Starting phenix.real_space_refine on Wed Mar 5 18:27:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvu_38719/03_2025/8xvu_38719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvu_38719/03_2025/8xvu_38719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xvu_38719/03_2025/8xvu_38719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvu_38719/03_2025/8xvu_38719.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvu_38719/03_2025/8xvu_38719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvu_38719/03_2025/8xvu_38719.cif" } resolution = 3.09 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= 1.000 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 28 5.16 5 C 2151 2.51 5 N 556 2.21 5 O 553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3288 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2367 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 288} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 496 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 63} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 425 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 55} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.63, per 1000 atoms: 0.80 Number of scatterers: 3288 At special positions: 0 Unit cell: (69.5125, 77.8125, 94.4125, 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 28 16.00 O 553 8.00 N 556 7.00 C 2151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 35 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 35 " distance=2.03 Simple disulfide: pdb=" SG CYS E 11 " - pdb=" SG CYS E 51 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 359.2 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 816 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 2 sheets defined 65.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'R' and resid 44 through 76 removed outlier: 3.601A pdb=" N PHE R 50 " --> pdb=" O ILE R 46 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 153 through 160 removed outlier: 3.832A pdb=" N THR R 156 " --> pdb=" O ARG R 153 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.588A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 Processing helix chain 'R' and resid 220 through 240 removed outlier: 3.662A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 330 removed outlier: 3.849A pdb=" N ALA R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 56 through 69 removed outlier: 3.807A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 removed outlier: 3.914A pdb=" N LYS E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AA2, first strand: chain 'D' and resid 49 through 52 removed outlier: 4.240A pdb=" N VAL D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 43 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL E 26 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE E 41 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N VAL E 28 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU E 39 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 636 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: 0.91 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1028 1.34 - 1.46: 732 1.46 - 1.58: 1553 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 3352 Sorted by residual: bond pdb=" N GLN E 13 " pdb=" CA GLN E 13 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.25e-02 6.40e+03 4.51e+00 bond pdb=" C GLN E 13 " pdb=" O GLN E 13 " ideal model delta sigma weight residual 1.235 1.253 -0.018 1.22e-02 6.72e+03 2.15e+00 bond pdb=" CA GLN E 13 " pdb=" C GLN E 13 " ideal model delta sigma weight residual 1.521 1.534 -0.014 1.24e-02 6.50e+03 1.20e+00 bond pdb=" CB VAL R 162 " pdb=" CG1 VAL R 162 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.07e-01 bond pdb=" CA LEU E 12 " pdb=" CB LEU E 12 " ideal model delta sigma weight residual 1.535 1.521 0.014 1.69e-02 3.50e+03 7.04e-01 ... (remaining 3347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 4274 0.88 - 1.77: 232 1.77 - 2.65: 33 2.65 - 3.54: 12 3.54 - 4.42: 10 Bond angle restraints: 4561 Sorted by residual: angle pdb=" O LEU E 12 " pdb=" C LEU E 12 " pdb=" N GLN E 13 " ideal model delta sigma