Starting phenix.real_space_refine on Wed Sep 17 03:38:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwa_38732/09_2025/8xwa_38732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwa_38732/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xwa_38732/09_2025/8xwa_38732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwa_38732/09_2025/8xwa_38732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xwa_38732/09_2025/8xwa_38732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwa_38732/09_2025/8xwa_38732.map" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.88, per 1000 atoms: 0.27 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: 0.20 Conformation dependent library (CDL) restraints added in 96.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.10 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: 0.49 Time building geometry restraints manager: 0.31 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: 1.640 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.770 Find NCS groups from input model: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.670 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG R 288 TYR 0.011 0.001 TYR R 49 PHE 0.004 0.001 PHE R 239 TRP 0.004 0.000 TRP R 207 HIS 0.002 0.000 HIS R 247 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 3366) covalent geometry : angle 0.45766 ( 4576) SS BOND : bond 0.00142 ( 6) SS BOND : angle 0.87914 ( 12) hydrogen bonds : bond 0.24058 ( 211) hydrogen bonds : angle 6.85887 ( 618) *********************** 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 : 0.127 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: 0.0775 time to fit residues: 11.7342 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 : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 0.0170 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.7822 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096905 restraints weight = 6030.842| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.23 r_work: 0.3149 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3372 Z= 0.156 Angle : 0.626 8.109 4588 Z= 0.328 Chirality : 0.043 0.209 565 Planarity : 0.004 0.024 558 Dihedral : 4.235 28.683 455 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.47 % Allowed : 15.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.42), residues: 420 helix: 2.07 (0.33), residues: 253 sheet: 0.46 (0.79), residues: 48 loop : -0.10 (0.57), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 48 TYR 0.014 0.001 TYR R 49 PHE 0.010 0.001 PHE R 183 TRP 0.005 0.001 TRP R 112 HIS 0.004 0.001 HIS D 19 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3366) covalent geometry : angle 0.62123 ( 4576) SS BOND : bond 0.00545 ( 6) SS BOND : angle 1.57638 ( 12) hydrogen bonds : bond 0.05579 ( 211) hydrogen bonds : angle 4.46362 ( 618) *********************** 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 101 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.163 Fit side-chains REVERT: D 27 ASN cc_start: 0.8487 (t0) cc_final: 0.8269 (t0) REVERT: D 46 ASN cc_start: 0.8434 (p0) cc_final: 0.8206 (p0) REVERT: D 48 ARG cc_start: 0.8299 (mtp180) cc_final: 0.7855 (ttm-80) REVERT: E 53 ASN cc_start: 0.8692 (t0) cc_final: 0.8374 (t0) REVERT: E 60 LYS cc_start: 0.9055 (mttt) cc_final: 0.8817 (mttm) REVERT: R 46 ILE cc_start: 0.8337 (mt) cc_final: 0.8090 (mp) REVERT: R 75 TYR cc_start: 0.7853 (t80) cc_final: 0.7577 (t80) REVERT: R 213 ILE cc_start: 0.9343 (tp) cc_final: 0.8999 (tp) REVERT: R 283 GLN cc_start: 0.8180 (tt0) cc_final: 0.7847 (pm20) outliers start: 9 outliers final: 5 residues processed: 98 average time/residue: 0.0703 time to fit residues: 8.3079 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 : 0.107 ------------------------------------------------------------------------------- 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 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.096587 restraints weight = 6018.195| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.25 r_work: 0.3143 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3449 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= 0.150 Angle : 0.557 6.373 4588 Z= 0.288 Chirality : 0.042 0.157 565 Planarity : 0.003 0.021 558 Dihedral : 3.951 23.535 455 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.47 % Allowed : 17.58 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.41), residues: 420 helix: 2.28 (0.33), residues: 249 sheet: 0.12 (0.76), residues: 48 loop : -0.32 (0.53), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 48 TYR 0.013 0.001 TYR R 49 PHE 0.010 0.001 PHE R 233 TRP 0.006 0.001 TRP R 264 HIS 0.002 0.001 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3366) covalent geometry : angle 0.55272 ( 4576) SS BOND : bond 0.00089 ( 6) SS BOND : angle 1.52280 ( 12) hydrogen bonds : bond 0.05080 ( 211) hydrogen bonds : angle 4.18236 ( 618) *********************** 