB ASN A 171 " ideal model delta sigma weight residual 110.24 114.05 -3.81 1.46e+00 4.69e-01 6.83e+00 ... (remaining 3312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 1188 17.92 - 35.83: 183 35.83 - 53.75: 36 53.75 - 71.67: 4 71.67 - 89.59: 3 Dihedral angle restraints: 1414 sinusoidal: 560 harmonic: 854 Sorted by residual: dihedral pdb=" CB CYS A 100 " pdb=" SG CYS A 100 " pdb=" SG CYS A 177 " pdb=" CB CYS A 177 " ideal model delta sinusoidal sigma weight residual -86.00 -156.72 70.72 1 1.00e+01 1.00e-02 6.43e+01 dihedral pdb=" CB GLU A 190 " pdb=" CG GLU A 190 " pdb=" CD GLU A 190 " pdb=" OE1 GLU A 190 " ideal model delta sinusoidal sigma weight residual 0.00 89.59 -89.59 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ARG A 90 " pdb=" CB ARG A 90 " pdb=" CG ARG A 90 " pdb=" CD ARG A 90 " ideal model delta sinusoidal sigma weight residual 180.00 125.46 54.54 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 1411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 221 0.031 - 0.062: 93 0.062 - 0.093: 37 0.093 - 0.124: 22 0.124 - 0.155: 5 Chirality restraints: 378 Sorted by residual: chirality pdb=" CB ILE A 78 " pdb=" CA ILE A 78 " pdb=" CG1 ILE A 78 " pdb=" CG2 ILE A 78 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CG LEU A 195 " pdb=" CB LEU A 195 " pdb=" CD1 LEU A 195 " pdb=" CD2 LEU A 195 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ASN A 171 " pdb=" N ASN A 171 " pdb=" C ASN A 171 " pdb=" CB ASN A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 375 not shown) Planarity restraints: 403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 171 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C ASN A 171 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A 171 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 172 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 199 " -0.028 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO A 200 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO A 31 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.021 5.00e-02 4.00e+02 ... (remaining 400 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 320 2.75 - 3.29: 2488 3.29 - 3.83: 3930 3.83 - 4.36: 4310 4.36 - 4.90: 7723 Nonbonded interactions: 18771 Sorted by model distance: nonbonded pdb=" O ASN A 171 " pdb=" ND2 ASN A 171 " model vdw 2.213 3.120 nonbonded pdb=" O PHE A 276 " pdb=" OG1 THR A 279 " model vdw 2.249 3.040 nonbonded pdb=" OH TYR A 284 " pdb=" O2 NIO A 401 " model vdw 2.276 3.040 nonbonded pdb=" OG SER A 140 " pdb=" OG1 THR A 143 " model vdw 2.294 3.040 nonbonded pdb=" O SER A 298 " pdb=" OG SER A 298 " model vdw 2.335 3.040 ... (remaining 18766 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: 0.340 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.780 Find NCS groups from input model: 0.020 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2444 Z= 0.255 Angle : 0.723 9.727 3317 Z= 0.386 Chirality : 0.046 0.155 378 Planarity : 0.005 0.043 403 Dihedral : 17.218 89.586 850 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.18 % Allowed : 29.13 % Favored : 69.69 % 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: 0.37 (0.51), residues: 289 helix: 0.93 (0.37), residues: 206 sheet: None (None), residues: 0 loop : -1.43 (0.70), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 93 HIS 0.004 0.001 HIS A 184 PHE 0.021 0.001 PHE A 95 TYR 0.012 0.001 TYR A 295 ARG 0.002 0.000 ARG A 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.341 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 0.1275 time to fit residues: 10.0858 Evaluate side-chains 62 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.0050 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2444 Z= 0.224 Angle : 0.594 6.529 3317 Z= 0.319 Chirality : 0.043 0.134 378 Planarity : 0.004 0.040 403 Dihedral : 4.703 35.048 316 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 9.06 % Allowed : 22.44 % Favored : 68.50 % 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: 0.64 (0.52), residues: 289 helix: 1.24 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.86 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 93 HIS 0.003 0.001 HIS A 55 PHE 0.011 0.001 PHE A 197 TYR 0.010 0.002 TYR A 295 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 0.255 Fit side-chains REVERT: A 205 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6213 (tt) REVERT: A 273 ASP cc_start: 0.6995 (t0) cc_final: 0.6756 (m-30) REVERT: A 274 LEU cc_start: 0.8191 (tp) cc_final: 0.7893 (mp) outliers start: 23 outliers final: 10 residues processed: 88 average time/residue: 0.1137 time to fit residues: 12.1169 Evaluate side-chains 77 