Starting phenix.real_space_refine on Tue Mar 3 13:50:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7saz_24959/03_2026/7saz_24959.cif Found real_map, /net/cci-nas-00/data/ceres_data/7saz_24959/03_2026/7saz_24959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7saz_24959/03_2026/7saz_24959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7saz_24959/03_2026/7saz_24959.map" model { file = "/net/cci-nas-00/data/ceres_data/7saz_24959/03_2026/7saz_24959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7saz_24959/03_2026/7saz_24959.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 25 5.16 5 C 3743 2.51 5 N 896 2.21 5 O 1044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5708 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1740 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain: "B" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1723 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain: "C" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 472 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "D" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 456 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "F" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Time building chain proxies: 1.64, per 1000 atoms: 0.29 Number of scatterers: 5708 At special positions: 0 Unit cell: (68.224, 75.712, 114.816, 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 25 16.00 O 1044 8.00 N 896 7.00 C 3743 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: 0.46 Conformation dependent library (CDL) restraints added in 402.3 milliseconds 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1294 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 77.6% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 6 through 22 Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 28 through 67 removed outlier: 3.706A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 101 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.547A pdb=" N VAL A 112 " --> pdb=" O ASP A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 130 through 150 Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 193 through 221 removed outlier: 3.712A pdb=" N LYS A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 29 removed outlier: 3.853A pdb=" N MET B 11 " --> pdb=" O PRO B 7 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 67 removed outlier: 3.673A pdb=" N GLY B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 101 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 132 through 152 removed outlier: 3.536A pdb=" N VAL B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.727A pdb=" N GLU B 190 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 218 Processing helix chain 'C' and resid 8 through 33 removed outlier: 3.719A pdb=" N PHE C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 65 removed outlier: 3.551A pdb=" N ALA C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 33 Processing helix chain 'D' and resid 43 through 63 removed outlier: 4.080A pdb=" N PHE D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 48 " --> pdb=" O GLY D 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 33 Processing helix chain 'E' and resid 43 through 65 removed outlier: 4.010A pdb=" N PHE E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR E 55 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 65 " --> pdb=" O PHE E 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 33 removed outlier: 4.684A pdb=" N TYR F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 63 removed outlier: 3.959A pdb=" N PHE F 47 " --> pdb=" O LEU F 43 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU F 48 " --> pdb=" O GLY F 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 33 Processing helix chain 'G' and resid 43 through 64 removed outlier: 4.079A pdb=" N PHE G 47 " --> pdb=" O LEU G 43 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA4, first strand: chain 'B' and resid 174 through 175 434 hydrogen bonds defined for protein. 