Starting phenix.real_space_refine on Mon Feb 10 23:33:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xwa_38732/02_2025/8xwa_38732.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xwa_38732/02_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_38732/02_2025/8xwa_38732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xwa_38732/02_2025/8xwa_38732.map" model { file = "/net/cci-nas-00/data/ceres_data/8xwa_38732/02_2025/8xwa_38732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xwa_38732/02_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-5592/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: 2.50, per 1000 atoms: 0.76 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: 0.65 Conformation dependent library (CDL) restraints added in 421.1 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: 0.34 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: 0.78 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: 0.560 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.530 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 3366 Z= 0.160 Angle : 0.458 4.790 4576 Z= 0.259 Chirality : 0.037 0.124 565 Planarity : 0.003 0.031 558 Dihedral : 13.515 89.864 1221 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.44), residues: 420 helix: 1.75 (0.35), residues: 247 sheet: 0.19 (0.80), residues: 48 loop : 0.24 (0.62), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 207 HIS 0.002 0.000 HIS R 247 PHE 0.004 0.001 PHE R 239 TYR 0.011 0.001 TYR R 49 ARG 0.002 0.000 ARG R 288 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.439 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: 0.1914 time to fit residues: 28.9340 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 : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096749 restraints weight = 5941.218| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.21 r_work: 0.3148 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3366 Z= 0.220 Angle : 0.611 7.882 4576 Z= 0.323 Chirality : 0.043 0.203 565 Planarity : 0.004 0.024 558 Dihedral : 4.179 27.869 455 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.02 % Allowed : 15.11 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.42), residues: 420 helix: 2.11 (0.33), residues: 253 sheet: 0.48 (0.79), residues: 48 loop : -0.08 (0.58), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 112 HIS 0.005 0.001 HIS D 34 PHE 0.010 0.001 PHE R 183 TYR 0.014 0.001 TYR R 49 ARG 0.006 0.001 ARG E 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.362 Fit side-chains REVERT: D 27 ASN cc_start: 0.8481 (t0) cc_final: 0.8262 (t0) REVERT: D 46 ASN cc_start: 0.8432 (p0) cc_final: 0.8207 (p0) REVERT: D 48 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7875 (ttm-80) REVERT: E 53 ASN cc_start: 0.8695 (t0) cc_final: 0.8377 (t0) REVERT: E 60 LYS cc_start: 0.9060 (mttt) cc_final: 0.8816 (mttm) REVERT: R 46 ILE cc_start: 0.8345 (mt) cc_final: 0.8096 (mp) REVERT: R 75 TYR cc_start: 0.7857 (t80) cc_final: 0.7587 (t80) REVERT: R 213 ILE cc_start: 0.9343 (tp) cc_final: 0.8998 (tp) REVERT: R 283 GLN cc_start: 0.8202 (tt0) cc_final: 0.7838 (pm20) outliers start: 11 outliers final: 5 residues processed: 99 average time/residue: 0.1658 time to fit residues: 19.5811 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 : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 217 SER Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 317 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 19 HIS R 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.115933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098075 restraints weight = 5861.273| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.23 r_work: 0.3170 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3366 Z= 0.174 Angle : 0.536 6.479 4576 Z= 0.276 Chirality : 0.042 0.147 565 Planarity : 0.004 0.027 558 Dihedral : 3.933 22.728 455 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.92 % Allowed : 18.41 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.42), residues: 420 helix: 2.33 (0.33), residues: 253 sheet: 0.21 (0.77), residues: 48 loop : -0.34 (0.54), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 207 HIS 0.003 0.000 HIS D 19 PHE 0.008 0.001 PHE R 97 TYR 0.013 0.001 TYR R 49 ARG 0.003 0.000 ARG E 48 *********************** 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 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.399 Fit side-chains REVERT: D 29 LYS cc_start: 0.8429 (ttpt) cc_final: 0.8223 (tmtt) REVERT: D 46 ASN cc_start: 0.8535 (p0) cc_final: 0.8266 (p0) REVERT: D 48 ARG cc_start: 0.8398 (mtp180) cc_final: 0.7913 (ttm-80) REVERT: D 53 ASN cc_start: 0.9282 (t0) cc_final: 0.8820 (t0) REVERT: E 53 ASN cc_start: 0.8649 (t0) cc_final: 0.8296 (t0) REVERT: R 46 ILE cc_start: 0.8193 (mt) cc_final: 0.7954 (mp) REVERT: R 75 TYR cc_start: 0.7877 (t80) cc_final: 0.7509 (t80) REVERT: R 213 ILE cc_start: 0.9356 (tp) cc_final: 0.9028 (tp) REVERT: R 283 GLN cc_start: 0.8344 (tt0) cc_final: 0.7951 (pm20) outliers start: 7 outliers final: 6 residues processed: 82 average time/residue: 0.1830 time to fit residues: 17.6760 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 : 0.318 ------------------------------------------------------------------------------- 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 313 ILE Chi-restraints excluded: chain R residue 317 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: 0.8980 chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 28 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.115563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097563 restraints weight = 5993.906| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.26 r_work: 0.3163 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3366 Z= 0.162 Angle : 0.520 6.539 4576 Z= 0.265 Chirality : 0.041 0.135 565 Planarity : 0.003 0.027 558 Dihedral : 3.722 20.355 455 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.30 % Allowed : 18.41 % 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: 2.05 (0.41), residues: 420 helix: 2.53 (0.33), residues: 251 sheet: 0.09 (0.75), residues: 48 loop : -0.63 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 207 HIS 0.001 0.000 HIS R 150 PHE 0.008 0.001 PHE R 183 TYR 0.013 0.001 TYR R 49 ARG 0.002 0.000 ARG R 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.385 Fit side-chains REVERT: D 45 LYS cc_start: 0.7330 (mtmm) cc_final: 0.7073 (mtmm) REVERT: D 46 ASN cc_start: 0.8627 (p0) cc_final: 0.8372 (p0) REVERT: D 48 ARG cc_start: 0.8440 (mtp180) cc_final: 0.7961 (ttm-80) REVERT: E 53 ASN cc_start: 0.8576 (t0) cc_final: 0.8137 (t0) REVERT: R 46 ILE cc_start: 0.8280 (mt) cc_final: 0.7957 (mp) REVERT: R 75 TYR cc_start: 0.7903 (t80) cc_final: 0.7548 (t80) REVERT: R 283 GLN cc_start: 0.8308 (tt0) cc_final: 0.7880 (pm20) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 0.1882 time to fit residues: 19.3458 Evaluate side-chains 80 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL 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: 0.0060 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.114085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.095892 restraints weight = 6056.627| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.26 r_work: 0.3130 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3366 Z= 0.236 Angle : 0.568 7.032 4576 Z= 0.288 Chirality : 0.042 0.142 565 Planarity : 0.003 0.029 558 Dihedral : 3.738 19.486 455 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.30 % Allowed : 20.60 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.41), residues: 420 helix: 2.47 (0.33), residues: 251 sheet: -0.08 (0.73), residues: 48 loop : -0.75 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 264 HIS 0.003 0.001 HIS D 34 PHE 0.013 0.001 PHE R 183 TYR 0.025 0.001 TYR R 49 ARG 0.002 0.000 ARG R 289 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8723 (p0) cc_final: 0.8441 (p0) REVERT: D 48 ARG cc_start: 0.8434 (mtp180) cc_final: 0.7956 (ttm-80) REVERT: E 49 LYS cc_start: 0.8810 (mppt) cc_final: 0.8583 (mmtm) REVERT: E 53 ASN cc_start: 0.8597 (t0) cc_final: 0.8026 (t0) REVERT: R 75 TYR cc_start: 0.7952 (t80) cc_final: 0.7605 (t80) REVERT: R 283 GLN cc_start: 0.8309 (tt0) cc_final: 