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 293 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2444 Z= 0.236 Angle : 0.602 6.490 3317 Z= 0.323 Chirality : 0.044 0.137 378 Planarity : 0.004 0.041 403 Dihedral : 4.587 31.762 314 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 10.24 % Allowed : 20.08 % Favored : 69.69 % 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: 0.64 (0.52), residues: 289 helix: 1.22 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.78 (0.75), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.003 0.001 HIS A 55 PHE 0.011 0.001 PHE A 244 TYR 0.008 0.002 TYR A 295 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 65 time to evaluate : 0.276 Fit side-chains REVERT: A 187 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6953 (mm-40) REVERT: A 205 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6210 (tt) REVERT: A 274 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8036 (mp) outliers start: 26 outliers final: 17 residues processed: 81 average time/residue: 0.1069 time to fit residues: 10.6595 Evaluate side-chains 83 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2444 Z= 0.244 Angle : 0.614 6.925 3317 Z= 0.324 Chirality : 0.044 0.149 378 Planarity : 0.004 0.040 403 Dihedral : 4.563 27.742 314 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 11.42 % Allowed : 20.87 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.52), residues: 289 helix: 1.16 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -1.75 (0.75), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.003 0.001 HIS A 161 PHE 0.011 0.001 PHE A 244 TYR 0.008 0.002 TYR A 87 ARG 0.002 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 68 time to evaluate : 0.262 Fit side-chains REVERT: A 205 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6224 (tt) REVERT: A 274 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7898 (mp) outliers start: 29 outliers final: 20 residues processed: 86 average time/residue: 0.1043 time to fit residues: 11.0563 Evaluate side-chains 87 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 293 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 19 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 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 0.032 2444 Z= 0.195 Angle : 0.601 7.300 3317 Z= 0.318 Chirality : 0.044 0.157 378 Planarity : 0.004 0.041 403 Dihedral : 4.468 26.040 314 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 10.63 % Allowed : 23.23 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.53), residues: 289 helix: 1.30 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -1.68 (0.76), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.010 0.001 TYR A 87 ARG 0.002 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 0.264 Fit side-chains REVERT: A 205 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6507 (tt) REVERT: A 274 LEU cc_start: 0.8198 (tp) cc_final: 0.7986 (mp) outliers start: 27 outliers final: 21 residues processed: 89 average time/residue: 0.1128 time to fit residues: 12.2137 Evaluate side-chains 88 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2444 Z= 0.218 Angle : 0.650 13.436 3317 Z= 0.336 Chirality : 0.045 0.148 378 Planarity : 0.004 0.041 403 Dihedral : 4.490 23.461 314 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 11.02 % Allowed : 24.80 % Favored : 64.17 % 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: 0.63 (0.52), residues: 289 helix: 1.18 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -1.72 (0.75), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 93 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.006 0.001 TYR A 269 ARG 0.003 0.000 ARG A 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 69 time to evaluate : 0.281 Fit side-chains REVERT: A 205 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6219 (tt) REVERT: A 274 LEU cc_start: 0.8232 (tp) cc_final: 0.8022 (mp) outliers start: 28 outliers final: 20 residues processed: 86 average time/residue: 0.1111 time to fit residues: 11.6902 Evaluate side-chains 89 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2444 Z= 0.219 Angle : 0.650 7.629 3317 Z= 0.338 Chirality : 0.046 0.139 378 Planarity : 0.004 0.041 403 Dihedral : 4.507 22.318 314 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 10.24 % Allowed : 24.80 % Favored : 64.96 % 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: 0.73 (0.53), residues: 289 helix: 1.24 (0.38), residues: 212 sheet: None (None), residues: 0 loop : -1.62 (0.75), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 93 HIS 0.003 0.001 HIS A 55 PHE 0.010 0.001 PHE A 244 TYR 0.006 0.001 TYR A 294 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 