1281 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: 0.86 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1786 1.34 - 1.46: 897 1.46 - 1.57: 3090 1.57 - 1.69: 0 1.69 - 1.80: 50 Bond restraints: 5823 Sorted by residual: bond pdb=" CG LEU B 42 " pdb=" CD2 LEU B 42 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.75e+00 bond pdb=" CG1 ILE D 59 " pdb=" CD1 ILE D 59 " ideal model delta sigma weight residual 1.513 1.452 0.061 3.90e-02 6.57e+02 2.43e+00 bond pdb=" CG MET B 11 " pdb=" SD MET B 11 " ideal model delta sigma weight residual 1.803 1.769 0.034 2.50e-02 1.60e+03 1.84e+00 bond pdb=" CA GLY F 40 " pdb=" C GLY F 40 " ideal model delta sigma weight residual 1.514 1.531 -0.016 1.41e-02 5.03e+03 1.37e+00 bond pdb=" CG1 ILE F 59 " pdb=" CD1 ILE F 59 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.35e+00 ... (remaining 5818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 7673 1.98 - 3.96: 126 3.96 - 5.94: 14 5.94 - 7.92: 2 7.92 - 9.90: 1 Bond angle restraints: 7816 Sorted by residual: angle pdb=" N GLU B 47 " pdb=" CA GLU B 47 " pdb=" CB GLU B 47 " ideal model delta sigma weight residual 110.12 114.89 -4.77 1.47e+00 4.63e-01 1.05e+01 angle pdb=" CA MET B 11 " pdb=" CB MET B 11 " pdb=" CG MET B 11 " ideal model delta sigma weight residual 114.10 107.86 6.24 2.00e+00 2.50e-01 9.74e+00 angle pdb=" C MET A 113 " pdb=" N ASP A 114 " pdb=" CA ASP A 114 " ideal model delta sigma weight residual 121.54 127.11 -5.57 1.91e+00 2.74e-01 8.50e+00 angle pdb=" C THR A 157 " pdb=" N TYR A 158 " pdb=" CA TYR A 158 " ideal model delta sigma weight residual 121.54 127.01 -5.47 1.91e+00 2.74e-01 8.20e+00 angle pdb=" C ILE A 12 " pdb=" N ASN A 13 " pdb=" CA ASN A 13 " ideal model delta sigma weight residual 121.14 116.17 4.97 1.75e+00 3.27e-01 8.06e+00 ... (remaining 7811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 2962 15.25 - 30.50: 323 30.50 - 45.74: 90 45.74 - 60.99: 10 60.99 - 76.24: 6 Dihedral angle restraints: 3391 sinusoidal: 1355 harmonic: 2036 Sorted by residual: dihedral pdb=" CA MET A 113 " pdb=" C MET A 113 " pdb=" N ASP A 114 " pdb=" CA ASP A 114 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA TYR A 158 " pdb=" C TYR A 158 " pdb=" N GLY A 159 " pdb=" CA GLY A 159 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PRO B 131 " pdb=" C PRO B 131 " pdb=" N GLU B 132 " pdb=" CA GLU B 132 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 3388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 665 0.050 - 0.101: 161 0.101 - 0.151: 12 0.151 - 0.202: 1 0.202 - 0.252: 1 Chirality restraints: 840 Sorted by residual: chirality pdb=" CG LEU B 42 " pdb=" CB LEU B 42 " pdb=" CD1 LEU B 42 " pdb=" CD2 LEU B 42 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ASP A 114 " pdb=" N ASP A 114 " pdb=" C ASP A 114 " pdb=" CB ASP A 114 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CA PRO A 131 " pdb=" N PRO A 131 " pdb=" C PRO A 131 " pdb=" CB PRO A 131 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.46e-01 ... (remaining 837 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 130 " -0.052 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO B 131 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 131 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 131 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 130 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 131 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 66 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO C 67 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 67 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 67 " 0.017 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 348 2.73 - 3.27: 6021 3.27 - 3.82: 9696 3.82 - 4.36: 11341 4.36 - 4.90: 19652 Nonbonded interactions: 47058 Sorted by model distance: nonbonded pdb=" OH TYR A 187 " pdb=" OE1 GLU B 30 " model vdw 2.188 3.040 nonbonded pdb=" NH2 ARG B 8 " pdb=" OE2 GLU C 56 " model vdw 2.237 3.120 nonbonded pdb=" ND2 ASN B 186 " pdb=" OE1 GLU B 190 " model vdw 2.285 3.120 nonbonded pdb=" O ILE F 59 " pdb=" OG SER F 63 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLU B 98 " pdb=" NZ LYS B 122 " model vdw 2.291 3.120 ... (remaining 47053 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 'A' and resid 6 through 220) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 10 through 65) selection = (chain 'D' and resid 10 through 65) selection = chain 'E' selection = (chain 'F' and resid 10 through 65) selection = (chain 'G' and resid 10 through 65) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.470 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 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 : 0.004 0.064 5823 Z= 0.188 Angle : 0.628 9.899 7816 Z= 0.354 Chirality : 0.041 0.252 840 Planarity : 0.004 0.077 997 Dihedral : 13.698 76.236 2097 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.67 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.31), residues: 708 helix: 1.14 (0.21), residues: 537 sheet: None (None), residues: 0 loop : -3.14 (0.40), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 182 TYR 0.020 0.002 TYR B 216 PHE 0.013 0.001 PHE A 123 TRP 0.005 0.001 TRP C 34 HIS 0.010 0.002 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 5823) covalent geometry : angle 0.62806 ( 7816) hydrogen bonds : bond 0.12606 ( 434) hydrogen bonds : angle 5.51055 ( 1281) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.164 Fit side-chains REVERT: A 173 ASP cc_start: 0.8789 (m-30) cc_final: 0.8425 (m-30) REVERT: B 100 MET cc_start: 0.8448 (mmp) cc_final: 0.8242 (mmt) REVERT: B 203 MET cc_start: 0.7223 (tpp) cc_final: 0.6960 (tpt) REVERT: B 207 ASP cc_start: 0.7846 (m-30) cc_final: 0.7641 (m-30) REVERT: C 10 LYS cc_start: 0.8166 (pptt) cc_final: 0.7060 (mptt) REVERT: D 14 MET cc_start: 0.8412 (ttm) cc_final: 0.8189 (ttp) REVERT: F 14 MET cc_start: 0.7609 (ttm) cc_final: 0.7184 (ttt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.5785 time to fit residues: 80.7725 Evaluate side-chains 94 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.111094 restraints weight = 6918.230| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.30 r_work: 0.3079 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5823 Z= 0.134 Angle : 0.512 6.061 7816 Z= 0.283 Chirality : 0.039 0.199 840 Planarity : 0.003 0.048 997 Dihedral : 4.476 25.757 752 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.11 % Favored : 96.75 % Rotamer: Outliers : 2.72 % Allowed : 11.88 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.31), residues: 708 helix: 1.83 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -3.08 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.015 0.001 TYR E 16 PHE 0.011 0.001 PHE A 75 TRP 0.003 0.001 TRP D 34 HIS 0.005 0.001 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 5823) covalent geometry : angle 0.51197 ( 7816) hydrogen bonds : bond 0.03994 ( 434) hydrogen bonds : angle 4.21723 ( 1281) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.176 Fit side-chains REVERT: A 13 ASN cc_start: 0.7630 (p0) cc_final: 0.6668 (m-40) REVERT: B 73 GLU cc_start: 0.7938 (pp20) cc_final: 0.7619 (tm-30) REVERT: B 100 MET cc_start: 0.8619 (mmp) cc_final: 0.8330 (mmt) REVERT: B 102 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8137 (pt0) REVERT: B 203 MET cc_start: 0.7735 (tpp) cc_final: 0.7252 (tpt) REVERT: B 207 ASP cc_start: 0.8402 (m-30) cc_final: 0.7986 (m-30) REVERT: D 14 MET cc_start: 0.8588 (ttm) cc_final: 0.8376 (ttp) REVERT: E 13 GLN cc_start: 0.8002 (tp40) cc_final: 0.7798 (tp40) REVERT: F 14 MET cc_start: 0.7486 (ttm) cc_final: 0.7225 (ttt) outliers start: 16 outliers final: 6 residues processed: 105 average time/residue: 0.5927 time to fit residues: 64.6861 Evaluate side-chains 89 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 45 optimal weight: 0.0570 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN B 172 ASN B 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.150077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112814 restraints weight = 6759.626| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.29 r_work: 0.3108 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5823 Z= 0.111 Angle : 0.465 5.792 7816 Z= 0.258 Chirality : 0.037 0.175 840 Planarity : 0.003 0.045 997 Dihedral : 4.179 25.412 752 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.21 % Allowed : 15.62 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.31), residues: 708 helix: 2.19 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -3.07 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 8 TYR 0.014 0.001 TYR E 16 PHE 0.009 0.001 PHE A 75 TRP 0.003 0.000 TRP C 34 HIS 0.003 0.001 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 5823) covalent geometry : angle 0.46544 ( 7816) hydrogen bonds : bond 0.03560 ( 434) hydrogen bonds : angle 3.91918 ( 1281) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7400 (p0) cc_final: 0.6720 (m-40) REVERT: A 58 GLN cc_start: 0.7537 (mt0) cc_final: 0.7331 (mt0) REVERT: A 61 GLU cc_start: 0.7677 (tp30) cc_final: 0.6965 (tm-30) REVERT: A 173 ASP cc_start: 0.9121 (m-30) cc_final: 0.8866 (m-30) REVERT: A 219 MET cc_start: 0.7665 (OUTLIER) cc_final: 0.7038 (mtp) REVERT: B 73 GLU cc_start: 0.7933 (pp20) cc_final: 0.7615 (tm-30) REVERT: D 14 MET cc_start: 0.8553 (ttm) cc_final: 0.8329 (ttp) REVERT: E 13 GLN cc_start: 0.8019 (tp40) cc_final: 0.7802 (tp40) outliers start: 13 outliers final: 3 residues processed: 103 average time/residue: 0.5879 time to fit residues: 