weight residual 121.92 124.45 -2.53 1.30e+00 5.92e-01 3.79e+00 angle pdb=" N ASN R 110 " pdb=" CA ASN R 110 " pdb=" C ASN R 110 " ideal model delta sigma weight residual 112.30 114.89 -2.59 1.36e+00 5.41e-01 3.64e+00 angle pdb=" C LEU E 12 " pdb=" N GLN E 13 " pdb=" CA GLN E 13 " ideal model delta sigma weight residual 122.73 119.71 3.02 1.62e+00 3.81e-01 3.48e+00 angle pdb=" CA LEU E 12 " pdb=" C LEU E 12 " pdb=" N GLN E 13 " ideal model delta sigma weight residual 117.88 115.40 2.48 1.40e+00 5.10e-01 3.13e+00 angle pdb=" CA ASN R 310 " pdb=" C ASN R 310 " pdb=" N PRO R 311 " ideal model delta sigma weight residual 120.77 119.14 1.63 9.70e-01 1.06e+00 2.82e+00 ... (remaining 4556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 1867 17.97 - 35.93: 136 35.93 - 53.90: 22 53.90 - 71.87: 10 71.87 - 89.83: 3 Dihedral angle restraints: 2038 sinusoidal: 786 harmonic: 1252 Sorted by residual: dihedral pdb=" CA PHE R 220 " pdb=" C PHE R 220 " pdb=" N ILE R 221 " pdb=" CA ILE R 221 " ideal model delta harmonic sigma weight residual 180.00 -164.56 -15.44 0 5.00e+00 4.00e-02 9.54e+00 dihedral pdb=" CB MET D 58 " pdb=" CG MET D 58 " pdb=" SD MET D 58 " pdb=" CE MET D 58 " ideal model delta sinusoidal sigma weight residual -60.00 -116.07 56.07 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CG ARG R 322 " pdb=" CD ARG R 322 " pdb=" NE ARG R 322 " pdb=" CZ ARG R 322 " ideal model delta sinusoidal sigma weight residual 90.00 131.26 -41.26 2 1.50e+01 4.44e-03 9.28e+00 ... (remaining 2035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 334 0.025 - 0.050: 138 0.050 - 0.075: 57 0.075 - 0.100: 21 0.100 - 0.125: 17 Chirality restraints: 567 Sorted by residual: chirality pdb=" CA ILE R 282 " pdb=" N ILE R 282 " pdb=" C ILE R 282 " pdb=" CB ILE R 282 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE E 41 " pdb=" N ILE E 41 " pdb=" C ILE E 41 " pdb=" CB ILE E 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA ILE E 18 " pdb=" N ILE E 18 " pdb=" C ILE E 18 " pdb=" CB ILE E 18 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 564 not shown) Planarity restraints: 556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 119 " 0.005 2.00e-02 2.50e+03 9.23e-03 8.52e-01 pdb=" C CYS R 119 " -0.016 2.00e-02 2.50e+03 pdb=" O CYS R 119 " 0.006 2.00e-02 2.50e+03 pdb=" N LYS R 120 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 214 " 0.014 5.00e-02 4.00e+02 2.14e-02 7.32e-01 pdb=" N PRO R 215 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 310 " 0.013 5.00e-02 4.00e+02 1.91e-02 5.81e-01 pdb=" N PRO R 311 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO R 311 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO R 311 " 0.011 5.00e-02 4.00e+02 ... (remaining 553 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 1188 2.88 - 3.39: 3317 3.39 - 3.89: 5236 3.89 - 4.40: 5667 4.40 - 4.90: 10128 Nonbonded interactions: 25536 Sorted by model distance: nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.377 3.040 nonbonded pdb=" NE ARG R 185 " pdb=" OD2 ASP R 199 " model vdw 2.396 3.120 nonbonded pdb=" OD1 ASP R 143 " pdb=" NH1 ARG R 159 " model vdw 2.446 3.120 nonbonded pdb=" O PHE R 97 " pdb=" OG1 THR R 100 " model vdw 2.468 3.040 nonbonded pdb=" O LEU R 125 " pdb=" ND2 ASN R 129 " model vdw 2.481 3.120 ... (remaining 25531 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 9 through 11 or (resid 12 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 36 or (resid 37 and (nam \ e N or name CA or name C or name O or name CB )) or resid 38 through 68)) selection = (chain 'E' and (resid 9 through 63 or (resid 64 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 67 or (resid 68 and (nam \ e N or name CA or name C or name O or name CB )))) } 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.610 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 0.028 3352 Z= 0.238 Angle : 0.511 4.423 4561 Z= 0.289 Chirality : 0.038 0.125 567 Planarity : 0.003 0.021 556 Dihedral : 13.713 89.833 1204 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.41), residues: 421 helix: 2.07 (0.32), residues: 261 sheet: 0.88 (0.75), residues: 51 loop : -0.08 (0.58), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 112 HIS 0.007 0.001 HIS R 150 PHE 0.010 0.001 PHE R 50 TYR 0.005 0.001 TYR R 267 ARG 0.003 0.000 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.343 Fit side-chains REVERT: R 48 LYS cc_start: 0.7110 (mttt) cc_final: 0.6814 (ttpp) REVERT: R 126 LYS cc_start: 0.8060 (tttt) cc_final: 0.7728 (ttpp) REVERT: R 243 MET cc_start: 0.7082 (mtm) cc_final: 0.6683 (mtt) REVERT: R 245 GLN cc_start: 0.8399 (mp10) cc_final: 0.7178 (tt0) REVERT: R 320 LYS cc_start: 0.8337 (ttmt) cc_final: 0.8104 (ttmm) REVERT: D 43 THR cc_start: 0.9014 (m) cc_final: 0.8637 (t) REVERT: D 53 ASN cc_start: 0.8942 (t0) cc_final: 0.8688 (t0) REVERT: E 27 LYS cc_start: 0.8584 (tttt) cc_final: 0.8258 (ttpp) REVERT: E 46 ASN cc_start: 0.8763 (p0) cc_final: 0.8291 (p0) REVERT: E 53 ASN cc_start: 0.8217 (t0) cc_final: 0.7936 (t0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1592 time to fit residues: 23.8932 Evaluate side-chains 90 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 ASN R 157 GLN R 323 HIS D 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.126162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.099747 restraints weight = 5270.098| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.42 r_work: 0.3080 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3352 Z= 0.309 Angle : 0.619 8.056 4561 Z= 0.311 Chirality : 0.042 0.131 567 Planarity : 0.004 0.022 556 Dihedral : 3.820 18.380 453 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.79 % Allowed : 13.65 % Favored : 83.57 % 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: 1.89 (0.41), residues: 421 helix: 1.94 (0.32), residues: 257 sheet: 0.81 (0.73), residues: 51 loop : -0.07 (0.59), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 112 HIS 0.014 0.002 HIS R 323 PHE 0.012 0.002 PHE R 97 TYR 0.011 0.002 TYR R 160 ARG 0.003 0.001 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: R 126 LYS cc_start: 0.8763 (tttt) cc_final: 0.8530 (ttpp) REVERT: R 160 TYR cc_start: 0.6410 (m-80) cc_final: 0.6181 (m-80) REVERT: R 245 GLN cc_start: 0.8653 (mp10) cc_final: 0.7281 (tt0) REVERT: R 276 LEU cc_start: 0.9357 (mt) cc_final: 0.9138 (mt) REVERT: R 280 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7849 (tm-30) REVERT: R 320 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8251 (ttmm) REVERT: D 30 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8562 (p) REVERT: D 39 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8432 (mt-10) REVERT: D 43 THR cc_start: 0.9100 (m) cc_final: 0.8787 (t) REVERT: D 53 ASN cc_start: 0.9014 (t0) cc_final: 0.8757 (t0) REVERT: D 58 MET cc_start: 0.8716 (mpp) cc_final: 0.8408 (tpt) REVERT: D 62 ILE cc_start: 0.9447 (mt) cc_final: 0.9072 (mt) REVERT: E 44 LEU cc_start: 0.8878 (mp) cc_final: 0.8444 (mm) REVERT: E 53 ASN cc_start: 0.8368 (t0) cc_final: 0.7965 (t0) outliers start: 10 outliers final: 2 residues processed: 97 average time/residue: 0.1664 time to fit residues: 19.7254 Evaluate side-chains 89 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.128415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101157 restraints weight = 5193.088| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.18 r_work: 0.3131 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3352 Z= 0.184 Angle : 0.549 5.726 4561 Z= 0.284 Chirality : 0.040 0.128 567 Planarity : 0.003 0.022 556 Dihedral : 4.042 24.184 453 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.95 % Allowed : 13.93 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.42), residues: 421 helix: 2.06 (0.32), residues: 262 sheet: 0.64 (0.74), residues: 52 loop : 0.16 (0.66), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 112 HIS 0.003 0.001 HIS R 150 PHE 0.007 0.001 PHE R 97 TYR 0.006 0.001 TYR R 86 ARG 0.002 0.000 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8630 (mp10) cc_final: 0.7265 (tt0) REVERT: R 280 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7751 (tm-30) REVERT: D 13 GLN cc_start: 0.8534 (mt0) cc_final: 0.8188 (mp10) REVERT: D 43 THR cc_start: 0.9091 (m) cc_final: 0.8817 (t) REVERT: D 53 ASN cc_start: 0.8927 (t0) cc_final: 0.8683 (t0) REVERT: D 