Starting phenix.real_space_refine on Tue Mar 3 19:49:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8crb_16807/03_2026/8crb_16807.cif Found real_map, /net/cci-nas-00/data/ceres_data/8crb_16807/03_2026/8crb_16807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8crb_16807/03_2026/8crb_16807.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8crb_16807/03_2026/8crb_16807.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8crb_16807/03_2026/8crb_16807.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8crb_16807/03_2026/8crb_16807.map" } resolution = 4.6 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= 0.001 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: 5 Type Number sf(0) Gaussians S 13 5.16 5 C 2743 2.51 5 N 738 2.21 5 O 885 1.98 5 H 4286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 8665 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3320 Classifications: {'peptide': 227} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 214} Chain: "B" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3187 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 198} Chain: "C" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2158 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131} Time building chain proxies: 1.74, per 1000 atoms: 0.20 Number of scatterers: 8665 At special positions: 0 Unit cell: (73.1, 81.6, 113.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 O 885 8.00 N 738 7.00 C 2743 6.00 H 4286 1.00 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: 0.71 Conformation dependent library (CDL) restraints added in 172.1 milliseconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1064 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 21.8% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.666A pdb=" N ASP A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 removed outlier: 4.321A pdb=" N SER A 146 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 125 through 130 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 211 through 215 Processing helix chain 'C' and resid 129 through 158 removed outlier: 3.584A pdb=" N ALA C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 189 through 198 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 236 through 264 Proline residue: C 250 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.546A pdb=" N THR A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.546A pdb=" N THR A 121 " --> pdb=" O TYR A 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 116 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 137 removed outlier: 3.518A pdb=" N SER A 134 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR A 190 " --> pdb=" O ASP A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 164 through 168 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.715A pdb=" N ASP B 86 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 39 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 122 removed outlier: 6.162A pdb=" N TYR B 176 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 118 through 122 removed outlier: 6.162A pdb=" N TYR B 176 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 198 hydrogen bonds defined for protein. 501 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: 1.89 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 4275 1.11 - 1.29: 732 1.29 - 1.46: 1380 1.46 - 1.64: 2361 1.64 - 1.81: 15 Bond restraints: 8763 Sorted by residual: bond pdb=" N SER A 49 " pdb=" H SER A 49 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ASN A 74 " pdb=" H ASN A 74 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N GLY B 69 " pdb=" H GLY B 69 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N ASN B 174 " pdb=" H ASN B 174 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" CD1 PHE A 160 " pdb=" HD1 PHE A 160 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 8758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 13930 3.08 - 6.15: 1519 6.15 - 9.23: 352 9.23 - 12.31: 8 12.31 - 15.39: 5 Bond angle restraints: 15814 Sorted by residual: angle pdb=" N PRO B 7 " pdb=" CA PRO B 7 " pdb=" C PRO B 7 " ideal model delta sigma weight residual 110.70 121.25 -10.55 1.22e+00 6.72e-01 7.48e+01 angle pdb=" C LYS B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta sigma weight residual 120.50 128.86 -8.36 1.34e+00 5.57e-01 3.89e+01 angle pdb=" CA PHE A 114 " pdb=" CB PHE A 114 " pdb=" CG