Starting phenix.real_space_refine on Wed Aug 5 07:41:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cvt_45966/08_2026/9cvt_45966.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cvt_45966/08_2026/9cvt_45966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cvt_45966/08_2026/9cvt_45966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cvt_45966/08_2026/9cvt_45966.map" model { file = "/net/cci-nas-00/data/ceres_data/9cvt_45966/08_2026/9cvt_45966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cvt_45966/08_2026/9cvt_45966.cif" } resolution = 4.41 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= 0.001 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: 5 Type Number sf(0) Gaussians P 182 5.49 5 S 32 5.16 5 C 5046 2.51 5 N 1608 2.21 5 O 2029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 8897 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1213 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Chain: "B" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1308 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 3, 'TRANS': 160} Chain: "C" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1337 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 1 Chain: "D" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1308 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain breaks: 1 Chain: "I" Number of atoms: 1851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1851 Classifications: {'DNA': 91} Link IDs: {'rna3p': 90} Chain: "J" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1880 Classifications: {'DNA': 91} Link IDs: {'rna3p': 90} Time building chain proxies: 1.59, per 1000 atoms: 0.18 Number of scatterers: 8897 At special positions: 0 Unit cell: (83.905, 114.46, 115.915, 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 32 16.00 P 182 15.00 O 2029 8.00 N 1608 7.00 C 5046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS B 103 " distance=2.04 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: 0.62 Conformation dependent library (CDL) restraints added in 289.9 milliseconds 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1254 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 1 sheets defined 72.7% alpha, 0.3% beta 89 base pairs and 143 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 23 through 48 Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.966A pdb=" N PHE A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 removed outlier: 3.758A pdb=" N LYS A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 removed outlier: 3.847A pdb=" N ASN A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 136 Processing helix chain 'A' and resid 142 through 153 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 22 through 48 removed outlier: 3.575A pdb=" N LEU B 26 " --> pdb=" O THR B 22 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU B 27 " --> pdb=" O LYS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 64 removed outlier: 3.546A pdb=" N PHE B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 removed outlier: 4.329A pdb=" N LYS B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 100 removed outlier: 3.931A pdb=" N THR B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 136 removed outlier: 3.694A pdb=" N VAL B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.574A pdb=" N HIS B 157 " --> pdb=" O ASP B 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 48 through 74 removed outlier: 3.667A pdb=" N ILE C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 132 through 136 removed outlier: 4.071A pdb=" N MET C 136 " --> pdb=" O ARG C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 158 Processing helix chain 'C' and resid 166 through 195 Processing helix chain 'C' and resid 201 through 213 Processing helix chain 'D' and resid 28 through 40 removed outlier: 3.672A pdb=" N THR D 32 " --> pdb=" O PRO D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 75 removed outlier: 3.541A pdb=" N ILE D 52 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 91 removed outlier: 3.668A pdb=" N MET D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 137 removed outlier: 4.368A pdb=" N LYS D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 removed outlier: 4.294A pdb=" N PHE D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 195 Processing helix chain 'D' and resid 201 through 212 removed outlier: 3.725A pdb=" N GLU D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 78 through 79 removed outlier: 3.639A pdb=" N ILE D 79 " --> pdb=" O HIS D 164 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 335 hydrogen bonds defined for protein. 