58 MET cc_start: 0.8558 (mpp) cc_final: 0.8209 (tpt) REVERT: E 44 LEU cc_start: 0.8900 (mp) cc_final: 0.8506 (mm) REVERT: E 48 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7977 (mp10) REVERT: E 53 ASN cc_start: 0.8317 (t0) cc_final: 0.7946 (t0) REVERT: E 66 MET cc_start: 0.8006 (mtt) cc_final: 0.7700 (mtm) outliers start: 7 outliers final: 4 residues processed: 92 average time/residue: 0.1532 time to fit residues: 17.0385 Evaluate side-chains 89 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 307 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.127707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101933 restraints weight = 5291.629| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.33 r_work: 0.3112 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3352 Z= 0.190 Angle : 0.524 5.167 4561 Z= 0.273 Chirality : 0.039 0.121 567 Planarity : 0.003 0.022 556 Dihedral : 3.898 24.910 453 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.95 % Allowed : 14.21 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.42), residues: 421 helix: 2.19 (0.32), residues: 260 sheet: 0.76 (0.75), residues: 52 loop : 0.14 (0.63), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 112 HIS 0.003 0.001 HIS R 150 PHE 0.008 0.001 PHE R 97 TYR 0.005 0.001 TYR R 86 ARG 0.002 0.000 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8599 (mp10) cc_final: 0.7219 (tt0) REVERT: R 280 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7674 (tm-30) REVERT: D 13 GLN cc_start: 0.8526 (mt0) cc_final: 0.8200 (mp10) REVERT: D 43 THR cc_start: 0.9102 (m) cc_final: 0.8812 (t) REVERT: D 53 ASN cc_start: 0.8889 (t0) cc_final: 0.8604 (t0) REVERT: D 58 MET cc_start: 0.8621 (mpp) cc_final: 0.8418 (tpt) REVERT: E 44 LEU cc_start: 0.8907 (mp) cc_final: 0.8507 (mm) REVERT: E 48 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7932 (mp10) REVERT: E 53 ASN cc_start: 0.8328 (t0) cc_final: 0.8004 (t0) REVERT: E 66 MET cc_start: 0.8074 (mtt) cc_final: 0.7830 (mtm) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 0.1596 time to fit residues: 17.0569 Evaluate side-chains 89 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 306 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.098067 restraints weight = 5288.983| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.42 r_work: 0.3046 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 3352 Z= 0.367 Angle : 0.605 5.266 4561 Z= 0.315 Chirality : 0.042 0.128 567 Planarity : 0.004 0.026 556 Dihedral : 4.150 24.008 453 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.23 % Allowed : 15.32 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.41), residues: 421 helix: 1.77 (0.32), residues: 259 sheet: 0.63 (0.75), residues: 52 loop : -0.13 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 112 HIS 0.007 0.001 HIS R 150 PHE 0.015 0.002 PHE R 233 TYR 0.006 0.001 TYR R 145 ARG 0.003 0.001 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8609 (mp10) cc_final: 0.7267 (tt0) REVERT: R 280 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7818 (tm-30) REVERT: R 297 ASP cc_start: 0.8298 (m-30) cc_final: 0.8096 (m-30) REVERT: D 6 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8175 (mm-30) REVERT: D 43 THR cc_start: 0.9105 (m) cc_final: 0.8813 (t) REVERT: D 53 ASN cc_start: 0.9013 (t0) cc_final: 0.8767 (t0) REVERT: E 44 LEU cc_start: 0.8981 (mp) cc_final: 0.8592 (mm) REVERT: E 48 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7904 (mp10) REVERT: E 53 ASN cc_start: 0.8403 (t0) cc_final: 0.8039 (t0) REVERT: E 66 MET cc_start: 0.7894 (mtt) cc_final: 0.7610 (mtm) outliers start: 8 outliers final: 7 residues processed: 88 average time/residue: 0.1557 time to fit residues: 16.4723 Evaluate side-chains 90 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.125336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099380 restraints weight = 5469.081| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.46 r_work: 0.3067 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3352 Z= 0.253 Angle : 0.566 5.351 4561 Z= 0.294 Chirality : 0.041 0.126 567 Planarity : 0.003 0.023 556 Dihedral : 4.043 23.238 453 