Starting phenix.real_space_refine on Fri May 9 17:25:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwa_38732/05_2025/8xwa_38732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwa_38732/05_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_38732/05_2025/8xwa_38732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwa_38732/05_2025/8xwa_38732.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwa_38732/05_2025/8xwa_38732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwa_38732/05_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-5687/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: 2.60, per 1000 atoms: 0.79 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: 0.71 Conformation dependent library (CDL) restraints added in 373.9 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: 0.30 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: 0.80 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: 0.750 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.910 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.740 ------------------------------------------------------------------------------- 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 3372 Z= 0.132 Angle : 0.459 4.790 4588 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 Details of bonding type rmsd hydrogen bonds : bond 0.24058 ( 211) hydrogen bonds : angle 6.85887 ( 618) SS BOND : bond 0.00142 ( 6) SS BOND : angle 0.87914 ( 12) covalent geometry : bond 0.00233 ( 3366) covalent geometry : angle 0.45766 ( 4576) *********************** 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 : 0.511 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: 0.2069 time to fit residues: 31.7770 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 : 0.347 ------------------------------------------------------------------------------- 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: 0.3980 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 = 0.114650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096776 restraints weight = 5938.244| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.21 r_work: 0.3150 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 3372 Z= 0.162 Angle : 0.621 8.115 4588 Z= 0.331 Chirality : 0.044 0.230 565 Planarity : 0.004 0.023 558 Dihedral : 4.161 28.437 455 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.75 % Allowed : 15.38 % 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: 1.96 (0.42), residues: 420 helix: 2.12 (0.33), residues: 253 sheet: 0.48 (0.79), residues: 48 loop : -0.08 (0.57), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 264 HIS 0.004 0.001 HIS D 19 PHE 0.009 0.001 PHE R 183 TYR 0.014 0.001 TYR R 49 ARG 0.006 0.001 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.05887 ( 211) hydrogen bonds : angle 4.50229 ( 618) SS BOND : bond 0.00443 ( 6) SS BOND : angle 2.09885 ( 12) covalent geometry : bond 0.00361 ( 3366) covalent geometry : angle 0.61249 ( 4576) *********************** 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: 10 poor density : 92 time to evaluate : 0.387 Fit side-chains REVERT: D 27 ASN cc_start: 0.8482 (t0) cc_final: 0.8260 (t0) REVERT: D 46 ASN cc_start: 0.8426 (p0) cc_final: 0.8200 (p0) REVERT: D 48 ARG cc_start: 0.8312 (mtp180) cc_final: 0.7861 (ttm-80) REVERT: D 53 ASN cc_start: 0.9215 (t0) cc_final: 0.8842 (t0) REVERT: E 53 ASN cc_start: 0.8697 (t0) cc_final: 0.8380 (t0) REVERT: E 60 LYS cc_start: 0.9054 (mttt) cc_final: 0.8813 (mttm) REVERT: R 46 ILE cc_start: 0.8343 (mt) cc_final: 0.8092 (mp) REVERT: R 75 TYR cc_start: 0.7851 (t80) cc_final: 0.7576 (t80) REVERT: R 213 ILE cc_start: 0.9337 (tp) cc_final: 0.8991 (tp) REVERT: R 283 GLN cc_start: 0.8210 (tt0) cc_final: 0.7843 (pm20) outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 0.1638 time to fit residues: 19.3354 Evaluate side-chains 79 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.0060 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.115664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097960 restraints weight = 5873.207| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.21 r_work: 0.3169 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3372 Z= 0.122 Angle : 0.541 6.916 4588 Z= 0.279 Chirality : 0.041 0.141 565 Planarity : 0.003 0.022 558 Dihedral : 3.908 22.532 455 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.47 % Allowed : 18.68 % Favored : 78.85 % 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: 2.00 (0.41), residues: 420 helix: 2.33 (0.33), residues: 249 sheet: 0.25 (0.77), residues: 48 loop : -0.32 (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 0.008 0.001 PHE R 97 TYR 0.013 0.001 TYR R 49 ARG 0.003 0.000 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 211) hydrogen bonds : angle 4.10443 ( 618) SS BOND : bond 0.00165 ( 6) SS BOND : angle 1.33347 ( 12) covalent geometry : bond 0.00268 ( 3366) covalent geometry : angle 0.53750 ( 4576) *********************** 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 88 