63.1661 Evaluate side-chains 89 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 63 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 102 GLN B 172 ASN B 213 GLN D 13 GLN G 33 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.109280 restraints weight = 6848.463| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.19 r_work: 0.3044 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5823 Z= 0.209 Angle : 0.550 7.197 7816 Z= 0.294 Chirality : 0.041 0.304 840 Planarity : 0.003 0.045 997 Dihedral : 4.336 22.677 752 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.06 % Allowed : 17.66 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.31), residues: 708 helix: 2.04 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -3.06 (0.41), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 8 TYR 0.017 0.002 TYR E 16 PHE 0.012 0.001 PHE D 60 TRP 0.005 0.001 TRP A 184 HIS 0.004 0.002 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 5823) covalent geometry : angle 0.54977 ( 7816) hydrogen bonds : bond 0.03880 ( 434) hydrogen bonds : angle 4.04176 ( 1281) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 111 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8159 (pt0) REVERT: A 219 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7110 (mtp) REVERT: B 73 GLU cc_start: 0.7943 (pp20) cc_final: 0.7629 (tm-30) REVERT: B 79 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8103 (mtpp) REVERT: B 100 MET cc_start: 0.8453 (mmp) cc_final: 0.8158 (mmt) REVERT: B 102 GLN cc_start: 0.8332 (pt0) cc_final: 0.7987 (pp30) REVERT: E 13 GLN cc_start: 0.8002 (tp40) cc_final: 0.7757 (tp40) outliers start: 18 outliers final: 8 residues processed: 96 average time/residue: 0.5902 time to fit residues: 59.1135 Evaluate side-chains 94 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 18 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN A 170 ASN B 172 ASN B 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.149653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.111969 restraints weight = 6945.503| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.29 r_work: 0.3098 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5823 Z= 0.114 Angle : 0.460 6.294 7816 Z= 0.255 Chirality : 0.037 0.190 840 Planarity : 0.003 0.047 997 Dihedral : 4.104 24.743 752 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.72 % Allowed : 19.19 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.31), residues: 708 helix: 2.28 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -3.05 (0.40), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 8 TYR 0.015 0.001 TYR E 16 PHE 0.009 0.001 PHE D 60 TRP 0.002 0.001 TRP C 34 HIS 0.003 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 5823) covalent geometry : angle 0.46034 ( 7816) hydrogen bonds : bond 0.03536 ( 434) hydrogen bonds : angle 3.88988 ( 1281) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 13 ASN cc_start: 0.7454 (p0) cc_final: 0.6687 (m-40) REVERT: A 58 GLN cc_start: 0.7555 (mt0) cc_final: 0.7340 (mt0) REVERT: A 61 GLU cc_start: 0.7705 (tp30) cc_final: 0.7095 (tm-30) REVERT: A 111 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: A 219 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7338 (mtp) REVERT: B 79 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8120 (mtpp) REVERT: B 102 GLN cc_start: 0.8364 (pt0) cc_final: 0.8005 (pp30) REVERT: E 13 GLN cc_start: 0.8013 (tp40) cc_final: 0.7747 (tp40) outliers start: 16 outliers final: 4 residues processed: 101 average time/residue: 0.5713 time to fit residues: 60.2281 Evaluate side-chains 96 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 207 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 172 ASN B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.149093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.111812 restraints weight = 6912.368| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.23 r_work: 0.3081 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5823 Z= 0.143 Angle : 0.519 14.468 7816 Z= 0.276 Chirality : 0.040 0.404 840 Planarity : 0.003 0.048 997 Dihedral : 4.104 23.637 752 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.89 % Allowed : 19.86 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.31), residues: 708 helix: 2.27 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -3.01 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 8 TYR 0.016 0.001 TYR E 16 PHE 0.010 0.001 PHE D 60 TRP 0.003 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 5823) covalent