Starting phenix.real_space_refine on Wed Aug 5 03:48:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/31ck_58291/08_2026/31ck_58291_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/31ck_58291/08_2026/31ck_58291.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/31ck_58291/08_2026/31ck_58291_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/31ck_58291/08_2026/31ck_58291_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/31ck_58291/08_2026/31ck_58291.map" default_real_map = "/net/cci-nas-00/data/ceres_data/31ck_58291/08_2026/31ck_58291.map" } resolution = 3.5 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= 0.005 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 26 5.16 5 C 2550 2.51 5 N 722 2.21 5 O 716 1.98 5 H 3991 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8009 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3951 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3952 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.48, per 1000 atoms: 0.18 Number of scatterers: 8009 At special positions: 0 Unit cell: (78, 75.92, 94.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 P 4 15.00 O 716 8.00 N 722 7.00 C 2550 6.00 H 3991 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: 0.60 Conformation dependent library (CDL) restraints added in 264.1 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 56.9% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.892A pdb=" N VAL A 56 " --> pdb=" O HIS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.880A pdb=" N PHE A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 134 Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 151 through 159 removed outlier: 4.566A pdb=" N LEU A 156 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 160 through 183 Processing helix chain 'A' and resid 187 through 208 removed outlier: 4.168A pdb=" N ILE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 224 Processing helix chain 'A' and resid 237 through 253 Processing helix chain 'B' and resid 34 through 42 Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'B' and resid 52 through 57 removed outlier: 3.893A pdb=" N VAL B 56 " --> pdb=" O HIS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 removed outlier: 3.880A pdb=" N PHE B 66 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 134 Proline residue: B 128 - end of helix Processing helix chain 'B' and resid 151 through 159 removed outlier: 4.565A pdb=" N LEU B 156 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Proline residue: B 157 - end of helix Processing helix chain 'B' and resid 160 through 183 Processing helix chain 'B' and resid 187 through 208 removed outlier: 4.318A pdb=" N ILE B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 224 Processing helix chain 'B' and resid 237 through 253 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.689A pdb=" N THR A 23 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A 33 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N MET A 21 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET A 102 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR A 111 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A 100 " --> pdb=" O TYR A 111 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER A 113 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASN A 98 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG A 115 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ARG A 96 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 93 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A 81 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 143 Processing sheet with id=AA3, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.689A pdb=" N THR B 23 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA B 33 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N MET B 21 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N MET B 102 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR B 111 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 100 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER B 113 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN B 98 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG B 115 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ARG B 96 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 93 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY B 81 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 140 through 143 226 hydrogen bonds defined for protein. 