PHE A 114 " ideal model delta sigma weight residual 113.80 119.77 -5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" CA PHE A 27 " pdb=" CB PHE A 27 " pdb=" CG PHE A 27 " ideal model delta sigma weight residual 113.80 119.39 -5.59 1.00e+00 1.00e+00 3.13e+01 angle pdb=" C GLY B 102 " pdb=" N PRO B 103 " pdb=" CA PRO B 103 " ideal model delta sigma weight residual 119.87 125.68 -5.81 1.04e+00 9.25e-01 3.12e+01 ... (remaining 15809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3783 17.77 - 35.55: 282 35.55 - 53.32: 102 53.32 - 71.10: 30 71.10 - 88.87: 8 Dihedral angle restraints: 4205 sinusoidal: 2281 harmonic: 1924 Sorted by residual: dihedral pdb=" CA PRO B 7 " pdb=" C PRO B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual -180.00 -150.74 -29.26 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA SER B 2 " pdb=" C SER B 2 " pdb=" N VAL B 3 " pdb=" CA VAL B 3 " ideal model delta harmonic sigma weight residual -180.00 -150.96 -29.04 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN C 234 " pdb=" C ASN C 234 " pdb=" N ASN C 235 " pdb=" CA ASN C 235 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 4202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 384 0.083 - 0.165: 226 0.165 - 0.248: 59 0.248 - 0.330: 11 0.330 - 0.412: 2 Chirality restraints: 682 Sorted by residual: chirality pdb=" CA ASN B 174 " pdb=" N ASN B 174 " pdb=" C ASN B 174 " pdb=" CB ASN B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CA TYR A 108 " pdb=" N TYR A 108 " pdb=" C TYR A 108 " pdb=" CB TYR A 108 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ASN A 218 " pdb=" N ASN A 218 " pdb=" C ASN A 218 " pdb=" CB ASN A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 679 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 37 " 0.307 2.00e-02 2.50e+03 1.40e-01 5.87e+02 pdb=" CG TYR B 37 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 37 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 TYR B 37 " -0.094 2.00e-02 2.50e+03 pdb=" CE1 TYR B 37 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 TYR B 37 " -0.074 2.00e-02 2.50e+03 pdb=" CZ TYR B 37 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 37 " 0.306 2.00e-02 2.50e+03 pdb=" HD1 TYR B 37 " -0.047 2.00e-02 2.50e+03 pdb=" HD2 TYR B 37 " -0.073 2.00e-02 2.50e+03 pdb=" HE1 TYR B 37 " -0.077 2.00e-02 2.50e+03 pdb=" HE2 TYR B 37 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 117 " 0.179 2.00e-02 2.50e+03 1.18e-01 5.53e+02 pdb=" CG TRP A 117 " 0.094 2.00e-02 2.50e+03 pdb=" CD1 TRP A 117 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TRP A 117 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP A 117 " -0.092 2.00e-02 2.50e+03 pdb=" CE2 TRP A 117 " -0.078 2.00e-02 2.50e+03 pdb=" CE3 TRP A 117 " -0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 117 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 117 " -0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP A 117 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 TRP A 117 " 0.101 2.00e-02 2.50e+03 pdb=" HE1 TRP A 117 " -0.153 2.00e-02 2.50e+03 pdb=" HE3 TRP A 117 " -0.188 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 117 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 117 " 0.005 2.00e-02 2.50e+03 pdb=" HH2 TRP A 117 " 0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 36 " -0.175 2.00e-02 2.50e+03 7.09e-02 2.01e+02 pdb=" CG TRP A 36 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 36 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 36 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP A 36 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TRP A 36 " 0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 36 " 0.069 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 36 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 36 " 0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 36 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP A 36 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 TRP A 36 " 0.106 2.00e-02 2.50e+03 pdb=" HE3 TRP A 36 " 0.079 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 36 " -0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 36 " 0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP A 36 " -0.090 2.00e-02 2.50e+03 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 639 2.19 - 2.79: 15350 2.79 - 3.39: 23731 3.39 - 4.00: 29777 4.00 - 4.60: 43550 Nonbonded interactions: 113047 Sorted by