Starting phenix.real_space_refine on Wed Sep 17 04:39:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5msh_3565/09_2025/5msh_3565.cif Found real_map, /net/cci-nas-00/data/ceres_data/5msh_3565/09_2025/5msh_3565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5msh_3565/09_2025/5msh_3565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5msh_3565/09_2025/5msh_3565.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5msh_3565/09_2025/5msh_3565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5msh_3565/09_2025/5msh_3565.map" } resolution = 4.25 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= 0.003 sd= 0.022 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 31 5.16 5 C 2732 2.51 5 N 719 2.21 5 O 805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s 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: 4287 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1422 Classifications: {'peptide': 182} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 163} Chain breaks: 1 Chain: "B" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2865 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 14, 'TRANS': 354} Time building chain proxies: 1.29, per 1000 atoms: 0.30 Number of scatterers: 4287 At special positions: 0 Unit cell: (92.4, 74.8, 99, 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 31 16.00 O 805 8.00 N 719 7.00 C 2732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.35 Conformation dependent library (CDL) restraints added in 193.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 12.9% alpha, 46.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 300 through 304 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.732A pdb=" N MET A 163 " --> pdb=" O PRO A 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 5.732A pdb=" N MET A 163 " --> pdb=" O PRO A 13 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA A 63 " --> pdb=" O ASN A 174 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN A 174 " --> pdb=" O ALA A 63 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 41 removed outlier: 3.654A pdb=" N ARG A 106 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 32 removed outlier: 5.989A pdb=" N LYS B 24 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE B 172 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 46 removed outlier: 6.330A pdb=" N VAL B 150 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP B 44 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N MET B 148 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N CYS B 87 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP B 111 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 202 removed outlier: 8.083A pdb=" N GLN B 188 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY B 356 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP B 190 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE B 354 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N LYS B 352 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN B 194 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY B 350 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TRP B 196 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 348 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LYS B 347 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR B 251 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 349 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 249 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE B 351 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS B 247 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASP B 353 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU B 245 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 202 removed outlier: 8.083A pdb=" N GLN B 188 " --> pdb=" O GLY B 356 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY B 356 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP B 190 " --> pdb=" O PHE B 354 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE B 354 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N LYS B 352 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN B 194 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLY B 350 " --> pdb=" O ASN B 194 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N TRP B 196 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 348 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LYS B 347 " --> pdb=" O THR B 251 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR B 251 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL B 349 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N GLU B 249 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE B 351 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS B 247 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ASP B 353 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLU B 245 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 210 through 214 174 hydrogen bonds defined for protein. 