630 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: 1.64 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 3985 1.03 - 1.23: 12 1.23 - 1.42: 1704 1.42 - 1.62: 2352 1.62 - 1.82: 54 Bond restraints: 8107 Sorted by residual: bond pdb=" N VAL A 187 " pdb=" CA VAL A 187 " ideal model delta sigma weight residual 1.459 1.477 -0.018 1.25e-02 6.40e+03 2.03e+00 bond pdb=" CB GLU A 77 " pdb=" CG GLU A 77 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.37e+00 bond pdb=" CA VAL A 187 " pdb=" CB VAL A 187 " ideal model delta sigma weight residual 1.540 1.555 -0.015 1.36e-02 5.41e+03 1.28e+00 bond pdb=" CG1 VAL A 187 " pdb="HG13 VAL A 187 " ideal model delta sigma weight residual 0.970 0.952 0.018 2.00e-02 2.50e+03 8.22e-01 bond pdb=" CB GLU A 121 " pdb=" CG GLU A 121 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.31e-01 ... (remaining 8102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 14212 1.46 - 2.92: 377 2.92 - 4.38: 38 4.38 - 5.84: 8 5.84 - 7.30: 5 Bond angle restraints: 14640 Sorted by residual: angle pdb=" N VAL A 187 " pdb=" CA VAL A 187 " pdb=" CB VAL A 187 " ideal model delta sigma weight residual 111.23 117.76 -6.53 1.65e+00 3.67e-01 1.56e+01 angle pdb=" C PRO A 186 " pdb=" N VAL A 187 " pdb=" CA VAL A 187 " ideal model delta sigma weight residual 121.97 128.55 -6.58 1.80e+00 3.09e-01 1.33e+01 angle pdb=" CB GLU A 77 " pdb=" CG GLU A 77 " pdb=" CD GLU A 77 " ideal model delta sigma weight residual 112.60 117.31 -4.71 1.70e+00 3.46e-01 7.68e+00 angle pdb=" CB MET A 169 " pdb=" CG MET A 169 " pdb=" SD MET A 169 " ideal model delta sigma weight residual 112.70 119.80 -7.10 3.00e+00 1.11e-01 5.61e+00 angle pdb=" CA GLU A 77 " pdb=" CB GLU A 77 " pdb=" CG GLU A 77 " ideal model delta sigma weight residual 114.10 118.56 -4.46 2.00e+00 2.50e-01 4.98e+00 ... (remaining 14635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3355 17.97 - 35.93: 353 35.93 - 53.90: 87 53.90 - 71.87: 20 71.87 - 89.83: 6 Dihedral angle restraints: 3821 sinusoidal: 2142 harmonic: 1679 Sorted by residual: dihedral pdb=" N VAL A 187 " pdb=" C VAL A 187 " pdb=" CA VAL A 187 " pdb=" CB VAL A 187 " ideal model delta harmonic sigma weight residual 123.40 132.17 -8.77 0 2.50e+00 1.60e-01 1.23e+01 dihedral pdb=" CA ASP A 25 " pdb=" CB ASP A 25 " pdb=" CG ASP A 25 " pdb=" OD1 ASP A 25 " ideal model delta sinusoidal sigma weight residual -30.00 -82.87 52.87 1 2.00e+01 2.50e-03 9.51e+00 dihedral pdb=" CA ASP B 25 " pdb=" CB ASP B 25 " pdb=" CG ASP B 25 " pdb=" OD1 ASP B 25 " ideal model delta sinusoidal sigma weight residual -30.00 -82.80 52.80 1 2.00e+01 2.50e-03 9.49e+00 ... (remaining 3818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 449 0.035 - 0.071: 127 0.071 - 0.106: 37 0.106 - 0.142: 13 0.142 - 0.177: 6 Chirality restraints: 632 Sorted by residual: chirality pdb=" CG LEU A 192 " pdb=" CB LEU A 192 " pdb=" CD1 LEU A 192 " pdb=" CD2 LEU A 192 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CG LEU B 192 " pdb=" CB LEU B 192 " pdb=" CD1 LEU B 192 " pdb=" CD2 LEU B 192 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA PRO A 186 " pdb=" N PRO A 186 " pdb=" C PRO A 186 " pdb=" CB PRO A 186 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.75e-01 ... (remaining 629 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 186 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C PRO A 186 " -0.030 2.00e-02 2.50e+03 pdb=" O PRO A 186 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 187 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 210 " -0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO B 211 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 211 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 211 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 210 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 211 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " 0.019 5.00e-02 4.00e+02 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 2445 2.33 - 2.90: 18033 2.90 - 3.47: 20912 3.47 - 4.03: 26986 4.03 - 4.60: 40759 Nonbonded interactions: 109135 Sorted by model distance: nonbonded pdb=" H THR A 189 " pdb=" HG1 THR A 189 " model vdw 1.766 2.100 nonbonded pdb=" H ILE A 123 " pdb="HG13 ILE A 123 " model vdw 1.831 2.270 nonbonded pdb=" H ILE B 123 " pdb="HG13 ILE B 123 " model vdw 1.832 2.270 nonbonded pdb=" H VAL B 246 " pdb="HG11 VAL B 246 " model vdw 1.904 