model distance: nonbonded pdb=" OD1 ASP A 73 " pdb=" HG SER A 75 " model vdw 1.584 2.450 nonbonded pdb=" H ASP A 73 " pdb=" HG LEU A 79 " model vdw 1.586 2.270 nonbonded pdb=" OD2 ASP C 199 " pdb=" HG SER C 214 " model vdw 1.601 2.450 nonbonded pdb=" OD1 ASP C 173 " pdb=" HG1 THR C 175 " model vdw 1.622 2.450 nonbonded pdb=" HG SER A 54 " pdb=" OD2 ASP C 246 " model vdw 1.625 2.450 ... (remaining 113042 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: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.640 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 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 : 0.013 0.043 4477 Z= 0.806 Angle : 1.985 10.554 6092 Z= 1.299 Chirality : 0.105 0.412 682 Planarity : 0.016 0.162 789 Dihedral : 14.753 88.871 1621 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 1.91 % Allowed : 10.07 % Favored : 88.02 % Rotamer: Outliers : 1.23 % Allowed : 5.33 % Favored : 93.44 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 11.11 % 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: -2.65 (0.30), residues: 576 helix: -1.56 (0.40), residues: 109 sheet: -1.03 (0.52), residues: 98 loop : -2.13 (0.28), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 62 TYR 0.279 0.029 TYR B 37 PHE 0.079 0.017 PHE A 114 TRP 0.144 0.030 TRP A 117 HIS 0.013 0.007 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.01317 ( 4477) covalent geometry : angle 1.98483 ( 6092) hydrogen bonds : bond 0.14355 ( 179) hydrogen bonds : angle 9.99043 ( 501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 PHE cc_start: 0.0318 (p90) cc_final: -0.0729 (p90) REVERT: A 67 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7382 (mpp80) REVERT: A 117 TRP cc_start: 0.7366 (m100) cc_final: 0.7067 (m100) REVERT: A 225 VAL cc_start: 0.7751 (t) cc_final: 0.7330 (t) REVERT: B 67 LYS cc_start: 0.7177 (pttt) cc_final: 0.6546 (ptpp) REVERT: B 159 VAL cc_start: 0.6504 (m) cc_final: 0.6280 (t) REVERT: B 180 SER cc_start: 0.8146 (p) cc_final: 0.7788 (t) REVERT: C 139 THR cc_start: 0.8712 (m) cc_final: 0.8502 (p) REVERT: C 143 LYS cc_start: 0.8901 (tttt) cc_final: 0.8693 (tttt) REVERT: C 153 ASN cc_start: 0.8141 (m-40) cc_final: 0.7855 (m-40) outliers start: 6 outliers final: 3 residues processed: 150 average time/residue: 0.2393 time to fit residues: 42.0092 Evaluate side-chains 105 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 174 ASN C 217 GLN C 234 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.127097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.105440 restraints weight = 48215.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.110110 restraints weight = 28748.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.113570 restraints weight = 19090.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.116013 restraints weight = 13518.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.117705 restraints weight = 10145.057| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6423 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4477 Z= 0.250 Angle : 0.884 7.470 6092 Z= 0.491 Chirality : 0.047 0.179 682 Planarity : 0.007 0.078 789 Dihedral : 8.676 37.889 630 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.46 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -2.72 (0.31), residues: 576 helix: -0.35 (0.45), residues: 107 sheet: -1.43 (0.39), residues: 150 loop : -2.59 (0.30), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 51 TYR 0.034 0.003 TYR B 37 PHE 0.021 0.003 PHE A 29 TRP 0.023 0.003 TRP A 47 HIS 0.004 0.002 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 4477) covalent geometry : angle 0.88384 ( 6092) hydrogen bonds : bond 0.05626 ( 179) hydrogen bonds : angle 7.72385 ( 501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.7688 (m100) cc_final: 0.7405 (m100) REVERT: A 67 ARG cc_start: 0.8161 (mtt180) cc_final: 0.7890 (mpt180) REVERT: A 82 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7687 (mt-10) REVERT: A 122 ARG cc_start: 0.6933 (ttm170) cc_final: 0.6441 (ttp-170) REVERT: A 124 THR cc_start: 0.7855 (m) cc_final: 0.6903 (m) REVERT: B 67 LYS cc_start: 0.7472 (pttt) cc_final: 0.6619 (ptpp) REVERT: B 74 LEU cc_start: 0.8883 (tt) cc_final: 0.8470 (tt) REVERT: B 84 GLU cc_start: 0.8238 (tp30) cc_final: 0.7646 (tm-30) REVERT: C 139 THR cc_start: 0.9189 (m) cc_final: 0.8978 (p) REVERT: C 141 GLU cc_start: 0.9655 (mt-10) cc_final: 0.9353 (mt-10) REVERT: C 199 ASP cc_start: 0.8015 (m-30) cc_final: 0.7747 (p0) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1864 time to fit residues: 27.1828 Evaluate side-chains 91 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN ** B 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.125841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.103959 restraints weight = 47411.