990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 228 hydrogen bonds 456 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 143 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1617 1.33 - 1.45: 2952 1.45 - 1.57: 4430 1.57 - 1.70: 362 1.70 - 1.82: 56 Bond restraints: 9417 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" C2' DG J 20 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT J -24 " pdb=" C2' DT J -24 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA I -22 " pdb=" C2' DA I -22 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC J 37 " pdb=" C2' DC J 37 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DA J -15 " pdb=" C2' DA J -15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 9412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 12894 2.04 - 4.09: 524 4.09 - 6.13: 36 6.13 - 8.18: 7 8.18 - 10.22: 3 Bond angle restraints: 13464 Sorted by residual: angle pdb=" O4' DG I 28 " pdb=" C4' DG I 28 " pdb=" C3' DG I 28 " ideal model delta sigma weight residual 106.00 102.82 3.18 6.00e-01 2.78e+00 2.81e+01 angle pdb=" C LEU A 97 " pdb=" N MET A 98 " pdb=" CA MET A 98 " ideal model delta sigma weight residual 120.68 112.41 8.27 1.70e+00 3.46e-01 2.36e+01 angle pdb=" O4' DG J -45 " pdb=" C1' DG J -45 " pdb=" N9 DG J -45 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.23e+01 angle pdb=" O4' DC I 7 " pdb=" C4' DC I 7 " pdb=" C3' DC I 7 " ideal model delta sigma weight residual 106.00 103.27 2.73 6.00e-01 2.78e+00 2.06e+01 angle pdb=" C3' DT I -39 " pdb=" O3' DT I -39 " pdb=" P DC I -38 " ideal model delta sigma weight residual 119.70 125.12 -5.42 1.20e+00 6.94e-01 2.04e+01 ... (remaining 13459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 4018 29.20 - 58.41: 1100 58.41 - 87.61: 116 87.61 - 116.81: 7 116.81 - 146.01: 5 Dihedral angle restraints: 5246 sinusoidal: 3337 harmonic: 1909 Sorted by residual: dihedral pdb=" CB CYS A 103 " pdb=" SG CYS A 103 " pdb=" SG CYS B 103 " pdb=" CB CYS B 103 " ideal model delta sinusoidal sigma weight residual 93.00 176.15 -83.15 1 1.00e+01 1.00e-02 8.45e+01 dihedral pdb=" C4' DC I 4 " pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sinusoidal sigma weight residual 220.00 73.99 146.01 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" C4' DC J 37 " pdb=" C3' DC J 37 " pdb=" O3' DC J 37 " pdb=" P DG J 38 " ideal model delta sinusoidal sigma weight residual 220.00 75.06 144.94 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 5243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1523 0.112 - 0.224: 37 0.224 - 0.336: 0 0.336 - 0.448: 0 0.448 - 0.560: 1 Chirality restraints: 1561 Sorted by residual: chirality pdb=" P DT I -39 " pdb=" OP1 DT I -39 " pdb=" OP2 DT I -39 " pdb=" O5' DT I -39 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.56 2.00e-01 2.50e+01 7.85e+00 chirality pdb=" CA CYS B 103 " pdb=" N CYS B 103 " pdb=" C CYS B 103 " pdb=" CB CYS B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA GLN C 174 " pdb=" N GLN C 174 " pdb=" C GLN C 174 " pdb=" CB GLN C 174 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.29e-01 ... (remaining 1558 not shown) Planarity restraints: 1049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 143 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO D 144 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 15 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO B 16 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 16 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 16 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 193 " -0.012 2.00e-02 2.50e+03 1.05e-02 2.21e+00 pdb=" CG TYR D 193 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR D 193 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 193 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR D 193 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 193 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR D 193 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 193 " 0.002 2.00e-02 2.50e+03 ... (remaining 1046 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1104 2.74 - 3.28: 9379 3.28 - 3.82: 18007 3.82 - 4.36: 19333 4.36 - 4.90: 27144 Nonbonded interactions: 74967 Sorted by model distance: nonbonded pdb=" N GLN D 135 " pdb=" OE1 GLN D 135 " model vdw 2.203 3.120 nonbonded pdb=" O TYR B 120 " pdb=" NE2 GLN B 124 " model vdw 2.204 3.120 nonbonded pdb=" O ILE D 191 " pdb=" OG SER D 194 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASP B 153 " pdb=" N LEU B 156 " model vdw 2.235 3.120 nonbonded pdb=" OE2 GLU B 24 " pdb=" OG SER B 25 " model vdw 2.242 3.040 ... (remaining 74962 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 9 through 15 or resid 22 through 165)) } ncs_group { reference = (chain 'C' and resid 15 through 212) selection = chain 'D' } 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: 8.