Starting phenix.real_space_refine on Sat Apr 26 19:51:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwa_38732/04_2025/8xwa_38732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwa_38732/04_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_38732/04_2025/8xwa_38732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwa_38732/04_2025/8xwa_38732.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwa_38732/04_2025/8xwa_38732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwa_38732/04_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-5669/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: 2.82, per 1000 atoms: 0.85 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: 0.80 Conformation dependent library (CDL) restraints added in 407.2 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: 0.33 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: 0.83 Time building geometry restraints manager: 0.97 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.250 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- 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 : 0.389 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: 0.1747 time to fit residues: 26.4546 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 : 0.369 ------------------------------------------------------------------------------- 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 = 0.096777 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: 4.45 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 : 0.351 Fit side-chains REVERT: D 27 ASN cc_start: 0.8484 (t0) cc_final: 0.8262 (t0) REVERT: D 46 ASN cc_start: 0.8427 (p0) cc_final: 0.8201 (p0) REVERT: D 48 ARG cc_start: 0.8313 (mtp180) cc_final: 0.7860 (ttm-80) REVERT: D 53 ASN cc_start: 0.9215 (t0) cc_final: 0.8842 (t0) REVERT: E 53 ASN cc_start: 0.8696 (t0) cc_final: 0.8379 (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: 0.8091 (mp) REVERT: R 75 TYR cc_start: 0.7850 (t80) cc_final: 0.7574 (t80) REVERT: R 213 ILE cc_start: 0.9338 (tp) cc_final: 0.8991 (tp) REVERT: R 283 GLN cc_start: 0.8210 (tt0) cc_final: 0.7842 (pm20) outliers start: 10 outliers final: 5 residues processed: 99 average time/residue: 0.1677 time to fit residues: 19.8702 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 : 0.407 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3552 r_free = 0.3552 target = 0.115421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097652 restraints weight = 5894.414| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.22 r_work: 0.3160 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3372 Z= 0.128 Angle : 0.546 6.781 4588 Z= 0.282 Chirality : 0.042 0.143 565 Planarity : 0.004 0.022 558 Dihedral : 3.917 22.428 455 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.47 % Allowed : 18.41 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.41), residues: 420 helix: 2.39 (0.33), residues: 247 sheet: 0.19 (0.77), residues: 48 loop : -0.36 (0.53), residues: 125 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 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 0.04827 ( 211) hydrogen bonds : angle 4.11541 ( 618) SS BOND : bond 0.00267 ( 6) SS BOND : angle 1.25744 ( 12) covalent geometry : bond 0.00285 ( 3366) covalent geometry : angle 0.54335 ( 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 86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.348 Fit side-chains REVERT: D 29 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8201 (tmtt) REVERT: D 46 ASN cc_start: 0.8535 (p0) cc_final: 0.8296 (p0) REVERT: D 48 ARG cc_start: 0.8432 (mtp180) cc_final: 0.7930 (ttm-80) REVERT: E 53 ASN cc_start: 0.8646 (t0) cc_final: 0.8244 (t0) REVERT: R 46 ILE cc_start: 0.8211 (mt) cc_final: 0.7968 (mp) REVERT: R 75 TYR cc_start: 0.7866 (t80) cc_final: 0.7498 (t80) REVERT: R 213 ILE cc_start: 0.9373 (tp) cc_final: 0.9037 (tp) REVERT: R 283 GLN cc_start: 0.8376 (tt0) cc_final: 0.7960 (pm20) outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 0.1864 time to fit residues: 18.2692 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 : 0.404 ------------------------------------------------------------------------------- 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: 4.