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.79 % Allowed : 15.60 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.42), residues: 421 helix: 1.89 (0.32), residues: 260 sheet: 0.74 (0.78), residues: 52 loop : -0.13 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 112 HIS 0.002 0.001 HIS R 150 PHE 0.010 0.001 PHE R 233 TYR 0.003 0.001 TYR R 131 ARG 0.002 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8603 (mp10) cc_final: 0.7255 (tt0) REVERT: R 280 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8068 (tm-30) REVERT: D 6 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8132 (mm-30) REVERT: D 43 THR cc_start: 0.9108 (m) cc_final: 0.8831 (t) REVERT: D 58 MET cc_start: 0.8519 (tpt) cc_final: 0.8247 (tpp) REVERT: E 44 LEU cc_start: 0.8942 (mp) cc_final: 0.8553 (mm) REVERT: E 48 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7981 (mp10) REVERT: E 53 ASN cc_start: 0.8402 (t0) cc_final: 0.8126 (t0) REVERT: E 66 MET cc_start: 0.7967 (mtt) cc_final: 0.7760 (mtm) outliers start: 10 outliers final: 6 residues processed: 89 average time/residue: 0.1505 time to fit residues: 16.3751 Evaluate side-chains 90 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 304 ILE Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 0.0010 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100214 restraints weight = 5288.311| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.45 r_work: 0.3075 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3352 Z= 0.227 Angle : 0.558 5.535 4561 Z= 0.291 Chirality : 0.040 0.129 567 Planarity : 0.003 0.022 556 Dihedral : 4.013 22.579 453 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.95 % Allowed : 15.88 % Favored : 82.17 % 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: 1.90 (0.42), residues: 421 helix: 1.98 (0.32), residues: 260 sheet: 0.71 (0.78), residues: 52 loop : -0.14 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.002 0.001 HIS R 306 PHE 0.009 0.001 PHE R 233 TYR 0.004 0.001 TYR R 131 ARG 0.001 0.000 ARG R 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.400 Fit side-chains REVERT: R 245 GLN cc_start: 0.8602 (mp10) cc_final: 0.7244 (tt0) REVERT: R 280 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8133 (tm-30) REVERT: D 6 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8081 (mm-30) REVERT: D 43 THR cc_start: 0.9117 (m) cc_final: 0.8838 (t) REVERT: D 58 MET cc_start: 0.8577 (tpt) cc_final: 0.8288 (tpp) REVERT: E 44 LEU cc_start: 0.8923 (mp) cc_final: 0.8546 (mm) REVERT: E 48 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7993 (mp10) REVERT: E 53 ASN cc_start: 0.8380 (t0) cc_final: 0.8071 (t0) REVERT: E 66 MET cc_start: 0.7965 (mtt) cc_final: 0.7721 (mtm) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.2121 time to fit residues: 22.2759 Evaluate side-chains 86 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.127038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101243 restraints weight = 5296.184| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.35 r_work: 0.3107 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3352 Z= 0.184 Angle : 0.549 5.956 4561 Z= 0.283 Chirality : 0.040 0.141 567 Planarity : 0.003 0.021 556 Dihedral : 3.952 21.044 453 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.67 % Allowed : 17.55 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.42), residues: 421 helix: 2.11 (0.32), residues: 256 sheet: 0.78 (0.79), residues: 52 loop : -0.25 (0.60), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 207 HIS 0.002 0.001 HIS R 306 PHE 0.007 0.001 PHE R 97 TYR 0.005 0.001 TYR R 86 ARG 0.001 0.000 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8551 (mp10) cc_final: 0.7221 (tt0) REVERT: D 6 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7992 (mm-30) REVERT: D 43 THR cc_start: 0.9113 (m) cc_final: 0.8851 (t) REVERT: D 56 SER cc_start: 0.9244 (t) cc_final: 0.8935 (m) REVERT: D 58 MET cc_start: 0.8514 (tpt) cc_final: 0.8157 (tpp) REVERT: E 44 LEU cc_start: 0.8914 (mp) cc_final: 0.8545 (mm) REVERT: E 53 ASN cc_start: 0.8353 (t0) cc_final: 0.8125 (t0) REVERT: E 66 MET cc_start: 0.8034 (mtt) cc_final: 0.7780 (mtm) outliers start: 