2.270 nonbonded pdb="HG21 VAL A 187 " pdb=" H VAL A 188 " model vdw 1.914 2.270 ... (remaining 109130 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' selection = (chain 'B' and (resid 6 through 91 or (resid 92 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 93 through 601)) } 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: 0.870 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.690 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 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 : 0.003 0.035 4116 Z= 0.131 Angle : 0.627 7.299 5610 Z= 0.320 Chirality : 0.042 0.177 632 Planarity : 0.004 0.036 688 Dihedral : 15.437 89.835 1562 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.85 % Favored : 96.95 % Rotamer: Outliers : 0.24 % Allowed : 26.20 % Favored : 73.56 % 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: 0.28 (0.38), residues: 492 helix: 0.61 (0.33), residues: 242 sheet: -1.25 (0.74), residues: 46 loop : 0.25 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 244 TYR 0.007 0.001 TYR A 190 PHE 0.008 0.001 PHE A 182 TRP 0.007 0.001 TRP B 181 HIS 0.011 0.002 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 4116) covalent geometry : angle 0.62713 / 0.32 ( 5610) hydrogen bonds : bond 0.20366 / 13.81 ( 226) hydrogen bonds : angle 7.19462 / 5.08 ( 630) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.234 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: A 10 GLN cc_start: 0.9284 (tp-100) cc_final: 0.8998 (tm-30) REVERT: A 55 MET cc_start: 0.8816 (ttp) cc_final: 0.8602 (ttp) REVERT: A 159 LEU cc_start: 0.9055 (tp) cc_final: 0.8746 (tp) REVERT: A 204 PHE cc_start: 0.8945 (t80) cc_final: 0.8677 (t80) REVERT: B 10 GLN cc_start: 0.9286 (tp-100) cc_final: 0.9001 (tm-30) REVERT: B 55 MET cc_start: 0.8814 (ttp) cc_final: 0.8599 (ttp) REVERT: B 77 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8321 (mp0) REVERT: B 159 LEU cc_start: 0.9040 (tp) cc_final: 0.8729 (tp) REVERT: B 169 MET cc_start: 0.9107 (mmt) cc_final: 0.8885 (mmm) outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.0911 time to fit residues: 11.3564 Evaluate side-chains 84 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.081452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.072606 restraints weight = 43490.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.075419 restraints weight = 15064.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.077100 restraints weight = 7341.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.078317 restraints weight = 4077.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.078887 restraints weight = 2411.309| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4116 Z= 0.173 Angle : 0.590 6.861 5610 Z= 0.313 Chirality : 0.040 0.229 632 Planarity : 0.004 0.032 688 Dihedral : 7.603 71.860 639 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.24 % Favored : 97.56 % Rotamer: Outliers : 2.88 % Allowed : 19.47 % Favored : 77.64 % 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: 1.03 (0.38), residues: 492 helix: 1.51 (0.32), residues: 260 sheet: -0.94 (0.59), residues: 64 loop : 0.23 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 96 TYR 0.009 0.001 TYR A 190 PHE 0.015 0.002 PHE B 182 TRP 0.005 0.001 TRP B 79 HIS 0.003 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 4116) covalent geometry : angle 0.58982 / 0.31 ( 5610) hydrogen bonds : bond 0.03877 / 2.69 ( 226) hydrogen bonds : angle 4.87433 / 3.42 ( 630) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.139 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: A 77 GLU cc_start: 0.8275 (mp0) cc_final: 0.8064 (mp0) REVERT: A 159 LEU cc_start: 0.9300 (tp) cc_final: 0.8952 (tp) REVERT: A 204 PHE cc_start: 0.9050 (t80) cc_final: 0.8775 (t80) REVERT: B 77 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8341 (mp0) REVERT: B 159 LEU cc_start: 0.9304 (tp) cc_final: 0.8966 (tp) REVERT: B 169 MET cc_start: 0.9252 (mmt) cc_final: 0.9012 (mmm) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.0762 time to fit residues: 10.0344 Evaluate side-chains 75 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.080199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.071240 restraints weight = 44601.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.073915 restraints weight = 15008.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.075643 restraints weight = 7274.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.076897 restraints weight = 4048.