Starting phenix.real_space_refine on Wed Mar 5 18:36:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwa_38732/03_2025/8xwa_38732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwa_38732/03_2025/8xwa_38732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xwa_38732/03_2025/8xwa_38732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwa_38732/03_2025/8xwa_38732.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwa_38732/03_2025/8xwa_38732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwa_38732/03_2025/8xwa_38732.cif" } resolution = 3.48 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 26 5.16 5 C 2156 2.51 5 N 567 2.21 5 O 552 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: 3301 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 502 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 62} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 433 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 55} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2366 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 287} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.74, per 1000 atoms: 0.83 Number of scatterers: 3301 At special positions: 0 Unit cell: (72.625, 74.7, 100.638, 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 26 16.00 O 552 8.00 N 567 7.00 C 2156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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 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 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: 0.70 Conformation dependent library (CDL) restraints added in 318.0 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 66.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... 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 68 removed outlier: 3.537A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 21 No H-bonds generated for 'chain 'E' and resid 19 through 21' Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'R' and resid 44 through 76 removed outlier: 4.041A pdb=" N LYS R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE R 50 " --> pdb=" O ILE R 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 100 removed outlier: 3.669A pdb=" N VAL R 85 " --> pdb=" O SER R 81 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 111 removed outlier: 3.691A pdb=" N VAL R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 149 removed outlier: 3.612A pdb=" N CYS R 119 " --> pdb=" O GLY R 115 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER R 123 " --> pdb=" O CYS R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 160 removed outlier: 3.905A pdb=" N THR R 156 " --> pdb=" O ARG R 153 " (cutoff:3.500A) removed outlier: 3.704A 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 Processing helix chain 'R' and resid 203 through 212 removed outlier: 3.682A pdb=" N MET R 209 " --> pdb=" O ALA R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 218 Processing helix chain 'R' and resid 220 through 239 removed outlier: 3.837A pdb=" N ARG R 236 " --> pdb=" O GLY R 232 " (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 305 removed outlier: 3.508A pdb=" N ILE R 301 " --> pdb=" O ASP R 297 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU R 305 " --> pdb=" O ILE R 301 " (cutoff:3.500A) 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: 3.600A pdb=" N ALA R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 49 through 52 removed outlier: 3.977A pdb=" N VAL D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 184 through 187 removed outlier: 3.689A pdb=" N ALA R 195 " --> pdb=" O VAL R 187 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 618 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: 0.78 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1033 1.35 - 1.47: 732 1.47 - 1.58: 1566 1.58 - 1.70: 0 1.70 - 1.82: 35 Bond restraints: 3366 Sorted by residual: bond pdb=" CA SER E 30 " pdb=" CB SER E 30 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.36e-02 5.41e+03 1.38e+01 bond pdb=" N LYS E 29 " pdb=" CA LYS