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.030 Find NCS groups from input model: 0.070 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 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 : 0.006 0.042 9418 Z= 0.502 Angle : 0.859 10.222 13466 Z= 0.702 Chirality : 0.048 0.560 1561 Planarity : 0.004 0.043 1049 Dihedral : 28.597 146.014 3989 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.77 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.71 (0.33), residues: 641 helix: 1.41 (0.25), residues: 437 sheet: None (None), residues: 0 loop : -1.63 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 149 TYR 0.024 0.002 TYR D 193 PHE 0.023 0.002 PHE B 160 TRP 0.008 0.001 TRP A 60 HIS 0.003 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.50 ( 9417) covalent geometry : angle 0.85894 / 0.70 (13464) SS BOND : bond 0.00586 / 0.31 ( 1) SS BOND : angle 0.30687 / 0.18 ( 2) hydrogen bonds : bond 0.10808 / 7.31 ( 563) hydrogen bonds : angle 4.27635 / 2.98 ( 1446) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ILE cc_start: 0.9176 (tt) cc_final: 0.8922 (tt) REVERT: B 31 ASN cc_start: 0.9370 (m110) cc_final: 0.9142 (m110) REVERT: B 120 TYR cc_start: 0.8981 (t80) cc_final: 0.8750 (t80) REVERT: B 126 MET cc_start: 0.7816 (ppp) cc_final: 0.7431 (ppp) REVERT: B 159 MET cc_start: 0.8286 (ptp) cc_final: 0.7896 (ptm) REVERT: C 79 ILE cc_start: 0.8728 (pt) cc_final: 0.8358 (pt) REVERT: D 65 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8358 (tm-30) REVERT: D 69 LEU cc_start: 0.9100 (mt) cc_final: 0.8793 (mt) REVERT: D 89 GLU cc_start: 0.9229 (pp20) cc_final: 0.8972 (pp20) REVERT: D 189 LEU cc_start: 0.9628 (tt) cc_final: 0.8745 (pp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0774 time to fit residues: 17.8666 Evaluate side-chains 122 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 overall best weight: 0.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN B 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.042299 restraints weight = 54943.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.043683 restraints weight = 31140.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.044635 restraints weight = 21446.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.045280 restraints weight = 16703.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.045665 restraints weight = 14184.254| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9418 Z= 0.159 Angle : 0.725 8.547 13466 Z= 0.420 Chirality : 0.049 0.272 1561 Planarity : 0.005 0.052 1049 Dihedral : 32.824 144.725 2656 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.52 % Favored : 95.16 % Rotamer: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.64 % 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: 0.76 (0.33), residues: 641 helix: 1.40 (0.24), residues: 447 sheet: None (None), residues: 0 loop : -1.65 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 13 TYR 0.016 0.002 TYR D 193 PHE 0.013 0.001 PHE D 148 TRP 0.005 0.001 TRP A 60 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.16 ( 9417) covalent geometry : angle 0.72476 / 0.42 (13464) SS BOND : bond 0.00356 / 0.19 ( 1) SS BOND : angle 0.59497 / 0.35 ( 2) hydrogen bonds : bond 0.05081 / 3.48 ( 563) hydrogen bonds : angle 3.59473 / 2.52 ( 1446) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ILE cc_start: 0.7335 (mt) cc_final: 0.7106 (mt) REVERT: A 46 ILE cc_start: 0.9144 (tt) cc_final: 0.8859 (tt) REVERT: A 48 ILE cc_start: 0.9323 (tp) cc_final: 0.9118 (tp) REVERT: A 120 TYR cc_start: 0.9072 (t80) cc_final: 0.8861 (t80) REVERT: B 31 ASN cc_start: 0.9378 (m110) cc_final: 0.9109 (m110) REVERT: B 120 TYR cc_start: 0.8948 (t80) cc_final: 0.8665 (t80) REVERT: B 126 MET cc_start: 0.7742 (ppp) cc_final: 0.7325 (ppp) REVERT: C 178 GLU cc_start: 0.8106 (pp20) cc_final: 0.7724 (pp20) REVERT: D 65 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 69 LEU cc_start: 0.9100 (mt) cc_final: 0.8712 (mt) REVERT: D 96 PHE cc_start: 0.8841 (m-80) cc_final: 0.8621 (m-80) REVERT: D 210 MET cc_start: 0.8851 (tpt) cc_final: 0.8496 (tpt) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.0740 time to fit residues: 17.5548 Evaluate side-chains 116 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 30.0000 chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 81 optimal weight: 40.0000 chunk 7 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.057993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.042090 restraints weight = 54983.