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.077610 restraints weight = 2396.924| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4116 Z= 0.172 Angle : 0.558 6.471 5610 Z= 0.298 Chirality : 0.039 0.213 632 Planarity : 0.004 0.035 688 Dihedral : 7.335 72.863 636 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.85 % Favored : 96.95 % Rotamer: Outliers : 2.88 % Allowed : 18.03 % Favored : 79.09 % 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: 1.18 (0.38), residues: 492 helix: 1.73 (0.32), residues: 260 sheet: -0.92 (0.61), residues: 62 loop : 0.11 (0.48), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 87 TYR 0.011 0.001 TYR A 190 PHE 0.020 0.002 PHE A 182 TRP 0.007 0.001 TRP A 181 HIS 0.005 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 4116) covalent geometry : angle 0.55827 / 0.30 ( 5610) hydrogen bonds : bond 0.03330 / 2.31 ( 226) hydrogen bonds : angle 4.54926 / 3.18 ( 630) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.128 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: A 77 GLU cc_start: 0.8241 (mp0) cc_final: 0.7962 (mp0) REVERT: A 195 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7894 (tp) REVERT: A 204 PHE cc_start: 0.9113 (t80) cc_final: 0.8859 (t80) REVERT: B 69 MET cc_start: 0.9241 (ttp) cc_final: 0.8951 (ttp) REVERT: B 77 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8304 (mp0) REVERT: B 169 MET cc_start: 0.9247 (mmt) cc_final: 0.9031 (mmm) REVERT: B 195 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7957 (tp) outliers start: 12 outliers final: 6 residues processed: 81 average time/residue: 0.0615 time to fit residues: 7.4308 Evaluate side-chains 74 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.081268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.072309 restraints weight = 44593.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.075006 restraints weight = 14914.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.076787 restraints weight = 7239.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.077988 restraints weight = 3980.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.078706 restraints weight = 2361.910| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4116 Z= 0.115 Angle : 0.516 5.688 5610 Z= 0.271 Chirality : 0.038 0.190 632 Planarity : 0.004 0.035 688 Dihedral : 7.191 76.189 636 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.85 % Favored : 96.95 % Rotamer: Outliers : 0.96 % Allowed : 16.59 % Favored : 82.45 % 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: 1.44 (0.38), residues: 492 helix: 1.96 (0.32), residues: 260 sheet: -0.68 (0.59), residues: 64 loop : 0.15 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 87 TYR 0.007 0.001 TYR A 190 PHE 0.012 0.001 PHE A 182 TRP 0.005 0.001 TRP B 79 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 4116) covalent geometry : angle 0.51574 / 0.27 ( 5610) hydrogen bonds : bond 0.03004 / 2.10 ( 226) hydrogen bonds : angle 4.23596 / 2.94 ( 630) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.157 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: A 69 MET cc_start: 0.9244 (ttp) cc_final: 0.9021 (ttp) REVERT: A 77 GLU cc_start: 0.8095 (mp0) cc_final: 0.7821 (mp0) REVERT: A 195 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7900 (tp) REVERT: A 204 PHE cc_start: 0.9103 (t80) cc_final: 0.8823 (t80) REVERT: B 69 MET cc_start: 0.9277 (ttp) cc_final: 0.9002 (ttp) REVERT: B 77 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8273 (mp0) REVERT: B 169 MET cc_start: 0.9129 (mmt) cc_final: 0.8927 (mmm) outliers start: 4 outliers final: 3 residues processed: 80 average time/residue: 0.0623 time to fit residues: 7.4404 Evaluate side-chains 73 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.076614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068445 restraints weight = 46268.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.071085 restraints weight = 16381.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.072740 restraints weight = 8238.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.073658 restraints weight = 4737.