E 29 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.19e-02 7.06e+03 3.06e+00 bond pdb=" N LEU R 34 " pdb=" CA LEU R 34 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N CYS E 9 " pdb=" CA CYS E 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N ALA D 1 " pdb=" CA ALA D 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 ... (remaining 3361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 4414 0.96 - 1.92: 125 1.92 - 2.87: 19 2.87 - 3.83: 11 3.83 - 4.79: 7 Bond angle restraints: 4576 Sorted by residual: angle pdb=" N ILE R 317 " pdb=" CA ILE R 317 " pdb=" C ILE R 317 " ideal model delta sigma weight residual 112.29 109.54 2.75 9.40e-01 1.13e+00 8.57e+00 angle pdb=" N VAL R 222 " pdb=" CA VAL R 222 " pdb=" C VAL R 222 " ideal model delta sigma weight residual 112.35 109.25 3.10 1.20e+00 6.94e-01 6.69e+00 angle pdb=" CA VAL R 222 " pdb=" C VAL R 222 " pdb=" N PRO R 223 " ideal model delta sigma weight residual 120.83 119.74 1.09 6.10e-01 2.69e+00 3.19e+00 angle pdb=" N CYS D 35 " pdb=" CA CYS D 35 " pdb=" C CYS D 35 " ideal model delta sigma weight residual 108.46 110.99 -2.53 1.51e+00 4.39e-01 2.81e+00 angle pdb=" C VAL R 222 " pdb=" CA VAL R 222 " pdb=" CB VAL R 222 " ideal model delta sigma weight residual 114.00 111.83 2.17 1.31e+00 5.83e-01 2.76e+00 ... (remaining 4571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 1867 17.97 - 35.95: 153 35.95 - 53.92: 24 53.92 - 71.89: 7 71.89 - 89.86: 2 Dihedral angle restraints: 2053 sinusoidal: 804 harmonic: 1249 Sorted by residual: dihedral pdb=" CB CYS D 11 " pdb=" SG CYS D 11 " pdb=" SG CYS D 51 " pdb=" CB CYS D 51 " ideal model delta sinusoidal sigma weight residual 93.00 164.70 -71.70 1 1.00e+01 1.00e-02 6.58e+01 dihedral pdb=" CA ASN R 47 " pdb=" C ASN R 47 " pdb=" N LYS R 48 " pdb=" CA LYS R 48 " ideal model delta harmonic sigma weight residual -180.00 -164.16 -15.84 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA LYS R 108 " pdb=" CB LYS R 108 " pdb=" CG LYS R 108 " pdb=" CD LYS R 108 " ideal model delta sinusoidal sigma weight residual -60.00 -115.32 55.32 3 1.50e+01 4.44e-03 9.34e+00 ... (remaining 2050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 353 0.025 - 0.050: 114 0.050 - 0.075: 59 0.075 - 0.099: 24 0.099 - 0.124: 15 Chirality restraints: 565 Sorted by residual: chirality pdb=" CA ILE D 18 " pdb=" N ILE D 18 " pdb=" C ILE D 18 " pdb=" CB ILE D 18 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA VAL D 3 " pdb=" N VAL D 3 " pdb=" C VAL D 3 " pdb=" CB VAL D 3 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.61e-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 -0.11 2.00e-01 2.50e+01 3.23e-01 ... (remaining 562 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 310 " -0.021 5.00e-02 4.00e+02 3.13e-02 1.56e+00 pdb=" N PRO R 311 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 311 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 311 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 56 " 0.017 5.00e-02 4.00e+02 2.57e-02 1.06e+00 pdb=" N PRO D 57 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO D 57 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 57 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 56 " -0.010 5.00e-02 4.00e+02 1.57e-02 3.96e-01 pdb=" N PRO E 57 " 0.027 5.00e-02 4.00e+02 pdb=" CA PRO E 57 " -0.008 5.00e-02 4.00e+02 pdb=" CD PRO E 57 " -0.009 5.00e-02 4.00e+02 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1255 2.90 - 3.40: 3246 3.40 - 3.90: 4985 3.90 - 4.40: 5567 4.40 - 4.90: 9628 Nonbonded interactions: 24681 Sorted by model distance: nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.398 3.040 nonbonded pdb=" O ILE R 213 " pdb=" OG SER R 217 " model vdw 2.420 3.040 nonbonded pdb=" O CYS D 9 " pdb=" NH2 ARG R 289 " model vdw 2.467 3.120 nonbonded pdb=" O LEU R 125 " pdb=" ND2 ASN R 129 " model vdw 2.469 3.120 nonbonded pdb=" OD1 ASP R 143 " pdb=" NH1 ARG R 159 " model vdw 2.485 3.120 ... (remaining 24676 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 20 or (resid 21 through 22 and (name N