0.7887 (pm20) outliers start: 12 outliers final: 9 residues processed: 82 average time/residue: 0.1960 time to fit residues: 18.9500 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 : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097105 restraints weight = 6125.992| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.28 r_work: 0.3154 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3366 Z= 0.176 Angle : 0.532 6.994 4576 Z= 0.269 Chirality : 0.040 0.121 565 Planarity : 0.003 0.028 558 Dihedral : 3.640 17.241 455 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.47 % Allowed : 21.98 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.41), residues: 420 helix: 2.53 (0.33), residues: 251 sheet: 0.00 (0.74), residues: 48 loop : -0.91 (0.49), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 207 HIS 0.001 0.000 HIS R 150 PHE 0.008 0.001 PHE R 183 TYR 0.018 0.001 TYR R 49 ARG 0.001 0.000 ARG R 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8738 (p0) cc_final: 0.8477 (p0) REVERT: D 48 ARG cc_start: 0.8448 (mtp180) cc_final: 0.7975 (ttm-80) REVERT: E 53 ASN cc_start: 0.8596 (t0) cc_final: 0.8035 (t0) REVERT: R 75 TYR cc_start: 0.7971 (t80) cc_final: 0.7645 (t80) REVERT: R 283 GLN cc_start: 0.8259 (tt0) cc_final: 0.7901 (pm20) outliers start: 9 outliers final: 7 residues processed: 82 average time/residue: 0.1823 time to fit residues: 17.7273 Evaluate side-chains 78 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 MET 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 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.113757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095403 restraints weight = 6091.530| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.26 r_work: 0.3125 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3366 Z= 0.249 Angle : 0.572 6.958 4576 Z= 0.289 Chirality : 0.042 0.131 565 Planarity : 0.003 0.027 558 Dihedral : 3.684 17.017 455 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.85 % Allowed : 19.51 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.41), residues: 420 helix: 2.50 (0.33), residues: 248 sheet: -0.23 (0.73), residues: 48 loop : -0.88 (0.49), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 207 HIS 0.003 0.001 HIS D 34 PHE 0.013 0.001 PHE R 183 TYR 0.019 0.001 TYR R 49 ARG 0.001 0.000 ARG R 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 34 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7625 (p90) REVERT: D 46 ASN cc_start: 0.8732 (p0) cc_final: 0.8469 (p0) REVERT: D 48 ARG cc_start: 0.8404 (mtp180) cc_final: 0.7957 (ttm-80) REVERT: E 49 LYS cc_start: 0.8756 (mppt) cc_final: 0.8541 (mmtm) REVERT: E 53 ASN cc_start: 0.8593 (t0) cc_final: 0.8114 (t0) REVERT: R 75 TYR cc_start: 0.8018 (t80) cc_final: 0.7726 (t80) REVERT: R 283 GLN cc_start: 0.8210 (tt0) cc_final: 0.7861 (pm20) outliers start: 14 outliers final: 10 residues processed: 82 average time/residue: 0.1919 time to fit residues: 18.6594 Evaluate side-chains 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.114305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096066 restraints weight = 5959.127| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.23 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: 0.8368 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3366 Z= 0.225 Angle : 0.557 7.098 4576 Z= 0.281 Chirality : 0.041 0.119 565 Planarity : 0.003 0.027 558 Dihedral : 3.656 17.518 455 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.30 % Allowed : 20.33 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.41), residues: 420 helix: 2.50 (0.33), residues: 248 sheet: -0.05 (0.73), residues: 50 loop : -1.03 (0.49), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 112 HIS 0.002 0.001 HIS R 150 PHE 0.013 0.001 PHE R 183 TYR 0.018 0.001 TYR R 49 ARG 0.001 0.000 ARG R 248 *********************** 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 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8727 (p0) cc_final: 0.8422 (p0) REVERT: D 48 ARG cc_start: 0.8382 (mtp180) cc_final: 0.7953 (ttm-80) REVERT: E 53 ASN cc_start: 0.8572 (t0) cc_final: 0.8128 (t0) REVERT: R 75 TYR cc_start: 0.7979 (t80) cc_final: 0.7698 (t80) REVERT: R 283 GLN cc_start: 0.8211 (tt0) cc_final: 0.7862 (pm20) outliers start: 12 outliers final: 10 residues processed: 82 average time/residue: 0.1965 time to fit residues: 19.2110 Evaluate side-chains 82 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 11 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.115388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097219 restraints weight = 5966.062| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.23 r_work: 0.3154 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3366 Z= 0.181 Angle : 0.561 7.292 4576 Z= 0.282 Chirality : 0.040 0.120 565 Planarity : 0.003 0.027 558 Dihedral : 3.646 17.348 455 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.30 % Allowed : 20.60 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.42), residues: 420 helix: 2.50 (0.33), residues: 250 sheet: -0.04 (0.73), residues: 50 loop : -1.21 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 207 HIS 0.002 0.000 HIS R 150 PHE 0.010 0.001 PHE R 183 TYR 0.019 0.001 TYR R 49 ARG 0.002 0.000 ARG D 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: D 46 ASN cc_start: 0.8746 (p0) cc_final: 0.8404 (p0) REVERT: D 48 ARG cc_start: 0.8359 (mtp180) cc_final: 0.7937 (ttm-80) REVERT: E 53 ASN cc_start: 0.8543 (t0) cc_final: 0.8119 (t0) REVERT: R 75 TYR cc_start: 0.7914 (t80) cc_final: 0.7620 (t80) REVERT: R 283 GLN cc_start: 0.8173 (tt0) cc_final: 0.7827 (pm20) outliers start: 12 outliers final: 10 residues processed: 86 average time/residue: 0.1818 time to fit residues: 18.4887 Evaluate side-chains 85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 82 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 overall best weight: 0.5700 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.097568 restraints weight = 5916.776| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.23 r_work: 0.3164 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3366 Z= 0.165 Angle : 0.552 7.411 4576 Z= 0.275 Chirality : 0.040 0.119 565 Planarity : 0.003 0.026 558 Dihedral : 3.616 17.185 455 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.02 % Allowed : 20.60 % 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: 1.80 (0.41), residues: 420 helix: 2.49 (0.33), residues: 250 sheet: 0.06 (0.73), residues: 50 loop : -1.20 (0.49), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 207 HIS 0.002 0.000 HIS D 34 PHE 0.007 0.001 PHE R 183 TYR 0.019 0.001 TYR R 49 ARG 0.002 0.000 ARG D 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: D 34 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7549 (p-80) REVERT: D 48 ARG cc_start: 0.8375 (mtp180) cc_final: 0.8040 (ttm-80) REVERT: E 53 ASN cc_start: 0.8503 (t0) cc_final: 0.8142 (t0) REVERT: R 75 TYR cc_start: 0.7925 (t80) cc_final: 0.7640 (t80) REVERT: R 283 GLN cc_start: 0.8178 (tt0) cc_final: 0.7836 (pm20) outliers start: 11 outliers final: 10 residues processed: 86 average time/residue: 0.1793 time to fit residues: 18.4333 Evaluate side-chains 86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 34 HIS Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 313 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.115646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097288 restraints weight = 6004.260| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.25 r_work: 0.3159 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3366 Z= 0.210 Angle : 0.577 7.241 4576 Z= 0.290 Chirality : 0.041 0.119 565 Planarity : 0.003 0.026 558 Dihedral : 3.640 16.139 455 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.57 % Allowed : 20.60 % 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: 1.72 (0.41), residues: 420 helix: 2.45 (0.34), residues: 250 sheet: 0.06 (0.73), residues: 50 loop : -1.28 (0.48), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 207 HIS 0.004 0.001 HIS D 34 PHE 0.010 0.001 PHE R 183 TYR 0.018 0.001 TYR R 49 ARG 0.002 0.000 ARG E 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1973.17 seconds wall clock time: 35 minutes 48.70 seconds (2148.70 seconds total)