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 : 0.114 Fit side-chains REVERT: D 29 LYS cc_start: 0.8442 (ttpt) cc_final: 0.8227 (tmtt) REVERT: D 46 ASN cc_start: 0.8540 (p0) cc_final: 0.8313 (p0) REVERT: D 48 ARG cc_start: 0.8413 (mtp180) cc_final: 0.7925 (ttm-80) REVERT: D 53 ASN cc_start: 0.9307 (t0) cc_final: 0.8853 (t0) REVERT: E 53 ASN cc_start: 0.8665 (t0) cc_final: 0.8265 (t0) REVERT: R 46 ILE cc_start: 0.8214 (mt) cc_final: 0.7978 (mp) REVERT: R 75 TYR cc_start: 0.7898 (t80) cc_final: 0.7557 (t80) REVERT: R 213 ILE cc_start: 0.9332 (tp) cc_final: 0.8984 (tp) REVERT: R 283 GLN cc_start: 0.8133 (tt0) cc_final: 0.7784 (pm20) outliers start: 9 outliers final: 6 residues processed: 83 average time/residue: 0.0759 time to fit residues: 7.4396 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 : 0.145 ------------------------------------------------------------------------------- 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 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 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.0370 chunk 28 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.0060 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.3452 ------------------------------------------------------------------------------- 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 = 0.116409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098486 restraints weight = 5831.374| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.24 r_work: 0.3178 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3372 Z= 0.109 Angle : 0.530 6.703 4588 Z= 0.269 Chirality : 0.041 0.151 565 Planarity : 0.003 0.025 558 Dihedral : 3.829 20.289 455 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.47 % Allowed : 19.51 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.41), residues: 420 helix: 2.45 (0.33), residues: 251 sheet: 0.16 (0.75), residues: 48 loop : -0.58 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 288 TYR 0.012 0.001 TYR R 49 PHE 0.008 0.001 PHE R 97 TRP 0.007 0.001 TRP R 207 HIS 0.001 0.000 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 3366) covalent geometry : angle 0.52452 ( 4576) SS BOND : bond 0.00232 ( 6) SS BOND : angle 1.51798 ( 12) hydrogen bonds : bond 0.04129 ( 211) hydrogen bonds : angle 3.94862 ( 618) *********************** 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 88 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.124 Fit side-chains REVERT: D 46 ASN cc_start: 0.8632 (p0) cc_final: 0.8375 (p0) REVERT: D 48 ARG cc_start: 0.8419 (mtp180) cc_final: 0.7940 (ttm-80) REVERT: E 48 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7575 (mtt90) REVERT: E 53 ASN cc_start: 0.8578 (t0) cc_final: 0.8135 (t0) REVERT: R 46 ILE cc_start: 0.8193 (mt) cc_final: 0.7880 (mp) REVERT: R 75 TYR cc_start: 0.7889 (t80) cc_final: 0.7535 (t80) REVERT: R 283 GLN cc_start: 0.8188 (tt0) cc_final: 0.7821 (pm20) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.0733 time to fit residues: 7.3495 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 : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 180 VAL 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 40 optimal weight: 0.0050 chunk 11 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097639 restraints weight = 5982.564| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.24 r_work: 0.3168 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4035 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= 0.114 Angle : 0.519 7.142 4588 Z= 0.265 Chirality : 0.040 0.120 565 Planarity : 0.003 0.027 558 Dihedral : 3.676 18.237 455 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.41), residues: 420 helix: 2.49 (0.33), residues: 251 sheet: 0.13 (0.74), residues: 48 loop : -0.73 (0.50), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 48 TYR 0.022 0.001 TYR R 49 PHE 0.008 0.001 PHE R 183 TRP 0.007 0.001 TRP R 264 HIS 0.002 0.000 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3366) covalent geometry : angle 0.51515 ( 4576) SS BOND : bond 0.00065 ( 6) SS BOND : angle 1.40898 ( 12) hydrogen bonds : bond 0.04089 ( 211) hydrogen bonds : angle 3.85385 ( 618) *********************** 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 88 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8747 (p0) cc_final: 0.8472 (p0) REVERT: D 48 ARG cc_start: 0.8432 (mtp180) cc_final: 0.7951 (ttm-80) REVERT: E 49 LYS cc_start: 0.8793 (mppt) cc_final: 0.8564 (mmtm) REVERT: E 53 ASN cc_start: 0.8560 (t0) cc_final: 0.8098 (t0) REVERT: R 46 ILE cc_start: 0.8245 (mt) cc_final: 0.8033 (mp) REVERT: R 75 TYR cc_start: 0.7925 (t80) cc_final: 0.7569 (t80) REVERT: R 283 GLN cc_start: 0.8201 (tt0) cc_final: 0.7797 (pm20) outliers start: 11 outliers final: 7 residues processed: 84 average time/residue: 0.0831 time to fit residues: 8.2362 Evaluate side-chains 83 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 82 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 30 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.116408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.098159 restraints weight = 5954.369| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.26 r_work: 0.3174 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3372 Z= 0.108 Angle : 0.523 6.939 4588 Z= 0.263 Chirality : 0.040 0.120 565 Planarity : 0.003 0.028 558 Dihedral : 3.607 16.880 455 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.20 % Allowed : 21.