or name C \ A or name C or name O or name CB )) or resid 23 through 28 or (resid 29 and (nam \ e N or name CA or name C or name O or name CB )) or resid 30 through 36 or (resi \ d 37 and (name N or name CA or name C or name O or name CB )) or resid 38 or (re \ sid 39 and (name N or name CA or name C or name O or name CB )) or resid 40 thro \ ugh 60 or (resid 61 and (name N or name CA or name C or name O or name CB )) or \ resid 62 through 63 or (resid 64 and (name N or name CA or name C or name O or n \ ame CB )) or resid 65 through 68)) selection = (chain 'E' and (resid 9 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 21 or (resid 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 through 68)) } 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: 0.580 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.360 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: 16.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.002 0.050 3366 Z= 0.160 Angle : 0.458 4.790 4576 Z= 0.259 Chirality : 0.037 0.124 565 Planarity : 0.003 0.031 558 Dihedral : 13.515 89.864 1221 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % 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: 1.63 (0.44), residues: 420 helix: 1.75 (0.35), residues: 247 sheet: 0.19 (0.80), residues: 48 loop : 0.24 (0.62), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 207 HIS 0.002 0.000 HIS R 247 PHE 0.004 0.001 PHE R 239 TYR 0.011 0.001 TYR R 49 ARG 0.002 0.000 ARG R 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 29 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8064 (ttpp) REVERT: D 48 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7669 (ttm-80) REVERT: D 56 SER cc_start: 0.9051 (t) cc_final: 0.8791 (p) REVERT: E 53 ASN cc_start: 0.8699 (t0) cc_final: 0.8299 (t0) REVERT: R 46 ILE cc_start: 0.8409 (mt) cc_final: 0.8077 (mm) REVERT: R 84 ASP cc_start: 0.7897 (m-30) cc_final: 0.7523 (m-30) REVERT: R 141 SER cc_start: 0.9073 (t) cc_final: 0.8771 (m) REVERT: R 262 LEU cc_start: 0.8148 (tp) cc_final: 0.7836 (mt) REVERT: R 283 GLN cc_start: 0.8042 (tt0) cc_final: 0.7662 (pm20) REVERT: R 287 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7360 (mp0) REVERT: R 320 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8947 (ttpt) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1836 time to fit residues: 27.8957 Evaluate side-chains 86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096748 restraints weight = 5941.218| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.21 r_work: 0.3148 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3366 Z= 0.220 Angle : 0.611 7.882 4576 Z= 0.323 Chirality : 0.043 0.203 565 Planarity : 0.004 0.024 558 Dihedral : 4.179 27.869 455 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.02 % Allowed : 15.11 % Favored : 81.87 % 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: 1.95 (0.42), residues: 420 helix: 2.11 (0.33), residues: 253 sheet: 0.48 (0.79), residues: 48 loop : -0.08 (0.58), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 112 HIS 0.005 0.001 HIS D 34 PHE 0.010 0.001 PHE R 183 TYR 0.014 0.001 TYR R 49 ARG 0.006 0.001 ARG E 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.357 Fit side-chains REVERT: D 27 ASN cc_start: 0.8482 (t0) cc_final: 0.8263 (t0) REVERT: D 46 ASN cc_start: 0.8432 (p0) cc_final: 0.8208 (p0) REVERT: D 48 ARG cc_start: 0.8332 (mtp180) cc_final: 0.7875 (ttm-80) REVERT: E 53 ASN cc_start: 0.8695 (t0) cc_final: 0.8377 (t0) REVERT: E 60 LYS cc_start: 0.9060 (mttt) cc_final: 0.8816 (mttm) REVERT: R 46 ILE cc_start: 0.8345 (mt) cc_final: 0.8096 (mp) REVERT: R 75 TYR cc_start: 0.7857 (t80) cc_final: 0.7585 (t80) REVERT: R 213 ILE cc_start: 0.9343 (tp) cc_final: 0.8998 (tp) REVERT: R 283 GLN cc_start: 0.8201 (tt0) cc_final: 0.7837 (pm20) outliers start: 11 outliers final: 5 residues processed: 99 average time/residue: 0.1642 time to fit residues: 19.3893 Evaluate side-chains 80 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 317 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 