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 0.2980 chunk 40 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.115801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097652 restraints weight = 6019.716| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.28 r_work: 0.3164 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3372 Z= 0.115 Angle : 0.531 6.707 4588 Z= 0.268 Chirality : 0.041 0.142 565 Planarity : 0.003 0.026 558 Dihedral : 3.803 20.204 455 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.75 % Allowed : 18.96 % Favored : 78.30 % 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: 2.48 (0.33), residues: 251 sheet: 0.17 (0.75), residues: 48 loop : -0.64 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 207 HIS 0.001 0.000 HIS R 150 PHE 0.008 0.001 PHE R 97 TYR 0.012 0.001 TYR R 49 ARG 0.002 0.000 ARG R 289 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 211) hydrogen bonds : angle 3.95577 ( 618) SS BOND : bond 0.00124 ( 6) SS BOND : angle 1.46867 ( 12) covalent geometry : bond 0.00252 ( 3366) covalent geometry : angle 0.52599 ( 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 86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: D 45 LYS cc_start: 0.7279 (mtmm) cc_final: 0.7028 (mtmm) REVERT: D 46 ASN cc_start: 0.8611 (p0) cc_final: 0.8350 (p0) REVERT: D 48 ARG cc_start: 0.8453 (mtp180) cc_final: 0.7958 (ttm-80) REVERT: E 53 ASN cc_start: 0.8571 (t0) cc_final: 0.8130 (t0) REVERT: R 46 ILE cc_start: 0.8279 (mt) cc_final: 0.7951 (mp) REVERT: R 75 TYR cc_start: 0.7884 (t80) cc_final: 0.7531 (t80) REVERT: R 283 GLN cc_start: 0.8338 (tt0) cc_final: 0.7899 (pm20) outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.1892 time to fit residues: 18.5851 Evaluate side-chains 80 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.112173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093875 restraints weight = 6115.841| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.26 r_work: 0.3096 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3372 Z= 0.222 Angle : 0.632 6.298 4588 Z= 0.322 Chirality : 0.044 0.140 565 Planarity : 0.004 0.029 558 Dihedral : 3.874 19.360 455 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.17 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: 1.71 (0.41), residues: 420 helix: 2.31 (0.33), residues: 250 sheet: -0.18 (0.73), residues: 48 loop : -0.82 (0.51), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.004 0.001 HIS R 150 PHE 0.016 0.002 PHE R 183 TYR 0.021 0.001 TYR R 49 ARG 0.002 0.000 ARG R 80 Details of bonding type rmsd hydrogen bonds : bond 0.05285 ( 211) hydrogen bonds : angle 4.18018 ( 618) SS BOND : bond 0.00140 ( 6) SS BOND : angle 1.68822 ( 12) covalent geometry : bond 0.00527 ( 3366) covalent geometry : angle 0.62657 ( 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 : 0.386 Fit side-chains REVERT: D 46 ASN cc_start: 0.8728 (p0) cc_final: 0.8430 (p0) REVERT: D 48 ARG cc_start: 0.8452 (mtp180) cc_final: 0.7974 (ttm-80) REVERT: E 49 LYS cc_start: 0.8798 (mppt) cc_final: 0.8586 (mmtm) REVERT: E 53 ASN cc_start: 0.8608 (t0) cc_final: 0.8014 (t0) REVERT: R 75 TYR cc_start: 0.7967 (t80) cc_final: 0.7680 (t80) REVERT: R 283 GLN cc_start: 0.8197 (tt0) cc_final: 0.7835 (pm20) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.1930 time to fit residues: 18.2388 Evaluate side-chains 74 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 2 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 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096071 restraints weight = 6163.553| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.27 r_work: 0.3135 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3372 Z= 0.128 Angle : 0.554 6.637 4588 Z= 0.281 Chirality : 0.041 0.123 565 Planarity : 0.003 0.028 558 Dihedral : 3.768 17.568 455 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: 1.91 (0.41), residues: 420 helix: 2.51 (0.33), residues: 248 sheet: -0.11 (0.75), residues: 48 loop : -0.78 (0.50), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 207 HIS 0.002 0.001 HIS R 150 PHE 0.011 0.001 PHE R 183 TYR 0.019 0.001 TYR R 49 ARG 0.001 0.000 ARG R 289 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 211) hydrogen bonds : angle 3.96288 ( 618) SS BOND : bond 0.00068 ( 6) SS BOND : angle 1.40071 ( 12) covalent geometry : bond 0.00291 ( 3366) covalent geometry : angle 0.54996 ( 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 84 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8723 (p0) cc_final: 0.8457 (p0) REVERT: D 48 ARG cc_start: 0.8462 (mtp180) cc_final: 0.7997 (ttm-80) REVERT: E 53 ASN cc_start: 0.8599 (t0) cc_final: 0.8063 (t0) REVERT: R 75 TYR cc_start: 0.7951 (t80) cc_final: 0.7637 (t80) REVERT: R 283 GLN