417 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: 0.77 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1083 1.32 - 1.45: 1049 1.45 - 1.57: 2218 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4398 Sorted by residual: bond pdb=" N PRO A 13 " pdb=" CA PRO A 13 " ideal model delta sigma weight residual 1.466 1.406 0.059 1.19e-02 7.06e+03 2.48e+01 bond pdb=" N PRO B 282 " pdb=" CA PRO B 282 " ideal model delta sigma weight residual 1.467 1.418 0.048 1.17e-02 7.31e+03 1.72e+01 bond pdb=" N PRO B 214 " pdb=" CA PRO B 214 " ideal model delta sigma weight residual 1.466 1.420 0.046 1.19e-02 7.06e+03 1.48e+01 bond pdb=" N PRO A 181 " pdb=" CA PRO A 181 " ideal model delta sigma weight residual 1.467 1.421 0.046 1.21e-02 6.83e+03 1.47e+01 bond pdb=" N PRO B 324 " pdb=" CA PRO B 324 " ideal model delta sigma weight residual 1.466 1.424 0.042 1.19e-02 7.06e+03 1.22e+01 ... (remaining 4393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 4957 1.80 - 3.61: 783 3.61 - 5.41: 178 5.41 - 7.22: 53 7.22 - 9.02: 19 Bond angle restraints: 5990 Sorted by residual: angle pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" O ARG A 77 " ideal model delta sigma weight residual 120.80 113.22 7.58 1.11e+00 8.12e-01 4.67e+01 angle pdb=" C GLY A 126 " pdb=" N PRO A 127 " pdb=" CA PRO A 127 " ideal model delta sigma weight residual 119.64 125.81 -6.17 1.01e+00 9.80e-01 3.73e+01 angle pdb=" C GLY A 1 " pdb=" N PRO A 2 " pdb=" CA PRO A 2 " ideal model delta sigma weight residual 119.56 125.71 -6.15 1.01e+00 9.80e-01 3.71e+01 angle pdb=" C GLU B 178 " pdb=" N PRO B 179 " pdb=" CA PRO B 179 " ideal model delta sigma weight residual 120.31 126.08 -5.77 9.80e-01 1.04e+00 3.46e+01 angle pdb=" C ASN A 152 " pdb=" N PRO A 153 " pdb=" CA PRO A 153 " ideal model delta sigma weight residual 119.84 127.08 -7.24 1.25e+00 6.40e-01 3.35e+01 ... (remaining 5985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 2515 17.09 - 34.18: 44 34.18 - 51.27: 11 51.27 - 68.36: 7 68.36 - 85.44: 6 Dihedral angle restraints: 2583 sinusoidal: 998 harmonic: 1585 Sorted by residual: dihedral pdb=" CA ARG A 77 " pdb=" C ARG A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta harmonic sigma weight residual 0.00 36.50 -36.50 0 5.00e+00 4.00e-02 5.33e+01 dihedral pdb=" C HIS B 66 " pdb=" N HIS B 66 " pdb=" CA HIS B 66 " pdb=" CB HIS B 66 " ideal model delta harmonic sigma weight residual -122.60 -131.97 9.37 0 2.50e+00 1.60e-01 1.40e+01 dihedral pdb=" N HIS B 66 " pdb=" C HIS B 66 " pdb=" CA HIS B 66 " pdb=" CB HIS B 66 " ideal model delta harmonic sigma weight residual 122.80 131.11 -8.31 0 2.50e+00 1.60e-01 1.11e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 505 0.083 - 0.166: 141 0.166 - 0.249: 17 0.249 - 0.333: 2 0.333 - 0.416: 1 Chirality restraints: 666 Sorted by residual: chirality pdb=" CA HIS B 66 " pdb=" N HIS B 66 " pdb=" C HIS B 66 " pdb=" CB HIS B 66 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CA MET B 231 " pdb=" N MET B 231 " pdb=" C MET B 231 " pdb=" CB MET B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA ASN B 233 " pdb=" N ASN B 233 " pdb=" C ASN B 233 " pdb=" CB ASN B 233 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 663 not shown) Planarity restraints: 772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 77 " -0.061 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C ARG A 77 " 0.216 2.00e-02 2.50e+03 pdb=" O ARG A 77 " -0.080 2.00e-02 2.50e+03 pdb=" N GLY A 78 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 128 " 0.052 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO B 129 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 47 " 0.036 2.00e-02 2.50e+03 1.75e-02 7.62e+00 pdb=" CG TRP A 47 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 47 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 47 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP A 47 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 47 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 47 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 47 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 47 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 47 " 0.017 2.00e-02 2.50e+03 ... (remaining 769 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1481 2.84 - 3.35: 3794 3.35 - 3.87: 7265 3.87 - 4.38: 8569 4.38 - 4.90: 14240 Nonbonded interactions: 35349 Sorted by model distance: nonbonded pdb=" O ASN B 128 " pdb=" OD1 ASN B 128 " model vdw 2.323 3.040 nonbonded pdb=" N GLU B 279 " pdb=" OE1 GLU B 279 " model vdw 2.326 3.120 nonbonded pdb=" OG SER B 366 " pdb=" N ARG B 367 " model vdw 2.420 3.120 nonbonded pdb=" O PHE A 133 " pdb=" CD1 PHE A 133 " model vdw 2.429 3.340 nonbonded pdb=" N GLU A 101 " pdb=" OE1 GLU A 101 " model vdw 2.467 3.120 ... (remaining 35344 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.520 Find NCS groups from input model: 0.010 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:1.