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.074523 restraints weight = 3158.286| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4116 Z= 0.165 Angle : 0.536 5.502 5610 Z= 0.284 Chirality : 0.038 0.190 632 Planarity : 0.004 0.033 688 Dihedral : 7.250 68.806 636 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.46 % Favored : 96.34 % Rotamer: Outliers : 2.64 % Allowed : 15.62 % Favored : 81.73 % 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: 1.35 (0.38), residues: 492 helix: 1.97 (0.32), residues: 260 sheet: -0.74 (0.59), residues: 64 loop : -0.03 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 87 TYR 0.009 0.001 TYR A 190 PHE 0.015 0.002 PHE B 182 TRP 0.005 0.001 TRP B 79 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 4116) covalent geometry : angle 0.53566 / 0.28 ( 5610) hydrogen bonds : bond 0.02994 / 2.09 ( 226) hydrogen bonds : angle 4.24204 / 2.96 ( 630) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.214 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: A 69 MET cc_start: 0.9306 (ttp) cc_final: 0.9015 (ttp) REVERT: A 77 GLU cc_start: 0.8131 (mp0) cc_final: 0.7861 (mp0) REVERT: A 195 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7867 (tp) REVERT: A 204 PHE cc_start: 0.9164 (t80) cc_final: 0.8936 (t80) REVERT: B 69 MET cc_start: 0.9304 (ttp) cc_final: 0.8976 (ttp) REVERT: B 77 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8288 (mp0) REVERT: B 195 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7962 (tp) outliers start: 11 outliers final: 7 residues processed: 77 average time/residue: 0.0722 time to fit residues: 8.3815 Evaluate side-chains 74 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.082091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.072707 restraints weight = 44691.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.075399 restraints weight = 14634.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.077187 restraints weight = 7041.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.078349 restraints weight = 3908.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.079017 restraints weight = 2372.494| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4116 Z= 0.148 Angle : 0.528 5.756 5610 Z= 0.278 Chirality : 0.038 0.177 632 Planarity : 0.004 0.034 688 Dihedral : 7.186 68.331 636 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.25 % Favored : 96.54 % Rotamer: Outliers : 2.16 % Allowed : 16.35 % Favored : 81.49 % 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: 1.31 (0.38), residues: 492 helix: 2.02 (0.32), residues: 260 sheet: -0.85 (0.59), residues: 62 loop : -0.17 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 244 TYR 0.008 0.001 TYR A 190 PHE 0.013 0.002 PHE A 182 TRP 0.004 0.001 TRP A 79 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 4116) covalent geometry : angle 0.52793 / 0.28 ( 5610) hydrogen bonds : bond 0.02950 / 2.06 ( 226) hydrogen bonds : angle 4.19314 / 2.92 ( 630) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 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: A 69 MET cc_start: 0.9300 (ttp) cc_final: 0.9032 (ttp) REVERT: A 195 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7854 (tp) REVERT: A 204 PHE cc_start: 0.9070 (t80) cc_final: 0.8771 (t80) REVERT: B 69 MET cc_start: 0.9287 (ttp) cc_final: 0.9010 (ttp) REVERT: B 77 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8157 (mp0) REVERT: B 195 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7964 (tp) outliers start: 9 outliers final: 7 residues processed: 74 average time/residue: 0.0712 time to fit residues: 7.9342 Evaluate side-chains 78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 248 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.080155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.071166 restraints weight = 45767.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.073909 restraints weight = 15179.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.075663 restraints weight = 7221.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.076832 restraints weight = 3986.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.077529 restraints weight = 2421.253| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4116 Z= 0.164 Angle : 0.538 6.258 5610 Z= 0.282 Chirality : 0.038 0.173 632 Planarity : 0.003 0.034 688 Dihedral : 7.240 66.471 636 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.05 % Favored : 96.75 % Rotamer: Outliers : 2.16 % Allowed : 17.07 % Favored : 80.77 % 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: 1.26 (0.38), residues: 492 helix: 1.97 (0.32), residues: 260 sheet: -0.85 (0.59), residues: 62 loop : -0.21 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 87 TYR 0.008 0.001 TYR B 190 PHE 0.014 0.002 PHE A 182 