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.41), residues: 420 helix: 2.65 (0.33), residues: 248 sheet: 0.11 (0.75), residues: 48 loop : -0.74 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 289 TYR 0.020 0.001 TYR R 49 PHE 0.009 0.001 PHE R 183 TRP 0.009 0.001 TRP R 207 HIS 0.002 0.000 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3366) covalent geometry : angle 0.51984 ( 4576) SS BOND : bond 0.00056 ( 6) SS BOND : angle 1.25352 ( 12) hydrogen bonds : bond 0.03916 ( 211) hydrogen bonds : angle 3.77822 ( 618) *********************** 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 86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8675 (p0) cc_final: 0.8420 (p0) REVERT: D 48 ARG cc_start: 0.8419 (mtp180) cc_final: 0.7959 (ttm-80) REVERT: E 53 ASN cc_start: 0.8486 (t0) cc_final: 0.7926 (t0) REVERT: R 46 ILE cc_start: 0.8269 (mt) cc_final: 0.8047 (mp) REVERT: R 77 ARG cc_start: 0.5816 (mtt180) cc_final: 0.5422 (mtt-85) REVERT: R 283 GLN cc_start: 0.8175 (tt0) cc_final: 0.7808 (pm20) outliers start: 8 outliers final: 6 residues processed: 83 average time/residue: 0.0807 time to fit residues: 7.9109 Evaluate side-chains 81 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain R residue 57 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 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.0770 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** 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 = 0.116012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097534 restraints weight = 6088.062| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.28 r_work: 0.3162 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4305 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= 0.119 Angle : 0.525 7.046 4588 Z= 0.266 Chirality : 0.040 0.127 565 Planarity : 0.003 0.027 558 Dihedral : 3.580 16.132 455 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.75 % Allowed : 21.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.41), residues: 420 helix: 2.69 (0.33), residues: 248 sheet: 0.04 (0.75), residues: 48 loop : -0.85 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 208 TYR 0.019 0.001 TYR R 49 PHE 0.010 0.001 PHE R 183 TRP 0.005 0.001 TRP R 264 HIS 0.001 0.000 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3366) covalent geometry : angle 0.52232 ( 4576) SS BOND : bond 0.00060 ( 6) SS BOND : angle 1.20651 ( 12) hydrogen bonds : bond 0.04028 ( 211) hydrogen bonds : angle 3.75083 ( 618) *********************** 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 83 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8013 (ttm-80) REVERT: E 53 ASN cc_start: 0.8502 (t0) cc_final: 0.8008 (t0) REVERT: R 75 TYR cc_start: 0.7778 (t80) cc_final: 0.7398 (t80) REVERT: R 77 ARG cc_start: 0.5827 (mtt180) cc_final: 0.5445 (mtt-85) REVERT: R 283 GLN cc_start: 0.8203 (tt0) cc_final: 0.7847 (pm20) outliers start: 10 outliers final: 9 residues processed: 80 average time/residue: 0.0783 time to fit residues: 7.4251 Evaluate side-chains 80 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 82 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 216 GLN ** 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 = 0.3554 r_free = 0.3554 target = 0.115684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097236 restraints weight = 6118.545| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.29 r_work: 0.3158 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4355 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= 0.122 Angle : 0.531 7.041 4588 Z= 0.266 Chirality : 0.040 0.120 565 Planarity : 0.003 0.028 558 Dihedral : 3.548 15.717 455 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 4.12 % Allowed : 19.78 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.41), residues: 420 helix: 2.67 (0.33), residues: 248 sheet: 0.04 (0.74), residues: 48 loop : -0.96 (0.48), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 185 TYR 0.019 0.001 TYR R 49 PHE 0.012 0.001 PHE R 183 TRP 0.009 0.001 TRP R 207 HIS 0.001 0.000 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 3366) covalent geometry : angle 0.52759 ( 4576) SS BOND : bond 0.00064 ( 6) SS BOND : angle 1.21820 ( 12) hydrogen bonds : bond 0.04051 ( 211) hydrogen bonds : angle 3.76712 ( 618) *********************** 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: 15 poor density : 71 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: D 48 