Starting phenix.real_space_refine on Sun Mar 10 14:50:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/03_2024/8k5b_36900_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/03_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_36900/03_2024/8k5b_36900.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/03_2024/8k5b_36900.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/03_2024/8k5b_36900_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5b_36900/03_2024/8k5b_36900_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 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-5265/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: 1.91, per 1000 atoms: 0.80 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: 1.04 Conformation dependent library (CDL) restraints added in 436.4 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... running ksdssp... Secondary structure from input PDB file: 9 helices and 1 sheets defined 69.1% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 30 through 53 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 60 through 88 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 98 through 130 Processing helix chain 'A' and resid 141 through 157 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.639A pdb=" N LYS A 164 " --> pdb=" O HIS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 217 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 226 through 260 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 270 through 294 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= A, first strand: chain 'A' and resid 169 through 171 150 hydrogen bonds defined for protein. 441 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: 0.60 Time building geometry restraints manager: 1.12 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: 2497 3.29 - 3.83: 3938 3.83 - 4.36: 4334 4.36 - 4.90: 7726 Nonbonded interactions: 18815 Sorted by model distance: nonbonded pdb=" O ASN A 171 " pdb=" ND2 ASN A 171 " model vdw 2.213 2.520 nonbonded pdb=" O PHE A 276 " pdb=" OG1 THR A 279 " model vdw 2.249 2.440 nonbonded pdb=" OH TYR A 284 " pdb=" O2 NIO A 401 " model vdw 2.276 2.440 nonbonded pdb=" OG SER A 140 " pdb=" OG1 THR A 143 " model vdw 2.294 2.440 nonbonded pdb=" O SER A 298 " pdb=" OG SER A 298 " model vdw 2.335 2.440 ... (remaining 18810 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: 0.010 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.820 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.060 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.670 ------------------------------------------------------------------------------- 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= 0.247 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 : 0.283 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 65 average time/residue: 0.1243 time to fit residues: 9.7504 Evaluate side-chains 62 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.246 ------------------------------------------------------------------------------- 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: 0.7980 chunk 21 optimal weight: 0.0670 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2444 Z= 0.199 Angle : 0.563 6.467 3317 Z= 0.300 Chirality : 0.043 0.130 378 Planarity : 0.004 0.040 403 Dihedral : 4.419 17.748 316 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.33 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: 0.75 (0.52), residues: 289 helix: 1.25 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -1.62 (0.76), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 93 HIS 0.003 0.001 HIS A 184 PHE 0.010 0.001 PHE A 244 TYR 0.006 0.001 TYR A 295 ARG 0.002 0.000 ARG A 251 *********************** 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 92 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 0.296 Fit side-chains REVERT: A 205 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6199 (tt) REVERT: A 269 TYR cc_start: 0.6783 (m-80) cc_final: 0.6319 (m-80) REVERT: A 274 LEU cc_start: 0.8185 (tp) cc_final: 0.7957 (mp) outliers start: 23 outliers final: 9 residues processed: 86 average time/residue: 0.1095 time to fit residues: 11.5456 Evaluate side-chains 75 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7680 moved from start: 0.0786 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= 0.242 Angle : 0.592 6.452 3317 Z= 0.312 Chirality : 0.043 0.138 378 Planarity : 0.004 0.039 403 Dihedral : 4.304 15.066 314 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 9.06 % Allowed : 23.23 % 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: 0.55 (0.52), residues: 289 helix: 1.15 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.77 (0.73), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 93 HIS 0.004 0.001 HIS A 189 PHE 0.012 0.001 PHE A 244 TYR 0.009 0.002 TYR A 87 ARG 0.002 0.000 ARG A 142 *********************** 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 88 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 65 time to evaluate : 0.280 Fit side-chains REVERT: A 205 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6240 (tt) outliers start: 23 outliers final: 15 residues processed: 79 average time/residue: 0.1112 time to fit residues: 10.7503 Evaluate side-chains 79 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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 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 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 12 