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0197 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 : 0.014 0.059 4398 Z= 0.905 Angle : 1.562 9.020 5990 Z= 1.032 Chirality : 0.074 0.416 666 Planarity : 0.009 0.125 772 Dihedral : 9.556 85.444 1561 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 1.47 % Allowed : 6.06 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.93 (0.34), residues: 545 helix: -2.30 (0.58), residues: 57 sheet: 0.82 (0.38), residues: 181 loop : -1.20 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 367 TYR 0.031 0.005 TYR B 100 PHE 0.026 0.004 PHE B 202 TRP 0.036 0.005 TRP A 47 HIS 0.003 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.01437 ( 4398) covalent geometry : angle 1.56186 ( 5990) hydrogen bonds : bond 0.14012 ( 152) hydrogen bonds : angle 8.28871 ( 417) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.6148 (tttt) cc_final: 0.4973 (mtmm) REVERT: A 89 GLN cc_start: 0.3743 (mt0) cc_final: 0.3304 (pt0) REVERT: B 24 LYS cc_start: -0.1135 (mttm) cc_final: -0.1570 (mttt) REVERT: B 200 LEU cc_start: 0.3159 (mt) cc_final: 0.2873 (mp) REVERT: B 347 LYS cc_start: 0.5153 (ttpt) cc_final: 0.4865 (pttt) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1113 time to fit residues: 8.6186 Evaluate side-chains 41 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.307115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5280 r_free = 0.5280 target = 0.301731 restraints weight = 8608.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.303373 restraints weight = 5641.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.304238 restraints weight = 3852.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.305122 restraints weight = 2856.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5316 r_free = 0.5316 target = 0.305550 restraints weight = 2066.202| |-----------------------------------------------------------------------------| r_work (final): 0.5315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0780 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4398 Z= 0.206 Angle : 0.786 7.604 5990 Z= 0.427 Chirality : 0.052 0.161 666 Planarity : 0.006 0.055 772 Dihedral : 5.873 30.286 587 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.77 % Favored : 95.05 % Rotamer: Outliers : 0.21 % Allowed : 1.27 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.74 (0.33), residues: 545 helix: -1.58 (0.66), residues: 52 sheet: 0.57 (0.39), residues: 170 loop : -0.89 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 143 TYR 0.015 0.002 TYR B 278 PHE 0.019 0.003 PHE A 32 TRP 0.019 0.003 TRP A 86 HIS 0.012 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 4398) covalent geometry : angle 0.78637 ( 5990) hydrogen bonds : bond 0.05341 ( 152) hydrogen bonds : angle 6.97273 ( 417) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.094 Fit side-chains REVERT: B 2 GLU cc_start: -0.0125 (mt-10) cc_final: -0.0613 (tm-30) outliers start: 1 outliers final: 1 residues processed: 54 average time/residue: 0.0691 time to fit residues: 4.7975 Evaluate side-chains 36 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 50.0000 chunk 32 optimal weight: 50.0000 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 20 optimal weight: 50.0000 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.5323 r_free = 0.5323 target = 0.305251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5281 r_free = 0.5281 target = 0.300873 restraints weight = 8698.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5294 r_free = 0.5294 target = 0.302169 restraints weight = 5830.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5302 r_free = 0.5302 target = 0.303069 restraints weight = 4081.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.303321 restraints weight = 2946.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.5310 r_free = 0.5310 target = 0.303916 restraints weight = 2466.841| |-----------------------------------------------------------------------------| r_work (final): 0.5310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0819 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4398 Z= 0.136 Angle : 0.626 5.645 5990 Z= 0.337 Chirality : 0.046 0.145 666 Planarity : 0.005 0.048 772 Dihedral : 5.196 27.475 587 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.67 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -0.49 (0.34), residues: 545 helix: -1.19 (0.70), residues: 52 sheet: 0.32 (0.38), residues: 184 loop : -0.51 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 97 TYR 0.014 0.002 TYR B 241 PHE 0.011 0.002 PHE A 32 TRP 0.008 0.001 TRP A 86 HIS 0.003 0.001 HIS B 331 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4398) covalent geometry : angle 0.62552 ( 5990) hydrogen bonds : bond 0.04191 ( 152) hydrogen bonds : angle 6.30327 ( 417) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: -0.1645 (mtp) cc_final: -0.1855 (tmm) REVERT: B 2 GLU cc_start: -0.0286 (mt-10) cc_final: -0.0698 (tm-30) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0865 time to fit residues: 3.9715 Evaluate side-chains 31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 10.0000 chunk 48 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.0980 chunk 6 optimal weight: 50.0000 chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 36 optimal weight: 50.0000 overall best weight: 7.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.301903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5242 r_free = 0.5242 target = 0.296979 restraints weight = 8652.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.298223 restraints weight = 6230.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5263 r_free = 0.5263 target = 0.299057 restraints weight = 4494.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5266 r_free = 0.5266 target = 0.299351 restraints weight = 3379.