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.043447 restraints weight = 31600.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.044385 restraints weight = 21952.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.045016 restraints weight = 17189.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045446 restraints weight = 14621.133| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9418 Z= 0.162 Angle : 0.697 8.135 13466 Z= 0.407 Chirality : 0.046 0.274 1561 Planarity : 0.004 0.050 1049 Dihedral : 32.831 145.234 2656 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.15 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.33), residues: 641 helix: 1.35 (0.24), residues: 447 sheet: None (None), residues: 0 loop : -1.66 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 93 TYR 0.013 0.001 TYR D 193 PHE 0.013 0.001 PHE B 58 TRP 0.004 0.001 TRP B 60 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 ( 9417) covalent geometry : angle 0.69684 / 0.41 (13464) SS BOND : bond 0.00467 / 0.25 ( 1) SS BOND : angle 0.43264 / 0.24 ( 2) hydrogen bonds : bond 0.04759 / 3.26 ( 563) hydrogen bonds : angle 3.46540 / 2.43 ( 1446) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ILE cc_start: 0.9154 (tt) cc_final: 0.8846 (tt) REVERT: A 48 ILE cc_start: 0.9334 (tp) cc_final: 0.9114 (tp) REVERT: A 75 ASP cc_start: 0.9360 (t0) cc_final: 0.9124 (m-30) REVERT: B 31 ASN cc_start: 0.9411 (m110) cc_final: 0.9143 (m-40) REVERT: B 120 TYR cc_start: 0.8956 (t80) cc_final: 0.8654 (t80) REVERT: B 126 MET cc_start: 0.7734 (ppp) cc_final: 0.7309 (ppp) REVERT: C 79 ILE cc_start: 0.8793 (pt) cc_final: 0.8435 (pt) REVERT: C 178 GLU cc_start: 0.8066 (pp20) cc_final: 0.7743 (pp20) REVERT: D 65 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8370 (tm-30) REVERT: D 69 LEU cc_start: 0.9101 (mt) cc_final: 0.8712 (mt) REVERT: D 89 GLU cc_start: 0.9189 (pp20) cc_final: 0.8989 (pp20) REVERT: D 189 LEU cc_start: 0.9655 (tt) cc_final: 0.9445 (tt) REVERT: D 210 MET cc_start: 0.8821 (tpt) cc_final: 0.8450 (tpt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.0745 time to fit residues: 16.7489 Evaluate side-chains 116 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 40.0000 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 70 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 30.0000 chunk 54 optimal weight: 7.9990 chunk 67 optimal weight: 40.0000 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.057219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.041323 restraints weight = 55939.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.042659 restraints weight = 31915.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.043594 restraints weight = 22102.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.044223 restraints weight = 17263.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.044610 restraints weight = 14670.029| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9418 Z= 0.169 Angle : 0.704 8.230 13466 Z= 0.408 Chirality : 0.046 0.277 1561 Planarity : 0.004 0.049 1049 Dihedral : 32.842 145.488 2656 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.62 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % 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: 0.72 (0.33), residues: 641 helix: 1.41 (0.24), residues: 447 sheet: None (None), residues: 0 loop : -1.77 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 105 TYR 0.014 0.001 TYR D 193 PHE 0.022 0.002 PHE A 76 TRP 0.004 0.001 TRP A 60 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.17 ( 9417) covalent geometry : angle 0.70442 / 0.41 (13464) SS BOND : bond 0.00255 / 0.13 ( 1) SS BOND : angle 0.47658 / 0.27 ( 2) hydrogen bonds : bond 0.04776 / 3.28 ( 563) hydrogen bonds : angle 3.44334 / 2.42 ( 1446) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.9325 (tp) cc_final: 0.9105 (tp) REVERT: A 75 ASP cc_start: 0.9423 (t0) cc_final: 0.9168 (m-30) REVERT: A 120 TYR cc_start: 0.9138 (t80) cc_final: 0.8870 (t80) REVERT: B 31 ASN cc_start: 0.9437 (m110) cc_final: 0.9141 (m-40) REVERT: B 120 TYR cc_start: 0.8969 (t80) cc_final: 0.8691 (t80) REVERT: B 126 MET cc_start: 0.7778 (ppp) cc_final: 0.7346 (ppp) REVERT: C 79 ILE cc_start: 0.8756 (pt) cc_final: 0.8474 (pt) REVERT: C 178 GLU cc_start: 0.8083 (pp20) cc_final: 0.7769 (pp20) REVERT: D 65 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8360 (tm-30) REVERT: D 69 LEU cc_start: 0.9101 (mt) cc_final: 0.8710 (mt) REVERT: D 143 ILE cc_start: 0.8782 (tp) cc_final: 0.8542 (tp) REVERT: D 210 MET cc_start: 0.8878 (tpt) cc_final: 0.8479 (tpt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0799 time to fit residues: 18.1208 Evaluate side-chains 111 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 65 optimal weight: 30.0000 chunk 64 optimal weight: 50.0000 chunk 42 optimal weight: 4.9990 chunk 73 optimal weight: 50.0000 chunk 39 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 79 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 43 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.038683 restraints weight = 57921.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.039917 restraints weight = 33519.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.040784 restraints weight = 23531.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.041362 restraints weight = 18581.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.041730 restraints weight = 15943.576| |-----------------------------------------------------------------------------| r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9418 Z= 0.290 Angle : 0.836 9.239 13466 Z= 0.475 Chirality : 0.050 0.254 1561 Planarity : 0.006 0.058 1049 Dihedral : 32.909 148.062 2656 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.71 % Favored : 92.98 % Rotamer: Outliers : 0.17 % Allowed : 4.36 % Favored : 95.47 % 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: 0.08 (0.32), residues: 641 helix: 0.92 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -2.01 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 147 TYR 0.017 0.002 TYR D 193 PHE 0.015 0.002 PHE D 148 TRP 0.007 0.001 TRP A 60 HIS 0.006 0.002 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.29 ( 9417) covalent geometry : angle 0.83631 / 0.48 (13464) SS BOND : bond 0.00438 / 0.23 ( 1) SS BOND : angle 1.19807 / 0.66 ( 2) hydrogen bonds : bond 0.07312 / 5.03 ( 563) hydrogen bonds : angle 4.13839 / 2.90 ( 1446) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.241 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: A 60 TRP cc_start: 0.8895 (m100) cc_final: 0.8651 (m100) REVERT: A 120 TYR cc_start: 0.9230 (t80) cc_final: 0.8938 (t80) REVERT: B 31 ASN cc_start: 0.9476 (m110) cc_final: 0.9187 (m-40) REVERT: B 126 MET cc_start: 0.7858 (ppp) cc_final: 0.7447 (ppp) REVERT: C 79 ILE cc_start: 0.8862 (pt) cc_final: 0.8589 (pt) REVERT: D 65 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8442 (tm-30) REVERT: D 69 LEU cc_start: 0.9149 (mt) cc_final: 0.8839 (mt) REVERT: D 143 ILE cc_start: 0.8999 (tp) cc_final: 0.8714 (tp) REVERT: D 210 MET cc_start: 0.8954 (tpt) cc_final: 0.8538 (tpt) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.0858 time to fit residues: 18.2348 Evaluate side-chains 110 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 3 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 chunk 71 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN B 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.040535 restraints weight = 54799.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.041861 restraints weight = 30607.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.042794 restraints weight = 20959.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043428 restraints weight = 16218.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.043847 restraints weight = 13675.807| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9418 Z= 0.157 Angle : 0.729 8.275 13466 Z= 0.417 Chirality : 0.047 0.277 1561 Planarity : 0.005 0.049 1049 Dihedral : 32.891 144.877 2656 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.84 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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: 0.51 (0.33), residues: 641 helix: 1.25 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -1.88 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 76 TYR 0.012 0.002 TYR B 120 PHE 0.019 0.002 PHE A 76 TRP 0.003 0.001 TRP A 60 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.16 ( 9417) covalent geometry : angle 0.72893 / 0.42 (13464) SS BOND : bond 0.00250 / 0.13 ( 1) SS BOND : angle 0.83355 / 0.47 ( 2) hydrogen bonds : bond 0.04892 / 3.37 ( 563) hydrogen bonds : angle 3.54879 / 2.51 ( 1446) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASN cc_start: 0.9485 (m110) cc_final: 0.9201 (m-40) REVERT: A 46 ILE cc_start: 0.9295 (tp) cc_final: 0.9095 (tp) REVERT: A 60 TRP cc_start: 0.8839 (m100) cc_final: 0.8584 (m100) REVERT: A 75 ASP cc_start: 0.9408 (t0) cc_final: 0.9182 (m-30) REVERT: A 120 TYR cc_start: 0.9171 (t80) cc_final: 0.8843 (t80) REVERT: B 31 ASN cc_start: 0.9427 (m110) cc_final: 0.9131 (m-40) REVERT: B 99 ARG cc_start: 0.9193 (mmt180) cc_final: 0.8834 (mmt180) REVERT: B 120 TYR cc_start: 0.9104 (t80) cc_final: 0.8734 (t80) REVERT: B 126 MET cc_start: 0.7824 (ppp) cc_final: 0.7409 (ppp) REVERT: C 79 ILE cc_start: 0.8801 (pt) cc_final: 0.8472 (pt) REVERT: C 178 GLU cc_start: 0.8176 (pp20) cc_final: 0.7775 (pp20) REVERT: D 65 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8340 (tm-30) REVERT: D 69 LEU cc_start: 0.9106 (mt) cc_final: 0.8755 (mt) REVERT: D 143 ILE cc_start: 0.8931 (tp) cc_final: 0.8677 (tp) REVERT: D 185 LEU cc_start: 0.9725 (mm) cc_final: 0.9456 (tp) REVERT: D 210 MET cc_start: 0.8871 (tpt) cc_final: 0.8429 (tpt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0741 time to fit residues: 16.7405 Evaluate side-chains 122 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 62 optimal weight: 7.9990 chunk 78 optimal weight: 40.0000 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 79 optimal weight: 40.0000 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.040263 restraints weight = 56601.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.041569 restraints weight = 32253.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.042490 restraints weight = 22334.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.043079 restraints weight = 17423.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.043530 restraints weight = 14820.820| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9418 Z= 0.176 Angle : 0.726 8.527 13466 Z= 0.418 Chirality : 0.047 0.276 1561 Planarity : 0.005 0.045 1049 Dihedral : 32.809 145.610 2656 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.62 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.33), residues: 641 helix: 1.28 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -1.85 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 76 TYR 0.017 0.002 TYR D 193 PHE 0.018 0.002 PHE D 148 TRP 0.004 0.001 TRP A 60 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.18 ( 9417) covalent geometry : angle 0.72633 / 0.42 (13464) SS BOND : bond 0.00347 / 0.18 ( 1) SS BOND : angle 0.96913 / 0.54 ( 2) hydrogen bonds : bond 0.05121 / 3.55 ( 563) hydrogen bonds : angle 3.60058 / 2.54 ( 1446) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.262 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: A 46 ILE cc_start: 0.9299 (tp) cc_final: 0.9088 (tp) REVERT: A 60 TRP cc_start: 0.8859 (m100) cc_final: 0.8586 (m100) REVERT: A 120 TYR cc_start: 0.9264 (t80) cc_final: 0.8943 (t80) REVERT: B 28 THR cc_start: 0.9736 (p) cc_final: 0.9535 (p) REVERT: B 31 ASN cc_start: 0.9446 (m110) cc_final: 0.9154 (m-40) REVERT: B 43 GLN cc_start: 0.9665 (mm-40) cc_final: 0.9448 (mm-40) REVERT: B 120 TYR cc_start: 0.9106 (t80) cc_final: 0.8776 (t80) REVERT: B 126 MET cc_start: 0.7836 (ppp) cc_final: 0.7417 (ppp) REVERT: C 79 ILE cc_start: 0.8835 (pt) cc_final: 0.8545 (pt) REVERT: C 178 GLU cc_start: 0.8187 (pp20) cc_final: 0.7809 (pp20) REVERT: D 65 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8364 (tm-30) REVERT: D 69 LEU cc_start: 0.9095 (mt) cc_final: 0.8761 (mt) REVERT: D 210 MET cc_start: 0.8862 (tpt) cc_final: 0.8436 (tpt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.0860 time to fit residues: 19.1528 Evaluate side-chains 119 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 43 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.039987 restraints weight = 57504.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.041290 restraints weight = 32674.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.042208 restraints weight = 22565.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.042840 restraints weight = 17643.