geometry : angle 0.51911 ( 7816) hydrogen bonds : bond 0.03609 ( 434) hydrogen bonds : angle 3.93346 ( 1281) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.173 Fit side-chains revert: symmetry clash REVERT: A 58 GLN cc_start: 0.7545 (mt0) cc_final: 0.7317 (mt0) REVERT: A 61 GLU cc_start: 0.7690 (tp30) cc_final: 0.7111 (tm-30) REVERT: A 111 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: A 219 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7286 (mtp) REVERT: B 73 GLU cc_start: 0.7903 (pp20) cc_final: 0.7535 (tm-30) REVERT: B 79 LYS cc_start: 0.8360 (mtpt) cc_final: 0.8078 (mtpp) REVERT: B 102 GLN cc_start: 0.8397 (pt0) cc_final: 0.8040 (pp30) REVERT: C 48 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8479 (mt) REVERT: E 13 GLN cc_start: 0.8005 (tp40) cc_final: 0.7727 (tp40) outliers start: 17 outliers final: 10 residues processed: 100 average time/residue: 0.5640 time to fit residues: 58.8869 Evaluate side-chains 103 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 7 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 0.0000 chunk 58 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.150591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.112782 restraints weight = 6881.729| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.29 r_work: 0.3104 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5823 Z= 0.114 Angle : 0.493 12.938 7816 Z= 0.264 Chirality : 0.039 0.380 840 Planarity : 0.003 0.051 997 Dihedral : 3.992 24.001 752 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.55 % Allowed : 20.71 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.31), residues: 708 helix: 2.36 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -2.90 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 8 TYR 0.013 0.001 TYR E 16 PHE 0.009 0.001 PHE D 60 TRP 0.002 0.000 TRP G 34 HIS 0.004 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5823) covalent geometry : angle 0.49303 ( 7816) hydrogen bonds : bond 0.03491 ( 434) hydrogen bonds : angle 3.84419 ( 1281) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7678 (tp30) cc_final: 0.7275 (tt0) REVERT: A 111 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: B 73 GLU cc_start: 0.7908 (pp20) cc_final: 0.7561 (tm-30) REVERT: B 79 LYS cc_start: 0.8372 (mtpt) cc_final: 0.8085 (mtpp) REVERT: C 48 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8499 (mt) REVERT: E 13 GLN cc_start: 0.8013 (tp40) cc_final: 0.7722 (tp40) outliers start: 15 outliers final: 7 residues processed: 105 average time/residue: 0.5575 time to fit residues: 61.2420 Evaluate side-chains 101 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 6 optimal weight: 0.0010 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124409 restraints weight = 6730.053| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.16 r_work: 0.3177 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5823 Z= 0.105 Angle : 0.481 12.321 7816 Z= 0.259 Chirality : 0.039 0.394 840 Planarity : 0.003 0.052 997 Dihedral : 3.919 23.663 752 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.55 % Allowed : 21.90 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.32), residues: 708 helix: 2.47 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.76 (0.42), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 8 TYR 0.015 0.001 TYR E 16 PHE 0.009 0.001 PHE D 60 TRP 0.003 0.000 TRP C 34 HIS 0.004 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 5823) covalent geometry : angle 0.48075 ( 7816) hydrogen bonds : bond 0.03419 ( 434) hydrogen bonds : angle 3.79934 ( 1281) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7639 (tp30) cc_final: 0.7266 (tt0) REVERT: A 219 MET cc_start: 0.8025 (mtp) cc_final: 0.7805 (mtp) REVERT: B 54 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7787 (pp) REVERT: B 73 GLU cc_start: 0.7881 (pp20) cc_final: 0.7536 (tm-30) REVERT: B 79 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8111 (mtpp) REVERT: C 48 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8568 (mt) REVERT: E 13 GLN cc_start: 0.8031 (tp40) cc_final: 0.7727 (tp40) outliers start: 15 outliers final: 8 residues processed: 108 average time/residue: 0.5393 time to fit residues: 61.0167 Evaluate side-chains 105 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 62 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 168 ASN B 63 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.150908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.113099 restraints weight = 