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.357 Fit side-chains REVERT: D 29 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8214 (tmtt) REVERT: D 46 ASN cc_start: 0.8527 (p0) cc_final: 0.8285 (p0) REVERT: D 48 ARG cc_start: 0.8393 (mtp180) cc_final: 0.7903 (ttm-80) REVERT: D 53 ASN cc_start: 0.9283 (t0) cc_final: 0.8809 (t0) REVERT: E 53 ASN cc_start: 0.8645 (t0) cc_final: 0.8292 (t0) REVERT: R 46 ILE cc_start: 0.8193 (mt) cc_final: 0.7909 (mp) REVERT: R 75 TYR cc_start: 0.7881 (t80) cc_final: 0.7513 (t80) REVERT: R 213 ILE cc_start: 0.9358 (tp) cc_final: 0.9031 (tp) REVERT: R 283 GLN cc_start: 0.8363 (tt0) cc_final: 0.7970 (pm20) outliers start: 9 outliers final: 6 residues processed: 85 average time/residue: 0.1820 time to fit residues: 18.2820 Evaluate side-chains 79 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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: 0.9980 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.115156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096987 restraints weight = 6046.369| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.28 r_work: 0.3150 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3372 Z= 0.128 Angle : 0.543 6.651 4588 Z= 0.277 Chirality : 0.041 0.141 565 Planarity : 0.003 0.027 558 Dihedral : 3.820 20.886 455 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.47 % Allowed : 19.78 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.41), residues: 420 helix: 2.47 (0.33), residues: 251 sheet: 0.16 (0.75), residues: 48 loop : -0.62 (0.52), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 207 HIS 0.002 0.000 HIS R 150 PHE 0.010 0.001 PHE R 183 TYR 0.027 0.001 TYR R 49 ARG 0.003 0.000 ARG R 289 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 211) hydrogen bonds : angle 3.99536 ( 618) SS BOND : bond 0.00238 ( 6) SS BOND : angle 1.37172 ( 12) covalent geometry : bond 0.00291 ( 3366) covalent geometry : angle 0.53935 ( 4576) *********************** 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 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8630 (p0) cc_final: 0.8363 (p0) REVERT: D 48 ARG cc_start: 0.8448 (mtp180) cc_final: 0.7943 (ttm-80) REVERT: E 53 ASN cc_start: 0.8581 (t0) cc_final: 0.8133 (t0) REVERT: R 46 ILE cc_start: 0.8253 (mt) cc_final: 0.8031 (mm) REVERT: R 75 TYR cc_start: 0.7901 (t80) cc_final: 0.7544 (t80) REVERT: R 283 GLN cc_start: 0.8313 (tt0) cc_final: 0.7898 (pm20) outliers start: 9 outliers final: 6 residues processed: 84 average time/residue: 0.1843 time to fit residues: 18.2646 Evaluate side-chains 77 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 30 optimal weight: 0.0980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.111613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.093129 restraints weight = 6142.777| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.27 r_work: 0.3080 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 3372 Z= 0.273 Angle : 0.676 6.628 4588 Z= 0.344 Chirality : 0.046 0.144 565 Planarity : 0.004 0.029 558 Dihedral : 3.982 20.398 455 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.85 % Allowed : 19.78 % 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: 1.53 (0.41), residues: 420 helix: 2.15 (0.33), residues: 249 sheet: -0.31 (0.74), residues: 48 loop : -0.79 (0.52), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP R 112 HIS 0.006 0.001 HIS R 150 PHE 0.017 0.002 PHE R 183 TYR 0.019 0.002 TYR R 49 ARG 0.003 0.001 ARG R 80 Details of bonding type rmsd hydrogen bonds : bond 0.05670 ( 211) hydrogen bonds : angle 4.31424 ( 618) SS BOND : bond 0.00187 ( 6) SS BOND : angle 1.77169 ( 12) covalent geometry : bond 0.00652 ( 3366) covalent geometry : angle 0.67118 ( 4576) *********************** 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 83 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8682 (p0) cc_final: 0.8421 (p0) REVERT: D 48 ARG cc_start: 0.8453 (mtp180) cc_final: 0.8003 (ttm-80) REVERT: E 49 LYS cc_start: 0.8814 (mppt) cc_final: 0.8572 (mmtm) REVERT: E 53 ASN cc_start: 0.8646 (t0) cc_final: 0.8056 (t0) REVERT: R 75 TYR cc_start: 0.7980 (t80) cc_final: 0.7722 (t80) REVERT: R 283 GLN cc_start: 0.8227 (tt0) cc_final: 0.7840 (pm20) outliers start: 14 outliers final: 8 residues processed: 80 average time/residue: 0.1891 time to fit residues: 17.9359 Evaluate side-chains 74 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 82 VAL 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 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: 0.5980 chunk 14 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 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 = 0.3534 r_free = 0.3534 target = 0.114565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096126 restraints weight = 6163.488| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.30 r_work: 0.3134 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3372 Z= 0.127 Angle : 0.555 6.612 4588 Z= 0.281 Chirality : 0.041 0.128 565 Planarity : 0.004 0.028 558 Dihedral : 3.800 17.865 455 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.75 % Allowed : 21.98 % 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: 1.85 (0.41), residues: 420 helix: 2.46 (0.33), residues: 248 sheet: -0.21 (0.75), residues: 48 loop : -0.78 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 207 HIS 0.002 0.001 HIS R 242 PHE 0.011 0.001 PHE R 183 TYR 0.017 0.001 TYR R 49 ARG 0.004 0.000 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.04452 ( 211) hydrogen bonds : angle 3.99278 ( 618) SS BOND : bond 0.00072 ( 6) SS BOND : angle 1.43579 ( 12) covalent geometry : bond 0.00286 ( 3366) covalent geometry : angle 0.55123 ( 4576) *********************** 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 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8727 (p0) cc_final: 0.8464 (p0) REVERT: D 48 ARG cc_start: 0.8472 (mtp180) cc_final: 0.7998 (ttm-80) REVERT: E 53 ASN cc_start: 0.8626 (t0) cc_final: 0.8093 (t0) REVERT: R 75 TYR cc_start: 0.7983 (t80) cc_final: 0.7688 (t80) REVERT: R 245 GLN cc_start: 0.5511 (tt0) cc_final: 0.5304 (tt0) REVERT: R 283 GLN cc_start: 0.8195 (tt0) cc_final: 0.7836 (pm20) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.1923 time to fit residues: 18.1193 Evaluate side-chains 74 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 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 16 GLN R 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096394 restraints weight = 6075.071| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.26 r_work: 0.3139 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3372 Z= 0.120 Angle : 0.536 7.248 4588 Z= 0.271 Chirality : 0.040 0.121 565 Planarity : 0.003 0.028 558 Dihedral : 3.711 16.628 455 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.02 % Allowed : 20.05 % Favored : 76.92 % 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: 1.87 (0.41), residues: 420 helix: 2.51 (0.33), residues: 248 sheet: -0.14 (0.75), residues: 48 loop : -0.87 (0.50), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 264 HIS 0.002 0.001 HIS D 34 PHE 0.009 0.001 PHE R 130 TYR 0.017 0.001 TYR R 49 ARG 0.003 0.000 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 211) hydrogen bonds : angle 3.85846 ( 618) SS BOND : bond 0.00077 ( 6) SS BOND : angle 1.33340 ( 12) covalent geometry : bond 0.00274 ( 3366) covalent geometry : angle 0.53186 ( 4576) *********************** 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 84 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 34 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7529 (p90) REVERT: D 46 ASN cc_start: 0.8728 (p0) cc_final: 0.8467 (p0) REVERT: D 48 ARG cc_start: 0.8426 (mtp180) cc_final: 0.8016 (ttm-80) REVERT: E 49 LYS cc_start: 0.8769 (mppt) cc_final: 0.8531 (mmtm) REVERT: E 53 ASN cc_start: 0.8589 (t0) cc_final: 0.8073 (t0) REVERT: R 75 TYR cc_start: 0.7997 (t80) cc_final: 0.7711 (t80) REVERT: R 283 GLN cc_start: 0.8187 (tt0) cc_final: 0.7809 (pm20) outliers start: 11 outliers final: 9 residues processed: 82 average time/residue: 0.1779 time to fit residues: 17.2991 Evaluate side-chains 81 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 82 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096440 restraints weight = 5960.033| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.23 r_work: 0.3138 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3372 Z= 0.129 Angle : 0.546 7.189 4588 Z= 0.276 Chirality : 0.040 0.120 565 Planarity : 0.003 0.027 558 Dihedral : 3.678 17.132 455 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.30 % Allowed : 20.05 % Favored : 76.65 % 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: 1.82 (0.41), residues: 420 helix: 2.52 (0.33), residues: 248 sheet: -0.28 (0.74), residues: 48 loop : -0.94 (0.49), residues: 124 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 0.011 0.001 PHE R 183 TYR 0.016 0.001 TYR R 49 ARG 0.002 0.000 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 211) hydrogen bonds : angle 3.85735 ( 618) SS BOND : bond 0.00073 ( 6) SS BOND : angle 1.30919 ( 12) covalent geometry : bond 0.00298 ( 3366) covalent geometry : angle 0.54283 ( 4576) *********************** 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 86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8728 (p0) cc_final: 0.8425 (p0) REVERT: D 48 ARG cc_start: 0.8444 (mtp180) cc_final: 0.8022 (ttm-80) REVERT: E 49 LYS cc_start: 0.8749 (mppt) cc_final: 0.8540 (mmtm) REVERT: E 53 ASN cc_start: 0.8569 (t0) cc_final: 0.8130 (t0) REVERT: R 75 TYR cc_start: 0.7978 (t80) cc_final: 0.7697 (t80) REVERT: R 283 GLN cc_start: 0.8206 (tt0) cc_final: 0.7816 (pm20) outliers start: 12 outliers final: 11 residues processed: 83 average time/residue: 0.1843 time to fit residues: 18.1061 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 : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 82 VAL 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 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: 0.4980 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.0570 chunk 4 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 129 