70 time to evaluate : 0.270 Fit side-chains REVERT: A 205 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6212 (tt) REVERT: A 239 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8274 (p) REVERT: A 274 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8008 (mp) outliers start: 26 outliers final: 20 residues processed: 84 average time/residue: 0.1135 time to fit residues: 11.7032 Evaluate side-chains 90 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 67 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2444 Z= 0.284 Angle : 0.704 11.086 3317 Z= 0.364 Chirality : 0.048 0.141 378 Planarity : 0.004 0.040 403 Dihedral : 4.602 18.505 314 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 9.06 % Allowed : 26.77 % Favored : 64.17 % 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: 0.64 (0.52), residues: 289 helix: 1.25 (0.38), residues: 207 sheet: None (None), residues: 0 loop : -1.72 (0.72), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 93 HIS 0.003 0.001 HIS A 55 PHE 0.011 0.001 PHE A 117 TYR 0.009 0.002 TYR A 294 ARG 0.002 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.264 Fit side-chains REVERT: A 205 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6284 (tt) REVERT: A 239 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8427 (p) REVERT: A 274 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8042 (mp) outliers start: 23 outliers final: 17 residues processed: 80 average time/residue: 0.1077 time to fit residues: 10.5826 Evaluate side-chains 85 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2444 Z= 0.229 Angle : 0.695 11.828 3317 Z= 0.357 Chirality : 0.047 0.133 378 Planarity : 0.004 0.041 403 Dihedral : 4.553 18.416 314 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 9.45 % Allowed : 25.20 % Favored : 65.35 % 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: 0.68 (0.53), residues: 289 helix: 1.31 (0.38), residues: 206 sheet: None (None), residues: 0 loop : -1.74 (0.72), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 197 TYR 0.007 0.001 TYR A 294 ARG 0.003 0.000 ARG A 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 69 time to evaluate : 0.264 Fit side-chains REVERT: A 205 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6600 (tt) REVERT: A 239 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8418 (p) REVERT: A 274 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7904 (tp) outliers start: 24 outliers final: 17 residues processed: 83 average time/residue: 0.1086 time to fit residues: 11.1026 Evaluate side-chains 86 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2444 Z= 0.235 Angle : 0.700 12.524 3317 Z= 0.358 Chirality : 0.047 0.138 378 Planarity : 0.004 0.041 403 Dihedral : 4.554 17.261 314 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 8.27 % Allowed : 25.98 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.52), residues: 289 helix: 1.28 (0.38), residues: 206 sheet: None (None), residues: 0 loop : -1.77 (0.72), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 93 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 197 TYR 0.007 0.001 TYR A 294 ARG 0.003 0.000 ARG A 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 0.223 Fit side-chains REVERT: A 205 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6516 (tt) REVERT: A 239 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8428 (p) REVERT: A 274 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7906 (tp) outliers start: 21 outliers final: 18 residues processed: 78 average time/residue: 0.1069 time to fit residues: 10.3074 Evaluate side-chains 88 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 chunk 11 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 ASN A 259 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.174252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.152003 restraints weight = 3264.395| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.03 r_work: 0.3630 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2444 Z= 0.216 Angle : 0.701 12.487 3317 Z= 0.360 Chirality : 0.047 0.134 378 Planarity : 0.004 0.041 403 Dihedral : 4.510 17.508 314 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 8.66 % Allowed : 25.59 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.53), residues: 289 helix: 1.27 (0.38), residues: 206 sheet: None (None), residues: 0 loop : -1.68 (0.73), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 59 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.010 0.001 TYR A 295 ARG 0.002 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 960.49 seconds wall clock time: 17 minutes 43.77 seconds (1063.77 seconds total)