6 outliers final: 6 residues processed: 90 average time/residue: 0.1410 time to fit residues: 15.7635 Evaluate side-chains 88 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.125228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.099747 restraints weight = 5397.703| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.60 r_work: 0.3067 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3352 Z= 0.314 Angle : 0.642 9.476 4561 Z= 0.329 Chirality : 0.042 0.166 567 Planarity : 0.004 0.024 556 Dihedral : 4.135 20.877 453 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.23 % Allowed : 17.27 % Favored : 80.50 % 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: 1.73 (0.41), residues: 421 helix: 1.79 (0.31), residues: 260 sheet: 0.77 (0.79), residues: 52 loop : -0.12 (0.62), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 112 HIS 0.003 0.001 HIS R 150 PHE 0.012 0.002 PHE R 233 TYR 0.005 0.001 TYR R 314 ARG 0.001 0.000 ARG R 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: D 6 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8116 (mm-30) REVERT: D 43 THR cc_start: 0.9087 (m) cc_final: 0.8817 (t) REVERT: D 56 SER cc_start: 0.9282 (t) cc_final: 0.8995 (m) REVERT: D 58 MET cc_start: 0.8539 (tpt) cc_final: 0.8211 (tpp) REVERT: E 44 LEU cc_start: 0.8838 (mp) cc_final: 0.8535 (mm) REVERT: E 53 ASN cc_start: 0.8385 (t0) cc_final: 0.8087 (t0) REVERT: E 66 MET cc_start: 0.8036 (mtt) cc_final: 0.7753 (mtm) outliers start: 8 outliers final: 6 residues processed: 88 average time/residue: 0.1506 time to fit residues: 16.2701 Evaluate side-chains 88 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.126039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100827 restraints weight = 5193.869| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.29 r_work: 0.3106 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3352 Z= 0.210 Angle : 0.623 10.304 4561 Z= 0.319 Chirality : 0.041 0.151 567 Planarity : 0.003 0.023 556 Dihedral : 4.076 20.649 453 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.67 % Allowed : 18.11 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.42), residues: 421 helix: 2.00 (0.32), residues: 256 sheet: 0.73 (0.79), residues: 52 loop : -0.21 (0.61), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 112 HIS 0.002 0.001 HIS R 306 PHE 0.007 0.001 PHE R 97 TYR 0.005 0.001 TYR R 55 ARG 0.001 0.000 ARG R 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: R 245 GLN cc_start: 0.8556 (mp10) cc_final: 0.7228 (tt0) REVERT: D 6 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8051 (mm-30) REVERT: D 43 THR cc_start: 0.9101 (m) cc_final: 0.8830 (t) REVERT: D 56 SER cc_start: 0.9304 (t) cc_final: 0.9000 (m) REVERT: D 58 MET cc_start: 0.8426 (tpt) cc_final: 0.8111 (tpp) REVERT: E 44 LEU cc_start: 0.8776 (mp) cc_final: 0.8494 (mm) REVERT: E 53 ASN cc_start: 0.8330 (t0) cc_final: 0.8094 (t0) REVERT: E 66 MET cc_start: 0.8075 (mtt) cc_final: 0.7820 (mtm) outliers start: 6 outliers final: 5 residues processed: 86 average time/residue: 0.1534 time to fit residues: 16.3659 Evaluate side-chains 87 residues out of total 376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 307 SER Chi-restraints excluded: chain D residue 30 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.0670 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101746 restraints weight = 5213.652| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.31 r_work: 0.3122 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3352 Z= 0.199 Angle : 0.609 9.981 4561 Z= 0.312 Chirality : 0.040 0.149 567 Planarity : 0.003 0.021 556 Dihedral : 3.993 20.184 453 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.39 % Allowed : 18.38 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.42), residues: 421 helix: 2.13 (0.32), residues: 256 sheet: 0.81 (0.85), residues: 47 loop : -0.16 (0.58), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 264 HIS 0.002 0.001 HIS R 306 PHE 0.007 0.001 PHE R 97 TYR 0.005 0.001 TYR R 55 ARG 0.001 0.000 ARG D 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.17 seconds wall clock time: 41 minutes 49.81 seconds (2509.81 seconds total)