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.108660 restraints weight = 28148.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.112006 restraints weight = 18686.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.114439 restraints weight = 13291.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.116175 restraints weight = 10002.096| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4477 Z= 0.237 Angle : 0.813 7.438 6092 Z= 0.453 Chirality : 0.046 0.179 682 Planarity : 0.007 0.077 789 Dihedral : 8.061 33.021 630 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.72 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.11 (0.31), residues: 576 helix: -0.23 (0.45), residues: 107 sheet: -1.88 (0.37), residues: 161 loop : -2.92 (0.30), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 110 TYR 0.021 0.002 TYR B 37 PHE 0.018 0.002 PHE A 114 TRP 0.020 0.003 TRP A 47 HIS 0.006 0.003 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 4477) covalent geometry : angle 0.81345 ( 6092) hydrogen bonds : bond 0.04954 ( 179) hydrogen bonds : angle 7.28257 ( 501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.7554 (m100) cc_final: 0.7180 (m100) REVERT: A 43 LYS cc_start: 0.6200 (mmtt) cc_final: 0.5020 (mttt) REVERT: A 68 PHE cc_start: 0.6407 (m-80) cc_final: 0.6192 (m-80) REVERT: A 115 GLU cc_start: 0.6541 (tm-30) cc_final: 0.5974 (tm-30) REVERT: A 122 ARG cc_start: 0.6829 (ttm170) cc_final: 0.6253 (ttp-170) REVERT: A 124 THR cc_start: 0.8044 (m) cc_final: 0.6792 (m) REVERT: B 67 LYS cc_start: 0.7457 (pttt) cc_final: 0.6587 (ptpp) REVERT: B 84 GLU cc_start: 0.8112 (tp30) cc_final: 0.7723 (tm-30) REVERT: B 137 VAL cc_start: 0.7362 (t) cc_final: 0.7151 (t) REVERT: C 153 ASN cc_start: 0.8536 (m-40) cc_final: 0.8243 (p0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.2106 time to fit residues: 27.6854 Evaluate side-chains 92 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 51 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 0.0570 chunk 44 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 overall best weight: 2.4102 ------------------------------------------------------------------------------- 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 = 0.4167 r_free = 0.4167 target = 0.128855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.106297 restraints weight = 47558.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.111168 restraints weight = 28190.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.114673 restraints weight = 18779.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.117215 restraints weight = 13403.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.118872 restraints weight = 10058.004| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4477 Z= 0.160 Angle : 0.712 6.934 6092 Z= 0.390 Chirality : 0.045 0.163 682 Planarity : 0.007 0.075 789 Dihedral : 7.321 32.924 630 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.81 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.86 (0.32), residues: 576 helix: 0.04 (0.46), residues: 107 sheet: -1.77 (0.40), residues: 148 loop : -2.75 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 19 TYR 0.020 0.002 TYR B 37 PHE 0.015 0.002 PHE B 101 TRP 0.013 0.002 TRP A 47 HIS 0.004 0.002 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4477) covalent geometry : angle 0.71230 ( 6092) hydrogen bonds : bond 0.04372 ( 179) hydrogen bonds : angle 6.64929 ( 501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.7540 (m100) cc_final: 0.7314 (m100) REVERT: A 43 LYS cc_start: 0.6142 (mmtt) cc_final: 0.5061 (mttt) REVERT: A 67 ARG cc_start: 0.8027 (mpt180) cc_final: 0.7619 (mpp-170) REVERT: A 115 GLU cc_start: 0.6145 (tm-30) cc_final: 0.5794 (tm-30) REVERT: A 122 ARG cc_start: 0.6688 (ttm170) cc_final: 0.6191 (ttp-170) REVERT: A 124 THR cc_start: 0.8001 (m) cc_final: 0.6670 (m) REVERT: A 154 CYS cc_start: 0.8078 (p) cc_final: 0.7868 (m) REVERT: B 67 LYS cc_start: 0.7436 (pttt) cc_final: 0.6502 (ptpp) REVERT: B 84 GLU cc_start: 0.8162 (tp30) cc_final: 0.7874 (tm-30) REVERT: B 137 VAL cc_start: 0.7300 (t) cc_final: 0.7084 (t) REVERT: C 141 GLU cc_start: 0.9658 (mt-10) cc_final: 0.8978 (mt-10) REVERT: C 217 GLN cc_start: 0.7356 (mt0) cc_final: 0.6531 (mt0) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2022 time to fit residues: 27.0293 Evaluate side-chains 96 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 39 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.127195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.105310 restraints weight = 48347.