cc_start: 0.8276 (tt0) cc_final: 0.7886 (pm20) outliers start: 11 outliers final: 9 residues processed: 82 average time/residue: 0.1923 time to fit residues: 18.6151 Evaluate side-chains 79 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 237 THR Chi-restraints excluded: chain R residue 274 ASP 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: 0.7980 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 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: 0.9990 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.095879 restraints weight = 6069.077| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.26 r_work: 0.3128 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4222 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= 0.136 Angle : 0.543 7.216 4588 Z= 0.275 Chirality : 0.041 0.128 565 Planarity : 0.003 0.027 558 Dihedral : 3.695 16.649 455 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.85 % Allowed : 20.33 % 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: 1.89 (0.41), residues: 420 helix: 2.52 (0.33), residues: 248 sheet: -0.13 (0.75), residues: 48 loop : -0.84 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 112 HIS 0.003 0.001 HIS R 242 PHE 0.011 0.001 PHE R 183 TYR 0.018 0.001 TYR R 49 ARG 0.001 0.000 ARG R 77 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 211) hydrogen bonds : angle 3.88058 ( 618) SS BOND : bond 0.00064 ( 6) SS BOND : angle 1.35511 ( 12) covalent geometry : bond 0.00315 ( 3366) covalent geometry : angle 0.53954 ( 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 87 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: D 34 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7544 (p90) REVERT: D 46 ASN cc_start: 0.8724 (p0) cc_final: 0.8459 (p0) REVERT: D 48 ARG cc_start: 0.8455 (mtp180) cc_final: 0.8021 (ttm-80) REVERT: E 49 LYS cc_start: 0.8757 (mppt) cc_final: 0.8518 (mmtm) REVERT: E 53 ASN cc_start: 0.8577 (t0) cc_final: 0.8089 (t0) REVERT: R 75 TYR cc_start: 0.7982 (t80) cc_final: 0.7689 (t80) REVERT: R 283 GLN cc_start: 0.8198 (tt0) cc_final: 0.7825 (pm20) outliers start: 14 outliers final: 11 residues processed: 82 average time/residue: 0.1794 time to fit residues: 17.4146 Evaluate side-chains 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 HIS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 = 0.3532 r_free = 0.3532 target = 0.114436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.096158 restraints weight = 5920.211| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.24 r_work: 0.3135 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4247 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= 0.131 Angle : 0.543 7.221 4588 Z= 0.274 Chirality : 0.041 0.119 565 Planarity : 0.003 0.027 558 Dihedral : 3.658 17.159 455 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.85 % Allowed : 20.05 % 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: 2.54 (0.33), residues: 248 sheet: -0.19 (0.75), residues: 48 loop : -0.96 (0.50), residues: 124 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 0.011 0.001 PHE R 183 TYR 0.018 0.001 TYR R 49 ARG 0.001 0.000 ARG R 77 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 211) hydrogen bonds : angle 3.87018 ( 618) SS BOND : bond 0.00073 ( 6) SS BOND : angle 1.32305 ( 12) covalent geometry : bond 0.00303 ( 3366) covalent geometry : angle 0.53931 ( 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 87 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8739 (p0) cc_final: 0.8441 (p0) REVERT: D 48 ARG cc_start: 0.8468 (mtp180) cc_final: 0.8031 (ttm-80) REVERT: E 53 ASN cc_start: 0.8549 (t0) cc_final: 0.8078 (t0) REVERT: R 75 TYR cc_start: 0.7979 (t80) cc_final: 0.7694 (t80) REVERT: R 283 GLN cc_start: 0.8222 (tt0) cc_final: 0.7829 (pm20) outliers start: 14 outliers final: 11 residues processed: 84 average time/residue: 0.1885 time to fit residues: 18.7415 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 : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 0.0000 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.0170 chunk 4 optimal weight: 0.0770 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.115883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097781 restraints weight = 5941.892| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.22 r_work: 0.3165 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3372 Z= 0.108 Angle : 0.554 7.588 4588 Z= 0.279 Chirality : 0.040 0.121 565 Planarity : 0.003 0.025 558 Dihedral : 3.644 