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.7661 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2444 Z= 0.195 Angle : 0.580 6.663 3317 Z= 0.305 Chirality : 0.043 0.148 378 Planarity : 0.004 0.040 403 Dihedral : 4.255 14.860 314 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 11.42 % Allowed : 23.23 % 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: 0.65 (0.52), residues: 289 helix: 1.21 (0.37), residues: 210 sheet: None (None), residues: 0 loop : -1.69 (0.74), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 93 HIS 0.003 0.001 HIS A 189 PHE 0.010 0.001 PHE A 244 TYR 0.014 0.002 TYR A 269 ARG 0.001 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 99 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 0.332 Fit side-chains REVERT: A 205 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6201 (tt) outliers start: 29 outliers final: 19 residues processed: 89 average time/residue: 0.1153 time to fit residues: 12.4272 Evaluate side-chains 83 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 63 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 293 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.0050 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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: 0.7659 moved from start: 0.1150 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= 0.190 Angle : 0.595 7.110 3317 Z= 0.310 Chirality : 0.045 0.158 378 Planarity : 0.004 0.040 403 Dihedral : 4.265 14.724 314 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 10.63 % Allowed : 24.80 % Favored : 64.57 % 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: 1.29 (0.38), residues: 210 sheet: None (None), residues: 0 loop : -1.70 (0.73), residues: 79 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 0.009 0.001 PHE A 244 TYR 0.012 0.002 TYR A 269 ARG 0.003 0.000 ARG A 22 *********************** 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 93 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 0.292 Fit side-chains REVERT: A 205 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6197 (tt) outliers start: 27 outliers final: 17 residues processed: 82 average time/residue: 0.0952 time to fit residues: 9.8911 Evaluate side-chains 81 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 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 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: 0.0980 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 2 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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: 0.7632 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2444 Z= 0.176 Angle : 0.628 14.041 3317 Z= 0.319 Chirality : 0.044 0.151 378 Planarity : 0.004 0.040 403 Dihedral : 4.203 14.729 314 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 9.84 % Allowed : 27.17 % Favored : 62.99 % 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: 0.81 (0.53), residues: 289 helix: 1.37 (0.38), residues: 209 sheet: None (None), residues: 0 loop : -1.72 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 93 HIS 0.003 0.001 HIS A 184 PHE 0.009 0.001 PHE A 244 TYR 0.011 0.002 TYR A 269 ARG 0.002 0.000 ARG A 22 *********************** 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 93 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 68 time to evaluate : 0.309 Fit side-chains REVERT: A 205 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6566 (tt) REVERT: A 269 TYR cc_start: 0.6879 (m-80) cc_final: 0.6617 (m-80) outliers start: 25 outliers final: 20 residues processed: 82 average time/residue: 0.1008 time to fit residues: 10.3143 Evaluate side-chains 86 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 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 43 LEU 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 160 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2444 Z= 0.193 Angle : 0.612 7.319 3317 Z= 0.314 Chirality : 0.046 0.156 378 Planarity : 0.004 0.039 403 Dihedral : 4.259 15.478 314 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 10.63 % Allowed : 26.38 % Favored : 62.99 % 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: 1.35 (0.38), residues: 209 sheet: None (None), residues: 0 loop : -1.72 (0.73), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 93 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 232 TYR 0.010 0.002 TYR A 87 ARG 0.002 0.000 ARG A 22 *********************** 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 92 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 65 time to evaluate : 0.260 Fit side-chains REVERT: A 205 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6188 (tt) REVERT: A 239 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8281 (p) outliers start: 27 outliers final: 20 residues processed: 79 average time/residue: 0.0878 time to fit residues: 8.7862 Evaluate side-chains 87 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 85 ASP Chi-restraints excluded: chain A residue 100 CYS 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 160 VAL 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 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 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: 1.9990 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 0.0060 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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: 0.7641 moved from start: 0.1372 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= 0.188 Angle : 0.640 13.030 3317 Z= 0.321 