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.109908 restraints weight = 28675.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.113205 restraints weight = 19226.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.115511 restraints weight = 13869.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.117199 restraints weight = 10631.226| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4477 Z= 0.227 Angle : 0.754 6.098 6092 Z= 0.416 Chirality : 0.045 0.164 682 Planarity : 0.008 0.073 789 Dihedral : 7.417 33.340 630 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.90 (0.32), residues: 576 helix: 0.26 (0.46), residues: 101 sheet: -1.78 (0.41), residues: 140 loop : -2.83 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 19 TYR 0.020 0.002 TYR B 37 PHE 0.022 0.003 PHE B 101 TRP 0.020 0.002 TRP A 47 HIS 0.007 0.003 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 4477) covalent geometry : angle 0.75422 ( 6092) hydrogen bonds : bond 0.04529 ( 179) hydrogen bonds : angle 6.77313 ( 501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 TRP cc_start: 0.7595 (m100) cc_final: 0.7321 (m100) REVERT: A 67 ARG cc_start: 0.7867 (mpt180) cc_final: 0.7614 (mpp-170) REVERT: A 81 LEU cc_start: 0.8517 (pt) cc_final: 0.8254 (pt) REVERT: A 122 ARG cc_start: 0.6758 (ttm170) cc_final: 0.6356 (ttp-170) REVERT: A 124 THR cc_start: 0.8026 (m) cc_final: 0.6920 (m) REVERT: A 154 CYS cc_start: 0.7845 (p) cc_final: 0.7631 (m) REVERT: B 67 LYS cc_start: 0.7286 (pttt) cc_final: 0.6309 (ptpp) REVERT: B 137 VAL cc_start: 0.7313 (t) cc_final: 0.7084 (t) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.2100 time to fit residues: 26.1434 Evaluate side-chains 89 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 0.0670 chunk 55 optimal weight: 0.9980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 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 = 0.4201 r_free = 0.4201 target = 0.131662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.108902 restraints weight = 45763.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.113670 restraints weight = 27753.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.117134 restraints weight = 18748.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.119370 restraints weight = 13607.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.121262 restraints weight = 10574.357| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4477 Z= 0.126 Angle : 0.633 5.535 6092 Z= 0.341 Chirality : 0.043 0.155 682 Planarity : 0.007 0.076 789 Dihedral : 6.467 26.598 630 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.94 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.42 (0.34), residues: 576 helix: 0.63 (0.48), residues: 101 sheet: -1.60 (0.42), residues: 145 loop : -2.42 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.017 0.001 TYR A 60 PHE 0.013 0.001 PHE A 29 TRP 0.009 0.001 TRP A 36 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4477) covalent geometry : angle 0.63320 ( 6092) hydrogen bonds : bond 0.03850 ( 179) hydrogen bonds : angle 6.10842 ( 501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8302 (pt) cc_final: 0.8067 (pt) REVERT: A 122 ARG cc_start: 0.6481 (ttm170) cc_final: 0.6238 (ttp-170) REVERT: A 124 THR cc_start: 0.8102 (m) cc_final: 0.6826 (m) REVERT: B 67 LYS cc_start: 0.7225 (pttt) cc_final: 0.6185 (ptpp) REVERT: B 84 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7563 (tm-30) REVERT: B 136 LEU cc_start: 0.8364 (mt) cc_final: 0.8053 (mt) REVERT: B 137 VAL cc_start: 0.7377 (t) cc_final: 0.7049 (t) REVERT: C 141 GLU cc_start: 0.9631 (mt-10) cc_final: 0.9091 (mt-10) REVERT: C 217 GLN cc_start: 0.7405 (mt0) cc_final: 0.6621 (mt0) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.1831 time to fit residues: 24.3470 Evaluate side-chains 91 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 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 = 0.4131 r_free = 0.4131 target = 0.126732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.104468 restraints weight = 47511.