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.5271 r_free = 0.5271 target = 0.299864 restraints weight = 2917.084| |-----------------------------------------------------------------------------| r_work (final): 0.5270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1132 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4398 Z= 0.179 Angle : 0.702 10.356 5990 Z= 0.377 Chirality : 0.049 0.164 666 Planarity : 0.006 0.054 772 Dihedral : 5.416 22.266 587 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.40 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -0.63 (0.35), residues: 545 helix: -0.85 (0.77), residues: 46 sheet: 0.10 (0.36), residues: 196 loop : -0.64 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 164 TYR 0.019 0.002 TYR B 325 PHE 0.025 0.003 PHE B 277 TRP 0.017 0.002 TRP A 86 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 4398) covalent geometry : angle 0.70224 ( 5990) hydrogen bonds : bond 0.04219 ( 152) hydrogen bonds : angle 6.56362 ( 417) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.169 Fit side-chains REVERT: B 2 GLU cc_start: -0.0352 (mt-10) cc_final: -0.0784 (tm-30) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0754 time to fit residues: 3.6533 Evaluate side-chains 33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 50.0000 chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 22 optimal weight: 40.0000 chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 50.0000 chunk 6 optimal weight: 50.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN B 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5269 r_free = 0.5269 target = 0.300858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5248 r_free = 0.5248 target = 0.298644 restraints weight = 8919.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5251 r_free = 0.5251 target = 0.299047 restraints weight = 6892.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5251 r_free = 0.5251 target = 0.299047 restraints weight = 5579.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5251 r_free = 0.5251 target = 0.299047 restraints weight = 5579.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5251 r_free = 0.5251 target = 0.299047 restraints weight = 5579.664| |-----------------------------------------------------------------------------| r_work (final): 0.5251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1315 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4398 Z= 0.178 Angle : 0.713 9.062 5990 Z= 0.382 Chirality : 0.049 0.249 666 Planarity : 0.006 0.061 772 Dihedral : 5.411 23.603 587 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -0.90 (0.35), residues: 545 helix: -1.13 (0.73), residues: 53 sheet: 0.26 (0.39), residues: 187 loop : -1.04 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 195 TYR 0.021 0.002 TYR A 93 PHE 0.030 0.002 PHE A 24 TRP 0.016 0.002 TRP B 190 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 4398) covalent geometry : angle 0.71330 ( 5990) hydrogen bonds : bond 0.04291 ( 152) hydrogen bonds : angle 6.58893 ( 417) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.186 Fit side-chains REVERT: B 140 MET cc_start: 0.3229 (tpt) cc_final: 0.2792 (tpt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0687 time to fit residues: 3.9541 Evaluate side-chains 36 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 40 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 48 optimal weight: 40.0000 chunk 26 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN ** B 233 ASN ** 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 = 0.5267 r_free = 0.5267 target = 0.300773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.5223 r_free = 0.5223 target = 0.295911 restraints weight = 8724.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5229 r_free = 0.5229 target = 0.296649 restraints weight = 6479.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.5232 r_free = 0.5232 target = 0.297005 restraints weight = 5105.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5232 r_free = 0.5232 target = 0.297005 restraints weight = 4478.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5232 r_free = 0.5232 target = 0.297005 restraints weight = 4478.603| |-----------------------------------------------------------------------------| r_work (final): 0.5232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1416 moved from start: 0.6713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4398 Z= 0.157 Angle : 0.654 6.785 5990 Z= 0.350 Chirality : 0.048 0.196 666 Planarity : 0.006 0.061 772 Dihedral : 5.191 22.528 587 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.95 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -0.90 (0.35), residues: 545 helix: -0.82 (0.77), residues: 47 sheet: 0.04 (0.38), residues: 195 loop : -0.97 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 315 TYR 0.016 0.002 TYR A 93 PHE 0.022 0.002 PHE A 24 TRP 0.014 0.001 TRP A 86 HIS 0.005 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4398) covalent geometry : angle 0.65436 ( 5990) hydrogen bonds : bond 0.03848 ( 152) hydrogen bonds : angle 6.58040 ( 417) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.163 Fit side-chains REVERT: B 59 THR cc_start: 0.3793 (t) cc_final: 0.3553 (t) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0656 time to fit residues: 3.6035 Evaluate side-chains 35 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 50.0000 chunk 15 optimal weight: 0.0030 chunk 48 optimal weight: 50.0000 chunk 6 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 30.0000 chunk 47 optimal weight: 40.0000 chunk 8 optimal weight: 6.9990 overall best weight: 3.