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.043232 restraints weight = 14966.647| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9418 Z= 0.192 Angle : 0.747 8.700 13466 Z= 0.426 Chirality : 0.047 0.274 1561 Planarity : 0.005 0.048 1049 Dihedral : 32.800 145.733 2656 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.24 % Favored : 93.29 % Rotamer: Outliers : 0.17 % Allowed : 1.92 % Favored : 97.91 % 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: 0.53 (0.33), residues: 641 helix: 1.25 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -1.80 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 149 TYR 0.017 0.002 TYR D 193 PHE 0.023 0.002 PHE D 148 TRP 0.004 0.001 TRP A 60 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.19 ( 9417) covalent geometry : angle 0.74679 / 0.43 (13464) SS BOND : bond 0.00275 / 0.14 ( 1) SS BOND : angle 0.94409 / 0.53 ( 2) hydrogen bonds : bond 0.05268 / 3.65 ( 563) hydrogen bonds : angle 3.66354 / 2.59 ( 1446) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 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: A 46 ILE cc_start: 0.9318 (tp) cc_final: 0.9093 (tp) REVERT: A 60 TRP cc_start: 0.8887 (m100) cc_final: 0.8619 (m100) REVERT: A 76 PHE cc_start: 0.8803 (m-80) cc_final: 0.8537 (m-10) REVERT: A 120 TYR cc_start: 0.9262 (t80) cc_final: 0.8966 (t80) REVERT: B 31 ASN cc_start: 0.9443 (m110) cc_final: 0.9186 (m110) REVERT: B 120 TYR cc_start: 0.9137 (t80) cc_final: 0.8749 (t80) REVERT: B 126 MET cc_start: 0.7870 (ppp) cc_final: 0.7469 (ppp) REVERT: C 79 ILE cc_start: 0.8824 (pt) cc_final: 0.8557 (pt) REVERT: C 89 GLU cc_start: 0.9176 (tp30) cc_final: 0.8975 (tp30) REVERT: D 33 GLN cc_start: 0.8980 (mp10) cc_final: 0.8764 (mp10) REVERT: D 65 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8386 (tm-30) REVERT: D 69 LEU cc_start: 0.9113 (mt) cc_final: 0.8766 (mt) REVERT: D 210 MET cc_start: 0.8851 (tpt) cc_final: 0.8422 (tpt) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.0873 time to fit residues: 19.3576 Evaluate side-chains 119 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 30.0000 chunk 7 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 40 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 71 optimal weight: 30.0000 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 60 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.055580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.039976 restraints weight = 56052.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.041275 restraints weight = 32143.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.042197 restraints weight = 22378.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.042818 restraints weight = 17515.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.043222 restraints weight = 14858.215| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9418 Z= 0.184 Angle : 0.748 8.510 13466 Z= 0.426 Chirality : 0.047 0.275 1561 Planarity : 0.005 0.062 1049 Dihedral : 32.788 145.463 2656 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.24 % Favored : 93.29 % Rotamer: Outliers : 0.17 % Allowed : 0.87 % Favored : 98.95 % 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: 0.53 (0.33), residues: 641 helix: 1.25 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -1.81 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 149 TYR 0.024 0.002 TYR D 193 PHE 0.025 0.002 PHE D 148 TRP 0.004 0.001 TRP A 60 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.18 ( 9417) covalent geometry : angle 0.74815 / 0.43 (13464) SS BOND : bond 0.00343 / 0.18 ( 1) SS BOND : angle 1.00681 / 0.57 ( 2) hydrogen bonds : bond 0.05151 / 3.58 ( 563) hydrogen bonds : angle 3.65501 / 2.58 ( 1446) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.280 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: A 46 ILE cc_start: 0.9321 (tp) cc_final: 0.9089 (tp) REVERT: A 60 TRP cc_start: 0.8898 (m100) cc_final: 0.8663 (m100) REVERT: A 76 PHE cc_start: 0.8851 (m-80) cc_final: 0.8549 (m-10) REVERT: A 120 TYR cc_start: 0.9262 (t80) cc_final: 0.8960 (t80) REVERT: B 31 ASN cc_start: 0.9448 (m110) cc_final: 0.9187 (m110) REVERT: B 120 TYR cc_start: 0.9105 (t80) cc_final: 0.8728 (t80) REVERT: B 126 MET cc_start: 0.7853 (ppp) cc_final: 0.7457 (ppp) REVERT: C 79 ILE cc_start: 0.8841 (pt) cc_final: 0.8608 (pt) REVERT: C 89 GLU cc_start: 0.9178 (tp30) cc_final: 0.8973 (tp30) REVERT: C 178 GLU cc_start: 0.8150 (pp20) cc_final: 0.7785 (pp20) REVERT: D 33 GLN cc_start: 0.8960 (mp10) cc_final: 0.8753 (mp10) REVERT: D 65 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8381 (tm-30) REVERT: D 69 LEU cc_start: 0.9099 (mt) cc_final: 0.8769 (mt) REVERT: D 189 LEU cc_start: 0.9663 (tt) cc_final: 0.9402 (tt) REVERT: D 210 MET cc_start: 0.8844 (tpt) cc_final: 0.8422 (tpt) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.0926 time to fit residues: 20.3081 Evaluate side-chains 114 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 40.0000 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.056253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.040641 restraints weight = 56147.