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.109108 restraints weight = 28595.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.112409 restraints weight = 19316.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.114819 restraints weight = 13962.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.116575 restraints weight = 10601.426| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 4477 Z= 0.244 Angle : 0.728 5.319 6092 Z= 0.401 Chirality : 0.044 0.160 682 Planarity : 0.007 0.075 789 Dihedral : 6.946 25.252 630 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.76 % Favored : 85.24 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.78 (0.33), residues: 576 helix: 0.48 (0.48), residues: 101 sheet: -1.83 (0.41), residues: 152 loop : -2.72 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 19 TYR 0.016 0.002 TYR B 37 PHE 0.018 0.002 PHE A 114 TRP 0.025 0.003 TRP A 36 HIS 0.006 0.003 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 4477) covalent geometry : angle 0.72788 ( 6092) hydrogen bonds : bond 0.04376 ( 179) hydrogen bonds : angle 6.43793 ( 501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7468 (mpp) cc_final: 0.7234 (mmp) REVERT: A 116 TYR cc_start: 0.6468 (t80) cc_final: 0.6104 (t80) REVERT: A 124 THR cc_start: 0.8015 (m) cc_final: 0.6754 (m) REVERT: B 67 LYS cc_start: 0.7209 (pttt) cc_final: 0.6172 (ptpp) REVERT: B 195 TYR cc_start: 0.7403 (m-80) cc_final: 0.7201 (m-80) REVERT: C 141 GLU cc_start: 0.9575 (mt-10) cc_final: 0.9274 (mt-10) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1995 time to fit residues: 23.9181 Evaluate side-chains 84 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 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 = 0.4198 r_free = 0.4198 target = 0.130811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.108065 restraints weight = 46775.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.113085 restraints weight = 27274.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.116542 restraints weight = 18056.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.119096 restraints weight = 12984.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.120965 restraints weight = 9774.922| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6320 moved from start: 0.6764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4477 Z= 0.129 Angle : 0.630 5.545 6092 Z= 0.340 Chirality : 0.043 0.152 682 Planarity : 0.006 0.076 789 Dihedral : 6.204 24.619 630 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.98 % Favored : 87.67 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.37 (0.34), residues: 576 helix: 0.73 (0.48), residues: 101 sheet: -1.54 (0.42), residues: 144 loop : -2.44 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 163 TYR 0.015 0.001 TYR A 60 PHE 0.013 0.002 PHE B 101 TRP 0.022 0.002 TRP A 36 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4477) covalent geometry : angle 0.62999 ( 6092) hydrogen bonds : bond 0.03768 ( 179) hydrogen bonds : angle 6.01182 ( 501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8423 (pt) cc_final: 0.8044 (pt) REVERT: A 191 SER cc_start: 0.8684 (p) cc_final: 0.8483 (p) REVERT: B 67 LYS cc_start: 0.7207 (pttt) cc_final: 0.6163 (ptpp) REVERT: C 141 GLU cc_start: 0.9645 (mt-10) cc_final: 0.9107 (mt-10) REVERT: C 217 GLN cc_start: 0.7473 (mt0) cc_final: 0.6705 (mt0) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1794 time to fit residues: 22.9062 Evaluate side-chains 86 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 0.0470 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 overall best weight: 3.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN B 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.128082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.105604 restraints weight = 47055.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.110440 restraints weight = 27990.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.113807 restraints weight = 18729.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.116171 restraints weight = 13485.