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5273 r_free = 0.5273 target = 0.301482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.296553 restraints weight = 8726.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5235 r_free = 0.5235 target = 0.297391 restraints weight = 6494.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.298031 restraints weight = 5095.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.298343 restraints weight = 4141.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.5245 r_free = 0.5245 target = 0.298431 restraints weight = 3601.023| |-----------------------------------------------------------------------------| r_work (final): 0.5244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1346 moved from start: 0.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4398 Z= 0.117 Angle : 0.578 6.053 5990 Z= 0.306 Chirality : 0.046 0.173 666 Planarity : 0.005 0.053 772 Dihedral : 4.721 18.317 587 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.59 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -0.73 (0.35), residues: 545 helix: -0.61 (0.78), residues: 47 sheet: 0.14 (0.38), residues: 197 loop : -0.87 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 95 TYR 0.015 0.001 TYR A 145 PHE 0.013 0.002 PHE B 62 TRP 0.006 0.001 TRP B 170 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 4398) covalent geometry : angle 0.57770 ( 5990) hydrogen bonds : bond 0.03401 ( 152) hydrogen bonds : angle 5.99582 ( 417) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.161 Fit side-chains REVERT: B 11 ASP cc_start: 0.3387 (p0) cc_final: 0.2737 (m-30) REVERT: B 136 TRP cc_start: -0.0168 (p-90) cc_final: -0.0490 (p-90) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0784 time to fit residues: 3.9648 Evaluate side-chains 32 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 7.9990 chunk 50 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 53 optimal weight: 50.0000 chunk 29 optimal weight: 10.0000 chunk 48 optimal weight: 50.0000 chunk 13 optimal weight: 40.0000 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** B 233 ASN ** 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 = 0.5257 r_free = 0.5257 target = 0.298754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.5243 r_free = 0.5243 target = 0.297239 restraints weight = 8790.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.5235 r_free = 0.5235 target = 0.296775 restraints weight = 7502.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.296979 restraints weight = 5986.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.296978 restraints weight = 5278.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.296978 restraints weight = 5277.541| |-----------------------------------------------------------------------------| r_work (final): 0.5237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1561 moved from start: 0.7594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4398 Z= 0.194 Angle : 0.734 11.736 5990 Z= 0.390 Chirality : 0.050 0.212 666 Planarity : 0.006 0.058 772 Dihedral : 5.508 25.993 587 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -1.03 (0.35), residues: 545 helix: -0.48 (0.86), residues: 40 sheet: -0.17 (0.39), residues: 184 loop : -1.01 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 95 TYR 0.027 0.002 TYR A 93 PHE 0.027 0.002 PHE A 24 TRP 0.019 0.002 TRP A 86 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 4398) covalent geometry : angle 0.73373 ( 5990) hydrogen bonds : bond 0.04210 ( 152) hydrogen bonds : angle 7.00603 ( 417) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.127 Fit side-chains REVERT: B 20 LEU cc_start: -0.0225 (mt) cc_final: -0.0516 (tt) REVERT: B 59 THR cc_start: 0.4027 (t) cc_final: 0.3770 (t) REVERT: B 89 MET cc_start: -0.2860 (tmm) cc_final: -0.4226 (tmm) REVERT: B 136 TRP cc_start: 0.0060 (p-90) cc_final: -0.0522 (p-90) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0550 time to fit residues: 2.7578 Evaluate side-chains 33 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 40.0000 chunk 28 optimal weight: 40.0000 chunk 40 optimal weight: 0.1980 chunk 33 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 18 optimal weight: 0.0470 chunk 35 optimal weight: 50.0000 chunk 30 optimal weight: 50.0000 overall best weight: 2.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5276 r_free = 0.5276 target = 0.301723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.5251 r_free = 0.5251 target = 0.299455 restraints weight = 8773.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5253 r_free = 0.5253 target = 0.299682 restraints weight = 6537.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.300200 restraints weight = 5514.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.300427 restraints weight = 4284.