HIS ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097482 restraints weight = 5863.957| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.18 r_work: 0.3158 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3366 Z= 0.189 Angle : 0.544 6.575 4576 Z= 0.281 Chirality : 0.042 0.155 565 Planarity : 0.004 0.028 558 Dihedral : 3.933 22.687 455 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.20 % Allowed : 18.13 % Favored : 79.67 % 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: 420 helix: 2.36 (0.33), residues: 249 sheet: 0.21 (0.77), residues: 48 loop : -0.34 (0.53), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 264 HIS 0.003 0.001 HIS D 19 PHE 0.009 0.001 PHE R 233 TYR 0.013 0.001 TYR R 49 ARG 0.003 0.000 ARG E 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.437 Fit side-chains REVERT: D 29 LYS cc_start: 0.8430 (ttpt) cc_final: 0.8221 (tmtt) REVERT: D 46 ASN cc_start: 0.8540 (p0) cc_final: 0.8304 (p0) REVERT: D 48 ARG cc_start: 0.8398 (mtp180) cc_final: 0.7915 (ttm-80) REVERT: D 53 ASN cc_start: 0.9284 (t0) cc_final: 0.8825 (t0) REVERT: E 53 ASN cc_start: 0.8662 (t0) cc_final: 0.8267 (t0) REVERT: R 46 ILE cc_start: 0.8204 (mt) cc_final: 0.7964 (mp) REVERT: R 75 TYR cc_start: 0.7864 (t80) cc_final: 0.7512 (t80) REVERT: R 213 ILE cc_start: 0.9369 (tp) cc_final: 0.9031 (tp) REVERT: R 283 GLN cc_start: 0.8342 (tt0) cc_final: 0.8015 (pm20) outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 0.1842 time to fit residues: 18.0443 Evaluate side-chains 78 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 15 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** 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 = 0.3550 r_free = 0.3550 target = 0.115346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.097307 restraints weight = 5994.521| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.26 r_work: 0.3158 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3366 Z= 0.165 Angle : 0.519 6.394 4576 Z= 0.265 Chirality : 0.041 0.135 565 Planarity : 0.003 0.027 558 Dihedral : 3.721 20.101 455 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.92 % Allowed : 19.51 % Favored : 78.57 % 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: 2.07 (0.41), residues: 420 helix: 2.52 (0.33), residues: 251 sheet: 0.10 (0.75), residues: 48 loop : -0.60 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 207 HIS 0.001 0.000 HIS R 150 PHE 0.009 0.001 PHE R 183 TYR 0.013 0.001 TYR R 49 ARG 0.001 0.000 ARG R 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8636 (p0) cc_final: 0.8382 (p0) REVERT: D 48 ARG cc_start: 0.8436 (mtp180) cc_final: 0.7963 (ttm-80) REVERT: E 53 ASN cc_start: 0.8588 (t0) cc_final: 0.8149 (t0) REVERT: R 46 ILE cc_start: 0.8285 (mt) cc_final: 0.7962 (mp) REVERT: R 75 TYR cc_start: 0.7901 (t80) cc_final: 0.7550 (t80) REVERT: R 283 GLN cc_start: 0.8313 (tt0) cc_final: 0.7918 (pm20) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 0.1896 time to fit residues: 17.9880 Evaluate side-chains 77 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 313 ILE 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 34 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.095844 restraints weight = 6051.435| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.25 r_work: 0.3132 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3366 Z= 0.240 Angle : 0.566 5.943 4576 Z= 0.290 Chirality : 0.042 0.135 565 Planarity : 0.004 0.027 558 Dihedral : 3.739 18.829 455 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.30 % Allowed : 20.33 % Favored : 76.37 % 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: 1.96 (0.41), residues: 420 helix: 2.52 (0.33), residues: 248 sheet: -0.11 (0.73), residues: 48 loop : -0.69 (0.50), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 207 HIS 0.003 0.001 HIS R 150 PHE 0.009 0.001 PHE R 183 TYR 0.026 0.001 TYR R 49 ARG 0.002 0.000 ARG R 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8755 (p0) cc_final: 0.8467 (p0) REVERT: D 48 ARG cc_start: 0.8437 (mtp180) cc_final: 0.7962 (ttm-80) REVERT: E 53 ASN cc_start: 0.8560 (t0) cc_final: 0.7941 (t0) REVERT: R 75 TYR cc_start: 0.7930 (t80) cc_final: 0.7594 (t80) REVERT: R 283 GLN cc_start: 0.8289 (tt0) cc_final: 0.7926 (pm20) outliers start: 12 outliers final: 7 residues processed: 84 average time/residue: 0.1899 time to fit residues: 18.9203 Evaluate side-chains 77 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.097064 restraints weight = 6140.595| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.28 r_work: 0.3158 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3366 Z= 0.179 Angle : 0.538 7.249 4576 Z= 0.271 Chirality : 0.041 0.122 565 Planarity : 0.003 0.027 558 Dihedral : 3.674 17.134 455 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.30 % Allowed : 20.88 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.41), residues: 420 helix: 2.53 (0.33), residues: 251 sheet: -0.09 (0.73), residues: 48 loop : -0.95 (0.49), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 207 HIS 0.002 0.000 HIS R 242 PHE 0.010 0.001 PHE R 183 TYR 0.018 0.001 TYR R 49 ARG 0.001 0.000 ARG R 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8753 (p0) cc_final: 0.8494 (p0) REVERT: D 48 ARG cc_start: 0.8463 (mtp180) cc_final: 0.7995 (ttm-80) REVERT: E 49 LYS cc_start: 0.8804 (mppt) cc_final: 0.8590 (mmtm) REVERT: E 53 ASN cc_start: 0.8599 (t0) cc_final: 0.8033 (t0) REVERT: R 75 TYR cc_start: 0.7985 (t80) cc_final: 0.7645 (t80) REVERT: R 283 GLN cc_start: 0.8242 (tt0) cc_final: 0.7882 (pm20) outliers start: 12 outliers final: 10 residues processed: 82 average time/residue: 0.1969 time to fit residues: 19.2281 Evaluate side-chains 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.114692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096356 restraints weight = 6059.842| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.26 r_work: 0.3138 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3366 Z= 0.205 Angle : 0.555 6.882 4576 Z= 0.279 Chirality : 0.041 0.136 565 Planarity : 0.003 0.027 558 Dihedral : 3.659 16.648 455 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.57 % Allowed : 20.88 % Favored : 75.55 % 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: 1.94 (0.41), residues: 420 helix: 2.60 (0.33), residues: 248 sheet: 0.02 (0.73), residues: 50 loop : -1.00 (0.49), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 207 HIS 0.003 0.001 HIS R 242 PHE 0.013 0.001 PHE R 183 TYR 0.019 0.001 TYR R 49 ARG 0.001 0.000 ARG R 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 34 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7518 (p90) REVERT: D 46 ASN cc_start: 0.8726 (p0) cc_final: 0.8452 (p0) REVERT: D 48 ARG cc_start: 0.8447 (mtp180) cc_final: 0.7987 (ttm-80) REVERT: E 53 ASN cc_start: 0.8587 (t0) cc_final: 0.8068 (t0) REVERT: R 75 TYR cc_start: 0.7953 (t80) cc_final: 0.7638 (t80) REVERT: R 283 GLN cc_start: 0.8205 (tt0) cc_final: 0.7862 (pm20) outliers start: 13 outliers final: 12 residues processed: 82 average time/residue: 0.1852 time to fit residues: 17.9227 Evaluate side-chains 84 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0770 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096683 restraints weight = 5913.128| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.23 r_work: 0.3146 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3366 Z= 0.182 Angle : 0.530 7.013 4576 Z= 0.267 Chirality : 0.040 0.120 565 Planarity : 0.003 0.027 558 Dihedral : 3.576 16.794 455 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.12 % Allowed : 19.78 % Favored : 76.10 % 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: 1.85 (0.41), residues: 420 helix: 2.55 (0.33), residues: 250 sheet: -0.00 (0.74), residues: 50 loop : -1.18 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 112 HIS 0.003 0.001 HIS R 242 PHE 0.009 0.001 PHE R 183 TYR 0.018 0.001 TYR R 49 ARG 0.001 0.000 ARG R 208 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8713 (p0) cc_final: 0.8383 (p0) REVERT: D 48 ARG cc_start: 0.8437 (mtp180) cc_final: 0.7994 (ttm-80) REVERT: E 53 ASN cc_start: 