Chirality : 0.045 0.151 378 Planarity : 0.004 0.039 403 Dihedral : 4.269 16.082 314 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 10.63 % Allowed : 26.77 % Favored : 62.60 % 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: 0.76 (0.53), residues: 289 helix: 1.34 (0.38), residues: 209 sheet: None (None), residues: 0 loop : -1.74 (0.73), residues: 80 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 0.009 0.001 PHE A 232 TYR 0.012 0.001 TYR A 87 ARG 0.001 0.000 ARG A 22 *********************** 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 93 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 66 time to evaluate : 0.307 Fit side-chains REVERT: A 195 LEU cc_start: 0.8441 (mp) cc_final: 0.8026 (tt) REVERT: A 205 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6181 (tt) REVERT: A 239 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8313 (p) outliers start: 27 outliers final: 21 residues processed: 80 average time/residue: 0.1039 time to fit residues: 10.4828 Evaluate side-chains 87 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 64 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 76 LEU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 100 CYS 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 160 VAL Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 196 GLU 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: 3.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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: 0.7638 moved from start: 0.1433 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= 0.190 Angle : 0.635 11.960 3317 Z= 0.321 Chirality : 0.046 0.156 378 Planarity : 0.004 0.039 403 Dihedral : 4.269 16.706 314 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 9.84 % Allowed : 27.56 % Favored : 62.60 % 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: 0.69 (0.52), residues: 289 helix: 1.28 (0.38), residues: 209 sheet: None (None), residues: 0 loop : -1.77 (0.72), residues: 80 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 0.012 0.001 PHE A 38 TYR 0.005 0.001 TYR A 294 ARG 0.001 0.000 ARG A 251 *********************** 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 89 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 64 time to evaluate : 0.328 Fit side-chains REVERT: A 205 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6178 (tt) REVERT: A 239 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8338 (p) outliers start: 25 outliers final: 20 residues processed: 76 average time/residue: 0.1064 time to fit residues: 10.1928 Evaluate side-chains 85 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 76 LEU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 100 CYS 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 160 VAL Chi-restraints excluded: chain A residue 171 ASN 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 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: 3.9990 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.0270 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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: 0.7639 moved from start: 0.1456 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= 0.191 Angle : 0.653 14.695 3317 Z= 0.327 Chirality : 0.046 0.151 378 Planarity : 0.004 0.039 403 Dihedral : 4.299 17.392 314 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 9.45 % Allowed : 27.56 % Favored : 62.99 % 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: 0.74 (0.52), residues: 289 helix: 1.47 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -1.93 (0.69), residues: 86 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 0.012 0.001 PHE A 38 TYR 0.013 0.001 TYR A 87 ARG 0.001 0.000 ARG A 111 ********************** 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: 24 poor density : 64 time to evaluate : 0.271 Fit side-chains REVERT: A 205 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6173 (tt) REVERT: A 239 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8342 (p) outliers start: 24 outliers final: 20 residues processed: 77 average time/residue: 0.0968 time to fit residues: 9.3372 Evaluate side-chains 85 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 63 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 76 LEU Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 100 CYS 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 160 VAL Chi-restraints excluded: chain A residue 171 ASN 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 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: 0.3980 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.171805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150035 restraints weight = 3275.753| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.01 r_work: 0.3618 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2444 Z= 0.195 Angle : 0.659 14.302 3317 Z= 0.329 Chirality : 0.046 0.153 378 Planarity : 0.004 0.039 403 Dihedral : 4.293 17.522 314 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 9.84 % Allowed : 27.95 % Favored : 62.20 % 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: 0.72 (0.52), residues: 289 helix: 1.46 (0.38), residues: 203 sheet: None (None), residues: 0 loop : -1.96 (0.69), residues: 86 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 0.011 0.001 PHE A 38 TYR 0.009 0.001 TYR A 269 ARG 0.001 0.000 ARG A 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 970.53 seconds wall clock time: 18 minutes 45.53 seconds (1125.53 seconds total)