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.300446 restraints weight = 3579.460| |-----------------------------------------------------------------------------| r_work (final): 0.5261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1359 moved from start: 0.7548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4398 Z= 0.112 Angle : 0.570 6.414 5990 Z= 0.301 Chirality : 0.046 0.162 666 Planarity : 0.005 0.053 772 Dihedral : 4.785 18.973 587 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -0.79 (0.35), residues: 545 helix: -0.58 (0.84), residues: 40 sheet: 0.05 (0.39), residues: 192 loop : -0.86 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 61 TYR 0.014 0.001 TYR A 145 PHE 0.012 0.001 PHE A 180 TRP 0.007 0.001 TRP A 86 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 4398) covalent geometry : angle 0.56994 ( 5990) hydrogen bonds : bond 0.03241 ( 152) hydrogen bonds : angle 6.14747 ( 417) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.108 Fit side-chains REVERT: B 59 THR cc_start: 0.4065 (t) cc_final: 0.3855 (t) REVERT: B 136 TRP cc_start: -0.0208 (p-90) cc_final: -0.0575 (p-90) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0710 time to fit residues: 3.3176 Evaluate side-chains 31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 22 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 50.0000 chunk 7 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 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 = 0.5254 r_free = 0.5254 target = 0.299091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.297366 restraints weight = 8757.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.297366 restraints weight = 8369.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.297366 restraints weight = 8369.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.297366 restraints weight = 8368.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5237 r_free = 0.5237 target = 0.297366 restraints weight = 8368.977| |-----------------------------------------------------------------------------| r_work (final): 0.5238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1565 moved from start: 0.8079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4398 Z= 0.186 Angle : 0.713 11.283 5990 Z= 0.377 Chirality : 0.049 0.190 666 Planarity : 0.006 0.059 772 Dihedral : 5.324 23.262 587 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -1.07 (0.35), residues: 545 helix: -0.81 (0.86), residues: 40 sheet: -0.04 (0.40), residues: 189 loop : -1.12 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 95 TYR 0.024 0.002 TYR A 93 PHE 0.020 0.002 PHE A 91 TRP 0.023 0.002 TRP A 86 HIS 0.005 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 4398) covalent geometry : angle 0.71348 ( 5990) hydrogen bonds : bond 0.04027 ( 152) hydrogen bonds : angle 6.95653 ( 417) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.185 Fit side-chains REVERT: B 59 THR cc_start: 0.4256 (t) cc_final: 0.4036 (t) REVERT: B 89 MET cc_start: -0.2648 (tmm) cc_final: -0.4100 (tmm) REVERT: B 136 TRP cc_start: 0.0035 (p-90) cc_final: -0.0489 (p-90) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0655 time to fit residues: 3.2019 Evaluate side-chains 31 residues out of total 474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 50.0000 chunk 50 optimal weight: 50.0000 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 5 optimal weight: 0.0470 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 53 optimal weight: 7.9990 overall best weight: 2.9684 ------------------------------------------------------------------------------- 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 = 0.5262 r_free = 0.5262 target = 0.300028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5238 r_free = 0.5238 target = 0.298003 restraints weight = 8739.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5242 r_free = 0.5242 target = 0.298389 restraints weight = 6700.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.298590 restraints weight = 5194.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.298590 restraints weight = 4487.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5244 r_free = 0.5244 target = 0.298590 restraints weight = 4487.846| |-----------------------------------------------------------------------------| r_work (final): 0.5244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1434 moved from start: 0.8093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4398 Z= 0.112 Angle : 0.583 6.186 5990 Z= 0.305 Chirality : 0.046 0.162 666 Planarity : 0.005 0.052 772 Dihedral : 4.786 17.957 587 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.19 % 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: -1.00 (0.35), residues: 545 helix: -0.80 (0.84), residues: 42 sheet: 0.06 (0.40), residues: 187 loop : -1.09 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 95 TYR 0.015 0.001 TYR B 325 PHE 0.018 0.002 PHE B 25 TRP 0.008 0.001 TRP A 86 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 4398) covalent geometry : angle 0.58313 ( 5990) hydrogen bonds : bond 0.03194 ( 152) hydrogen bonds : angle 6.25602 ( 417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 787.58 seconds wall clock time: 14 minutes 20.99 seconds (860.99 seconds total)