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.117977 restraints weight = 10298.911| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4477 Z= 0.168 Angle : 0.650 5.554 6092 Z= 0.354 Chirality : 0.043 0.152 682 Planarity : 0.007 0.074 789 Dihedral : 6.352 24.317 630 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.37 % Favored : 86.28 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.58 (0.34), residues: 576 helix: 0.65 (0.49), residues: 103 sheet: -1.72 (0.41), residues: 151 loop : -2.61 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 87 TYR 0.013 0.002 TYR B 99 PHE 0.018 0.002 PHE B 101 TRP 0.014 0.002 TRP A 36 HIS 0.006 0.002 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4477) covalent geometry : angle 0.64959 ( 6092) hydrogen bonds : bond 0.03890 ( 179) hydrogen bonds : angle 6.11247 ( 501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.7529 (mpp) cc_final: 0.7325 (mmp) REVERT: B 67 LYS cc_start: 0.7256 (pttt) cc_final: 0.6398 (ptpp) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1710 time to fit residues: 20.5565 Evaluate side-chains 83 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 0.0170 chunk 10 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.131779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.110189 restraints weight = 46781.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.114871 restraints weight = 27881.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.118192 restraints weight = 18714.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.120552 restraints weight = 13434.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.122098 restraints weight = 10222.190| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.7101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4477 Z= 0.117 Angle : 0.602 5.642 6092 Z= 0.322 Chirality : 0.043 0.145 682 Planarity : 0.006 0.073 789 Dihedral : 5.807 23.237 630 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.46 % Favored : 88.19 % Rotamer: Outliers : 0.20 % Allowed : 0.61 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.30 (0.34), residues: 576 helix: 0.87 (0.50), residues: 103 sheet: -1.41 (0.42), residues: 144 loop : -2.49 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 163 TYR 0.018 0.001 TYR C 228 PHE 0.009 0.001 PHE B 101 TRP 0.021 0.002 TRP A 36 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4477) covalent geometry : angle 0.60210 ( 6092) hydrogen bonds : bond 0.03561 ( 179) hydrogen bonds : angle 5.75112 ( 501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8313 (pt) cc_final: 0.8027 (pt) REVERT: A 124 THR cc_start: 0.6919 (m) cc_final: 0.6707 (m) REVERT: B 67 LYS cc_start: 0.7014 (pttt) cc_final: 0.6143 (ptpp) REVERT: C 141 GLU cc_start: 0.9615 (mt-10) cc_final: 0.9081 (mt-10) REVERT: C 163 ARG cc_start: 0.7226 (mtp180) cc_final: 0.6839 (mtp85) REVERT: C 217 GLN cc_start: 0.7373 (mt0) cc_final: 0.6582 (mt0) REVERT: C 236 PRO cc_start: 0.8640 (Cg_endo) cc_final: 0.8359 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.1725 time to fit residues: 20.8784 Evaluate side-chains 84 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 37 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.129383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.107224 restraints weight = 46484.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.111935 restraints weight = 28264.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.115300 restraints weight = 19035.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.117732 restraints weight = 13683.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.119247 restraints weight = 10359.952| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.7154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4477 Z= 0.149 Angle : 0.613 5.462 6092 Z= 0.331 Chirality : 0.042 0.161 682 Planarity : 0.006 0.068 789 Dihedral : 5.900 22.608 630 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.50 % Favored : 87.15 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -2.38 (0.34), residues: 576 helix: 0.92 (0.49), residues: 103 sheet: -1.55 (0.41), residues: 148 loop : -2.53 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 80 TYR 0.017 0.002 TYR C 228 PHE 0.017 0.002 PHE B 101 TRP 0.017 0.002 TRP A 36 HIS 0.005 0.002 HIS A 178 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4477) covalent geometry : angle 0.61301 ( 6092) hydrogen bonds : bond 0.03605 ( 179) hydrogen bonds : angle 5.76903 ( 501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1798.50 seconds wall clock time: 31 minutes 21.47 seconds (1881.47 seconds total)