17.359 455 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.20 % Allowed : 22.25 % 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: 1.86 (0.42), residues: 420 helix: 2.56 (0.33), residues: 250 sheet: 0.18 (0.75), residues: 50 loop : -1.28 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 207 HIS 0.002 0.000 HIS R 242 PHE 0.008 0.001 PHE R 130 TYR 0.019 0.001 TYR R 49 ARG 0.002 0.000 ARG D 8 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 211) hydrogen bonds : angle 3.76958 ( 618) SS BOND : bond 0.00083 ( 6) SS BOND : angle 1.19352 ( 12) covalent geometry : bond 0.00235 ( 3366) covalent geometry : angle 0.55139 ( 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 87 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8712 (p0) cc_final: 0.8394 (p0) REVERT: D 48 ARG cc_start: 0.8405 (mtp180) cc_final: 0.8001 (ttm-80) REVERT: E 53 ASN cc_start: 0.8514 (t0) cc_final: 0.8083 (t0) REVERT: R 75 TYR cc_start: 0.7990 (t80) cc_final: 0.7697 (t80) REVERT: R 283 GLN cc_start: 0.8211 (tt0) cc_final: 0.7853 (pm20) outliers start: 8 outliers final: 6 residues processed: 84 average time/residue: 0.1800 time to fit residues: 17.9206 Evaluate side-chains 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 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 83 THR 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 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 3 optimal weight: 0.0470 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 36 optimal weight: 0.0170 overall best weight: 0.3316 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.116937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.098711 restraints weight = 5858.546| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.21 r_work: 0.3186 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3372 Z= 0.100 Angle : 0.520 7.296 4588 Z= 0.260 Chirality : 0.040 0.121 565 Planarity : 0.003 0.025 558 Dihedral : 3.538 16.384 455 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.92 % Allowed : 21.98 % 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: 1.86 (0.42), residues: 420 helix: 2.56 (0.33), residues: 250 sheet: 0.27 (0.76), residues: 50 loop : -1.32 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 207 HIS 0.001 0.000 HIS D 34 PHE 0.007 0.001 PHE R 130 TYR 0.019 0.001 TYR R 49 ARG 0.002 0.000 ARG E 48 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 211) hydrogen bonds : angle 3.68526 ( 618) SS BOND : bond 0.00107 ( 6) SS BOND : angle 1.15843 ( 12) covalent geometry : bond 0.00213 ( 3366) covalent geometry : angle 0.51705 ( 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 87 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8771 (p0) cc_final: 0.8481 (p0) REVERT: D 48 ARG cc_start: 0.8340 (mtp180) cc_final: 0.7980 (ttm-80) REVERT: E 53 ASN cc_start: 0.8443 (t0) cc_final: 0.8125 (t0) REVERT: R 75 TYR cc_start: 0.7990 (t80) cc_final: 0.7728 (t80) REVERT: R 283 GLN cc_start: 0.8245 (tt0) cc_final: 0.7890 (pm20) outliers start: 7 outliers final: 6 residues processed: 84 average time/residue: 0.2353 time to fit residues: 23.6107 Evaluate side-chains 84 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 83 THR 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: 0.5980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3565 r_free = 0.3565 target = 0.116463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097944 restraints weight = 5977.205| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.26 r_work: 0.3168 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4616 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= 0.117 Angle : 0.558 7.368 4588 Z= 0.282 Chirality : 0.040 0.119 565 Planarity : 0.003 0.026 558 Dihedral : 3.481 16.502 455 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.91 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: 1.88 (0.42), residues: 420 helix: 2.60 (0.33), residues: 250 sheet: 0.20 (0.74), residues: 50 loop : -1.34 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 207 HIS 0.002 0.001 HIS R 242 PHE 0.009 0.001 PHE R 130 TYR 0.019 0.001 TYR R 49 ARG 0.002 0.000 ARG D 8 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 211) hydrogen bonds : angle 3.69945 ( 618) SS BOND : bond 0.00090 ( 6) SS BOND : angle 1.19836 ( 12) covalent geometry : bond 0.00268 ( 3366) covalent geometry : angle 0.55580 ( 4576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2244.73 seconds wall clock time: 39 minutes 25.55 seconds (2365.55 seconds total)