0.8564 (t0) cc_final: 0.8098 (t0) REVERT: R 75 TYR cc_start: 0.7999 (t80) cc_final: 0.7700 (t80) REVERT: R 283 GLN cc_start: 0.8161 (tt0) cc_final: 0.7833 (pm20) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.1840 time to fit residues: 18.5483 Evaluate side-chains 83 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096837 restraints weight = 5975.240| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.22 r_work: 0.3151 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3366 Z= 0.192 Angle : 0.564 7.181 4576 Z= 0.282 Chirality : 0.040 0.119 565 Planarity : 0.003 0.026 558 Dihedral : 3.600 17.010 455 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.30 % Allowed : 20.60 % Favored : 76.10 % 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: 1.81 (0.42), residues: 420 helix: 2.54 (0.33), residues: 250 sheet: -0.06 (0.73), residues: 50 loop : -1.23 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 207 HIS 0.003 0.001 HIS R 242 PHE 0.012 0.001 PHE R 183 TYR 0.019 0.001 TYR R 49 ARG 0.001 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: D 34 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7810 (p90) REVERT: D 46 ASN cc_start: 0.8715 (p0) cc_final: 0.8377 (p0) REVERT: D 48 ARG cc_start: 0.8430 (mtp180) cc_final: 0.7991 (ttm-80) REVERT: E 53 ASN cc_start: 0.8536 (t0) cc_final: 0.8107 (t0) REVERT: R 75 TYR cc_start: 0.7980 (t80) cc_final: 0.7697 (t80) REVERT: R 283 GLN cc_start: 0.8155 (tt0) cc_final: 0.7791 (pm20) outliers start: 12 outliers final: 10 residues processed: 82 average time/residue: 0.1835 time to fit residues: 17.9240 Evaluate side-chains 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.0470 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097123 restraints weight = 5905.191| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.21 r_work: 0.3165 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3366 Z= 0.180 Angle : 0.556 7.257 4576 Z= 0.278 Chirality : 0.040 0.120 565 Planarity : 0.003 0.026 558 Dihedral : 3.614 17.010 455 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.02 % Allowed : 20.88 % Favored : 76.10 % 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: 1.81 (0.41), residues: 420 helix: 2.53 (0.33), residues: 250 sheet: 0.01 (0.73), residues: 50 loop : -1.24 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 207 HIS 0.003 0.001 HIS R 242 PHE 0.009 0.001 PHE R 183 TYR 0.019 0.001 TYR R 49 ARG 0.002 0.000 ARG D 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: D 34 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7810 (p90) REVERT: D 48 ARG cc_start: 0.8432 (mtp180) cc_final: 0.8045 (ttm-80) REVERT: E 53 ASN cc_start: 0.8505 (t0) cc_final: 0.8112 (t0) REVERT: R 75 TYR cc_start: 0.7966 (t80) cc_final: 0.7686 (t80) REVERT: R 283 GLN cc_start: 0.8178 (tt0) cc_final: 0.7822 (pm20) outliers start: 11 outliers final: 9 residues processed: 83 average time/residue: 0.1824 time to fit residues: 18.0513 Evaluate side-chains 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0670 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 34 HIS ** 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 = 0.3561 r_free = 0.3561 target = 0.116218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097810 restraints weight = 5956.946| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.24 r_work: 0.3167 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3366 Z= 0.175 Angle : 0.566 7.201 4576 Z= 0.284 Chirality : 0.040 0.119 565 Planarity : 0.003 0.025 558 Dihedral : 3.649 16.963 455 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.02 % Allowed : 21.70 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.42), residues: 420 helix: 2.57 (0.33), residues: 250 sheet: 0.02 (0.73), residues: 50 loop : -1.28 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 207 HIS 0.002 0.001 HIS R 242 PHE 0.008 0.001 PHE R 183 TYR 0.019 0.001 TYR R 49 ARG 0.005 0.000 ARG E 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2066.41 seconds wall clock time: 36 minutes 10.54 seconds (2170.54 seconds total)