TRP 0.004 0.001 TRP A 181 HIS 0.003 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 4116) covalent geometry : angle 0.53797 / 0.28 ( 5610) hydrogen bonds : bond 0.02922 / 2.03 ( 226) hydrogen bonds : angle 4.20342 / 2.93 ( 630) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.154 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: A 69 MET cc_start: 0.9314 (ttp) cc_final: 0.9041 (ttp) REVERT: A 195 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7889 (tp) REVERT: A 204 PHE cc_start: 0.9103 (t80) cc_final: 0.8789 (t80) REVERT: B 69 MET cc_start: 0.9300 (ttp) cc_final: 0.9004 (ttp) REVERT: B 77 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8164 (mp0) REVERT: B 195 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7965 (tp) outliers start: 9 outliers final: 7 residues processed: 75 average time/residue: 0.0764 time to fit residues: 8.5414 Evaluate side-chains 77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 248 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.081272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.072193 restraints weight = 44800.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.074928 restraints weight = 14622.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.076715 restraints weight = 7015.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.077877 restraints weight = 3858.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.078563 restraints weight = 2340.402| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4116 Z= 0.122 Angle : 0.521 5.723 5610 Z= 0.268 Chirality : 0.038 0.153 632 Planarity : 0.003 0.035 688 Dihedral : 7.070 67.545 636 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.24 % Favored : 97.56 % Rotamer: Outliers : 1.68 % Allowed : 17.31 % Favored : 81.01 % 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: 1.45 (0.38), residues: 492 helix: 2.12 (0.32), residues: 260 sheet: -0.71 (0.58), residues: 64 loop : -0.12 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 164 TYR 0.007 0.001 TYR A 190 PHE 0.010 0.001 PHE A 182 TRP 0.004 0.001 TRP A 181 HIS 0.004 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 4116) covalent geometry : angle 0.52098 / 0.27 ( 5610) hydrogen bonds : bond 0.02773 / 1.93 ( 226) hydrogen bonds : angle 4.00422 / 2.78 ( 630) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.220 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: A 69 MET cc_start: 0.9326 (ttp) cc_final: 0.9044 (ttp) REVERT: A 77 GLU cc_start: 0.8386 (mp0) cc_final: 0.7987 (mp0) REVERT: A 142 ILE cc_start: 0.9264 (mp) cc_final: 0.8876 (tp) REVERT: A 195 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7936 (tp) REVERT: A 204 PHE cc_start: 0.9091 (t80) cc_final: 0.8768 (t80) REVERT: B 69 MET cc_start: 0.9332 (ttp) cc_final: 0.9025 (ttp) REVERT: B 77 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8128 (mp0) REVERT: B 142 ILE cc_start: 0.9255 (mp) cc_final: 0.8866 (tp) REVERT: B 195 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7977 (tp) outliers start: 7 outliers final: 4 residues processed: 74 average time/residue: 0.0736 time to fit residues: 8.1140 Evaluate side-chains 68 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.079627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.070617 restraints weight = 45455.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.073262 restraints weight = 15114.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.075005 restraints weight = 7265.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.076189 restraints weight = 4087.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.076724 restraints weight = 2512.095| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4116 Z= 0.166 Angle : 0.550 5.845 5610 Z= 0.287 Chirality : 0.038 0.153 632 Planarity : 0.003 0.033 688 Dihedral : 7.227 65.067 636 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.86 % Favored : 95.93 % Rotamer: Outliers : 1.92 % Allowed : 16.59 % Favored : 81.49 % 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: 1.43 (0.38), residues: 492 helix: 2.07 (0.32), residues: 260 sheet: -0.45 (0.57), residues: 64 loop : -0.18 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 87 TYR 0.009 0.001 TYR A 190 PHE 0.014 0.002 PHE B 182 TRP 0.005 0.001 TRP A 181 HIS 0.003 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 4116) covalent geometry : angle 0.54955 / 0.29 ( 5610) hydrogen bonds : bond 0.02843 / 1.98 ( 226) hydrogen bonds : angle 