6893.802| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.28 r_work: 0.3132 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5823 Z= 0.120 Angle : 0.506 12.420 7816 Z= 0.271 Chirality : 0.040 0.422 840 Planarity : 0.003 0.052 997 Dihedral : 3.877 23.416 752 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.38 % Allowed : 22.41 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.32), residues: 708 helix: 2.44 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.69 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 8 TYR 0.016 0.001 TYR E 16 PHE 0.009 0.001 PHE D 60 TRP 0.003 0.001 TRP B 184 HIS 0.004 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5823) covalent geometry : angle 0.50645 ( 7816) hydrogen bonds : bond 0.03460 ( 434) hydrogen bonds : angle 3.80506 ( 1281) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.7009 (mppt) REVERT: A 61 GLU cc_start: 0.7680 (tp30) cc_final: 0.7319 (tt0) REVERT: A 168 ASN cc_start: 0.7929 (m-40) cc_final: 0.7642 (m-40) REVERT: A 219 MET cc_start: 0.8085 (mtp) cc_final: 0.7883 (mtp) REVERT: B 73 GLU cc_start: 0.7896 (pp20) cc_final: 0.7559 (tm-30) REVERT: B 79 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8109 (mtpp) REVERT: B 82 LYS cc_start: 0.8253 (tptt) cc_final: 0.7342 (tttm) REVERT: C 48 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8595 (mt) REVERT: E 13 GLN cc_start: 0.8034 (tp40) cc_final: 0.7726 (tp40) outliers start: 14 outliers final: 7 residues processed: 101 average time/residue: 0.5828 time to fit residues: 61.5038 Evaluate side-chains 102 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.110552 restraints weight = 7005.909| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.29 r_work: 0.3067 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5823 Z= 0.158 Angle : 0.537 12.328 7816 Z= 0.285 Chirality : 0.041 0.446 840 Planarity : 0.003 0.050 997 Dihedral : 3.976 22.942 752 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.21 % Allowed : 23.26 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.31), residues: 708 helix: 2.29 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.64 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 8 TYR 0.019 0.001 TYR E 16 PHE 0.011 0.001 PHE D 60 TRP 0.004 0.001 TRP A 184 HIS 0.003 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 5823) covalent geometry : angle 0.53672 ( 7816) hydrogen bonds : bond 0.03579 ( 434) hydrogen bonds : angle 3.90691 ( 1281) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1416 Ramachandran restraints generated. 708 Oldfield, 0 Emsley, 708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7651 (tp30) cc_final: 0.7269 (tt0) REVERT: A 219 MET cc_start: 0.8021 (mtp) cc_final: 0.7707 (mtp) REVERT: B 73 GLU cc_start: 0.7893 (pp20) cc_final: 0.7549 (tm-30) REVERT: B 79 LYS cc_start: 0.8347 (mtpt) cc_final: 0.8034 (mtpp) REVERT: B 82 LYS cc_start: 0.8125 (tptt) cc_final: 0.7211 (tttm) REVERT: C 48 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8464 (mt) REVERT: E 13 GLN cc_start: 0.8024 (tp40) cc_final: 0.7719 (tp40) outliers start: 13 outliers final: 8 residues processed: 102 average time/residue: 0.5547 time to fit residues: 59.1681 Evaluate side-chains 99 residues out of total 589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 204 MET Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain G residue 59 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 39 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 121 GLN A 168 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.111562 restraints weight = 6756.635| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.26 r_work: 0.3082 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5823 Z= 0.132 Angle : 0.518 12.164 7816 Z= 0.277 Chirality : 0.041 0.444 840 Planarity : 0.003 0.051 997 Dihedral : 3.942 23.356 752 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.38 % Allowed : 22.75 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.31), residues: 708 helix: 2.33 (0.21), residues: 539 sheet: None (None), residues: 0 loop : -2.62 (0.43), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 8 TYR 0.018 0.001 TYR E 16 PHE 0.010 0.001 PHE D 60 TRP 0.002 0.001 TRP A 184 HIS 0.004 0.001 HIS G 33 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 5823) covalent geometry : angle 0.51820 ( 7816) hydrogen bonds : bond 0.03532 ( 434) hydrogen bonds : angle 3.87696 ( 1281) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.05 seconds wall clock time: 37 minutes 56.54 seconds (2276.54 seconds total)