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.041965 restraints weight = 32073.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.042901 restraints weight = 22258.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.043525 restraints weight = 17362.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.043922 restraints weight = 14782.468| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9418 Z= 0.159 Angle : 0.732 8.418 13466 Z= 0.415 Chirality : 0.047 0.282 1561 Planarity : 0.005 0.048 1049 Dihedral : 32.737 144.710 2656 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.46 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.33), residues: 641 helix: 1.31 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -1.84 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 13 TYR 0.023 0.002 TYR D 193 PHE 0.019 0.002 PHE D 148 TRP 0.003 0.001 TRP A 60 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 ( 9417) covalent geometry : angle 0.73154 / 0.42 (13464) SS BOND : bond 0.00340 / 0.18 ( 1) SS BOND : angle 0.92443 / 0.53 ( 2) hydrogen bonds : bond 0.04697 / 3.26 ( 563) hydrogen bonds : angle 3.51199 / 2.48 ( 1446) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1282 Ramachandran restraints generated. 641 Oldfield, 0 Emsley, 641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.8825 (tpt90) cc_final: 0.8595 (mtp85) REVERT: A 46 ILE cc_start: 0.9308 (tp) cc_final: 0.9073 (tp) REVERT: A 76 PHE cc_start: 0.8854 (m-80) cc_final: 0.8532 (m-10) REVERT: A 120 TYR cc_start: 0.9246 (t80) cc_final: 0.8936 (t80) REVERT: B 28 THR cc_start: 0.9716 (p) cc_final: 0.9508 (p) REVERT: B 31 ASN cc_start: 0.9432 (m110) cc_final: 0.9145 (m-40) REVERT: B 120 TYR cc_start: 0.9078 (t80) cc_final: 0.8730 (t80) REVERT: B 126 MET cc_start: 0.7823 (ppp) cc_final: 0.7430 (ppp) REVERT: C 178 GLU cc_start: 0.8125 (pp20) cc_final: 0.7756 (pp20) REVERT: D 33 GLN cc_start: 0.8965 (mp10) cc_final: 0.8741 (mp10) REVERT: D 65 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8338 (tm-30) REVERT: D 69 LEU cc_start: 0.9083 (mt) cc_final: 0.8751 (mt) REVERT: D 189 LEU cc_start: 0.9625 (tt) cc_final: 0.9370 (tt) REVERT: D 210 MET cc_start: 0.8805 (tpt) cc_final: 0.8459 (tpt) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0887 time to fit residues: 20.1287 Evaluate side-chains 118 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 40.0000 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 47 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 65 optimal weight: 30.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 43 GLN A 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.055955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.040477 restraints weight = 54960.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.041815 restraints weight = 31382.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.042749 restraints weight = 21694.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.043380 restraints weight = 16888.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.043733 restraints weight = 14288.824| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9418 Z= 0.160 Angle : 0.734 9.044 13466 Z= 0.415 Chirality : 0.047 0.282 1561 Planarity : 0.004 0.048 1049 Dihedral : 32.701 144.938 2656 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.77 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 0.61 (0.34), residues: 641 helix: 1.32 (0.24), residues: 448 sheet: None (None), residues: 0 loop : -1.80 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 13 TYR 0.024 0.002 TYR D 193 PHE 0.017 0.002 PHE D 148 TRP 0.002 0.001 TRP A 60 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 ( 9417) covalent geometry : angle 0.73369 / 0.41 (13464) SS BOND : bond 0.00343 / 0.18 ( 1) SS BOND : angle 0.92795 / 0.52 ( 2) hydrogen bonds : bond 0.04761 / 3.30 ( 563) hydrogen bonds : angle 3.52859 / 2.49 ( 1446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1911.10 seconds wall clock time: 33 minutes 31.48 seconds (2011.48 seconds total)