4.09947 / 2.84 ( 630) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.224 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: A 69 MET cc_start: 0.9340 (ttp) cc_final: 0.9052 (ttp) REVERT: A 142 ILE cc_start: 0.9208 (mp) cc_final: 0.8801 (tp) REVERT: A 195 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7910 (tp) REVERT: A 204 PHE cc_start: 0.9168 (t80) cc_final: 0.8910 (t80) REVERT: B 69 MET cc_start: 0.9333 (ttp) cc_final: 0.9031 (ttp) REVERT: B 77 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8186 (mp0) REVERT: B 142 ILE cc_start: 0.9198 (mp) cc_final: 0.8790 (tp) REVERT: B 195 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7978 (tp) outliers start: 8 outliers final: 5 residues processed: 68 average time/residue: 0.0746 time to fit residues: 7.6485 Evaluate side-chains 71 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.079904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.070983 restraints weight = 45497.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.073675 restraints weight = 14997.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.075427 restraints weight = 7208.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.076514 restraints weight = 4000.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.077220 restraints weight = 2496.537| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4116 Z= 0.134 Angle : 0.544 6.577 5610 Z= 0.282 Chirality : 0.038 0.139 632 Planarity : 0.003 0.034 688 Dihedral : 7.119 65.290 636 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.44 % Favored : 97.36 % Rotamer: Outliers : 1.68 % Allowed : 16.59 % Favored : 81.73 % 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: 1.47 (0.38), residues: 492 helix: 2.12 (0.32), residues: 260 sheet: -0.43 (0.61), residues: 62 loop : -0.23 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 87 TYR 0.008 0.001 TYR A 190 PHE 0.012 0.001 PHE A 182 TRP 0.004 0.001 TRP A 181 HIS 0.004 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 4116) covalent geometry : angle 0.54389 / 0.28 ( 5610) hydrogen bonds : bond 0.02804 / 1.95 ( 226) hydrogen bonds : angle 3.97946 / 2.75 ( 630) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.136 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: A 69 MET cc_start: 0.9338 (ttp) cc_final: 0.9062 (ttp) REVERT: A 77 GLU cc_start: 0.8309 (mp0) cc_final: 0.8067 (mp0) REVERT: A 142 ILE cc_start: 0.9191 (mp) cc_final: 0.8805 (tp) REVERT: A 195 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7881 (tp) REVERT: A 204 PHE cc_start: 0.9130 (t80) cc_final: 0.8864 (t80) REVERT: B 69 MET cc_start: 0.9339 (ttp) cc_final: 0.9043 (ttp) REVERT: B 77 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8190 (mp0) REVERT: B 142 ILE cc_start: 0.9181 (mp) cc_final: 0.8793 (tp) REVERT: B 195 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7956 (tp) outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 0.0792 time to fit residues: 8.1243 Evaluate side-chains 69 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.079966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.071297 restraints weight = 45263.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.073929 restraints weight = 15329.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.075640 restraints weight = 7469.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.076806 restraints weight = 4197.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.077444 restraints weight = 2587.040| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4116 Z= 0.114 Angle : 0.524 6.342 5610 Z= 0.270 Chirality : 0.038 0.141 632 Planarity : 0.003 0.035 688 Dihedral : 7.013 68.523 636 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.03 % Favored : 97.76 % Rotamer: Outliers : 1.20 % Allowed : 17.07 % Favored : 81.73 % 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: 1.60 (0.38), residues: 492 helix: 2.24 (0.32), residues: 260 sheet: -0.31 (0.63), residues: 62 loop : -0.21 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 164 TYR 0.006 0.001 TYR A 190 PHE 0.009 0.001 PHE A 182 TRP 0.004 0.001 TRP B 79 HIS 0.004 0.001 HIS B 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 4116) covalent geometry : angle 0.52374 / 0.27 ( 5610) hydrogen bonds : bond 0.02679 / 1.87 ( 226) hydrogen bonds : angle 3.82256 / 2.62 ( 630) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1424.71 seconds wall clock time: 24 minutes 50.47 seconds (1490.47 seconds total)