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 = 0.3551 r_free = 0.3551 target = 0.115966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097665 restraints weight = 5978.803| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.23 r_work: 0.3162 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3372 Z= 0.111 Angle : 0.533 7.469 4588 Z= 0.270 Chirality : 0.040 0.120 565 Planarity : 0.003 0.027 558 Dihedral : 3.639 16.843 455 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.20 % Allowed : 21.43 % 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: 1.79 (0.41), residues: 420 helix: 2.49 (0.33), residues: 250 sheet: 0.17 (0.74), residues: 50 loop : -1.27 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 264 HIS 0.001 0.000 HIS R 150 PHE 0.007 0.001 PHE R 97 TYR 0.017 0.001 TYR R 49 ARG 0.002 0.000 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 211) hydrogen bonds : angle 3.73588 ( 618) SS BOND : bond 0.00076 ( 6) SS BOND : angle 1.26017 ( 12) covalent geometry : bond 0.00243 ( 3366) covalent geometry : angle 0.52956 ( 4576) *********************** 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 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8701 (p0) cc_final: 0.8367 (p0) REVERT: D 48 ARG cc_start: 0.8376 (mtp180) cc_final: 0.7993 (ttm-80) REVERT: E 48 ARG cc_start: 0.8159 (mtt90) cc_final: 0.7881 (mtt90) REVERT: E 53 ASN cc_start: 0.8501 (t0) cc_final: 0.8087 (t0) REVERT: R 75 TYR cc_start: 0.7992 (t80) cc_final: 0.7702 (t80) REVERT: R 283 GLN cc_start: 0.8191 (tt0) cc_final: 0.7837 (pm20) outliers start: 8 outliers final: 8 residues processed: 80 average time/residue: 0.1796 time to fit residues: 17.1984 Evaluate side-chains 81 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 82 VAL 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 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: 0.0770 chunk 14 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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 129 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 = 0.3571 r_free = 0.3571 target = 0.117170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098837 restraints weight = 5886.232| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.23 r_work: 0.3182 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 3372 Z= 0.102 Angle : 0.526 7.328 4588 Z= 0.264 Chirality : 0.040 0.120 565 Planarity : 0.003 0.026 558 Dihedral : 3.596 16.327 455 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.37 % Allowed : 22.53 % 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: 1.84 (0.41), residues: 420 helix: 2.51 (0.33), residues: 250 sheet: 0.33 (0.74), residues: 50 loop : -1.26 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 207 HIS 0.002 0.000 HIS D 34 PHE 0.007 0.001 PHE R 130 TYR 0.017 0.001 TYR R 49 ARG 0.003 0.000 ARG R 294 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 211) hydrogen bonds : angle 3.66993 ( 618) SS BOND : bond 0.00103 ( 6) SS BOND : angle 1.15745 ( 12) covalent geometry : bond 0.00216 ( 3366) covalent geometry : angle 0.52360 ( 4576) ********************** 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 80 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8762 (p0) cc_final: 0.8435 (p0) REVERT: D 48 ARG cc_start: 0.8347 (mtp180) cc_final: 0.7978 (ttm-80) REVERT: E 53 ASN cc_start: 0.8470 (t0) cc_final: 0.8148 (t0) REVERT: R 46 ILE cc_start: 0.8292 (mt) cc_final: 0.8079 (mp) REVERT: R 75 TYR cc_start: 0.7980 (t80) cc_final: 0.7708 (t80) REVERT: R 283 GLN cc_start: 0.8242 (tt0) cc_final: 0.7858 (pm20) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.1863 time to fit residues: 17.1811 Evaluate side-chains 77 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 71 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- 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 129 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 = 0.3548 r_free = 0.3548 target = 0.115501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.096997 restraints weight = 6016.438| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.27 r_work: 0.3150 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3372 Z= 0.132 Angle : 0.567 7.476 4588 Z= 0.287 Chirality : 0.040 0.120 565 Planarity : 0.004 0.038 558 Dihedral : 3.618 16.451 455 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.92 % Allowed : 22.80 % 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: 1.77 (0.42), residues: 420 helix: 2.50 (0.34), residues: 250 sheet: 0.14 (0.73), residues: 50 loop : -1.32 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 264 HIS 0.002 0.001 HIS R 150 PHE 0.009 0.001 PHE R 130 TYR 0.016 0.001 TYR R 49 ARG 0.009 0.000 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 211) hydrogen bonds : angle 3.69852 ( 618) SS BOND : bond 0.00075 ( 6) SS BOND : angle 1.25022 ( 12) covalent geometry : bond 0.00306 ( 3366) covalent geometry : angle 0.56393 ( 4576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2038.55 seconds wall clock time: 35 minutes 56.91 seconds (2156.91 seconds total)