ARG cc_start: 0.8394 (mtp180) cc_final: 0.7996 (ttm-80) REVERT: E 53 ASN cc_start: 0.8504 (t0) cc_final: 0.8065 (t0) REVERT: R 75 TYR cc_start: 0.7858 (t80) cc_final: 0.7507 (t80) REVERT: R 283 GLN cc_start: 0.8156 (tt0) cc_final: 0.7877 (pm20) outliers start: 15 outliers final: 10 residues processed: 81 average time/residue: 0.0830 time to fit residues: 7.9342 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 : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS ** R 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097399 restraints weight = 6042.785| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.28 r_work: 0.3159 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3372 Z= 0.123 Angle : 0.552 7.230 4588 Z= 0.279 Chirality : 0.040 0.146 565 Planarity : 0.003 0.028 558 Dihedral : 3.560 15.729 455 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.57 % Allowed : 21.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.41), residues: 420 helix: 2.67 (0.33), residues: 248 sheet: 0.16 (0.73), residues: 50 loop : -1.06 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 48 TYR 0.019 0.001 TYR R 49 PHE 0.009 0.001 PHE R 183 TRP 0.005 0.001 TRP R 264 HIS 0.002 0.000 HIS R 150 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3366) covalent geometry : angle 0.54907 ( 4576) SS BOND : bond 0.00068 ( 6) SS BOND : angle 1.19934 ( 12) hydrogen bonds : bond 0.04042 ( 211) hydrogen bonds : angle 3.75161 ( 618) *********************** 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 86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: D 34 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.7097 (p-80) REVERT: D 48 ARG cc_start: 0.8372 (mtp180) cc_final: 0.7975 (ttm-80) REVERT: E 53 ASN cc_start: 0.8480 (t0) cc_final: 0.8054 (t0) REVERT: R 75 TYR cc_start: 0.7892 (t80) cc_final: 0.7512 (t80) REVERT: R 283 GLN cc_start: 0.8148 (tt0) cc_final: 0.7868 (pm20) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.0706 time to fit residues: 6.8334 Evaluate side-chains 83 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.0470 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.0670 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.116565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098076 restraints weight = 5980.513| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.25 r_work: 0.3174 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 3372 Z= 0.109 Angle : 0.546 7.318 4588 Z= 0.274 Chirality : 0.040 0.128 565 Planarity : 0.003 0.030 558 Dihedral : 3.552 17.554 455 Min Nonbonded Distance : 2.615 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.41), residues: 420 helix: 2.63 (0.33), residues: 250 sheet: 0.27 (0.74), residues: 50 loop : -1.26 (0.47), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.019 0.001 TYR R 49 PHE 0.011 0.001 PHE R 183 TRP 0.010 0.001 TRP R 207 HIS 0.003 0.000 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3366) covalent geometry : angle 0.54282 ( 4576) SS BOND : bond 0.00167 ( 6) SS BOND : angle 1.19525 ( 12) hydrogen bonds : bond 0.03879 ( 211) hydrogen bonds : angle 3.74185 ( 618) ********************** 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 83 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: D 48 ARG cc_start: 0.8422 (mtp180) cc_final: 0.8019 (ttm-80) REVERT: E 53 ASN cc_start: 0.8482 (t0) cc_final: 0.8062 (t0) REVERT: R 75 TYR cc_start: 0.7902 (t80) cc_final: 0.7505 (t80) REVERT: R 283 GLN cc_start: 0.8135 (tt0) cc_final: 0.7867 (pm20) outliers start: 11 outliers final: 10 residues processed: 80 average time/residue: 0.0803 time to fit residues: 7.5898 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 : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 66 MET 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 243 MET Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 0.3980 chunk 7 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.117046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098389 restraints weight = 6119.500| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.31 r_work: 0.3185 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 3372 Z= 0.109 Angle : 0.542 7.268 4588 Z= 0.272 Chirality : 0.040 0.129 565 Planarity : 0.003 0.029 558 Dihedral : 3.523 17.271 455 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.42), residues: 420 helix: 2.64 (0.33), residues: 250 sheet: 0.33 (0.74), residues: 50 loop : -1.29 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 8 TYR 0.019 0.001 TYR R 49 PHE 0.008 0.001 PHE R 130 TRP 0.005 0.001 TRP R 264 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 3366) covalent geometry : angle 0.53926 ( 4576) SS BOND : bond 0.00079 ( 6) SS BOND : angle 1.17407 ( 12) hydrogen bonds : bond 0.03770 ( 211) hydrogen bonds : angle 3.68446 ( 618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1009.26 seconds wall clock time: 18 minutes 17.76 seconds (1097.76 seconds total)