Starting phenix.real_space_refine on Wed Jul 1 22:47:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b33_44124/07_2026/9b33_44124.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b33_44124/07_2026/9b33_44124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b33_44124/07_2026/9b33_44124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b33_44124/07_2026/9b33_44124.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b33_44124/07_2026/9b33_44124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b33_44124/07_2026/9b33_44124.map" } resolution = 4.07 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= 0.002 sd= 0.015 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 Ca 2 9.91 5 Zn 2 6.06 5 S 4 5.16 5 C 2281 2.51 5 N 604 2.21 5 O 726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3619 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1806 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1809 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 225} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 0.91, per 1000 atoms: 0.25 Number of scatterers: 3619 At special positions: 0 Unit cell: (70.1324, 67.435, 93.0603, 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) Zn 2 29.99 Ca 2 19.99 S 4 16.00 O 726 8.00 N 604 7.00 C 2281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.22 Conformation dependent library (CDL) restraints added in 81.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 24 " 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 884 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.674A pdb=" N VAL E 5 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER E 94 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY E 92 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER E 215 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 95 " --> pdb=" O GLY E 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'E' and resid 49 through 52 Processing sheet with id=AA4, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.851A pdb=" N TYR E 77 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 154 through 155 Processing sheet with id=AA6, first strand: chain 'E' and resid 110 through 111 removed outlier: 3.517A pdb=" N PHE E 111 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 28 through 29 removed outlier: 3.685A pdb=" N SER F 94 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER F 215 " --> pdb=" O ARG F 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 24 through 26 Processing sheet with id=AA9, first strand: chain 'F' and resid 47 through 48 removed outlier: 3.583A pdb=" N PHE F 197 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLU F 192 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE F 111 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR F 194 " --> pdb=" O TRP F 109 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP F 109 " --> pdb=" O THR F 194 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR F 196 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE F 111 " --> pdb=" O PHE F 128 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE F 128 " --> pdb=" O PHE F 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 47 through 48 removed outlier: 3.583A pdb=" N PHE F 197 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLU F 192 " --> pdb=" O PHE F 111 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE F 111 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR F 194 " --> pdb=" O TRP F 109 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TRP F 109 " --> pdb=" O THR F 194 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR F 196 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 50 through 53 55 hydrogen bonds defined for protein. 123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.33 Time building geometry restraints manager: 0.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1083 1.33 - 1.45: 668 1.45 - 1.57: 1937 1.57 - 1.69: 3 1.69 - 1.81: 8 Bond restraints: 3699 Sorted by residual: bond pdb=" CA ASN F 14 " pdb=" CB ASN F 14 " ideal model delta sigma weight residual 1.524 1.424 0.099 1.37e-02 5.33e+03 5.27e+01 bond pdb=" C SER E 21 " pdb=" N TYR E 22 " ideal model delta sigma weight residual 1.327 1.261 0.066 1.39e-02 5.18e+03 2.25e+01 bond pdb=" C LEU F 85 " pdb=" N PRO F 86 " ideal model delta sigma weight residual 1.331 1.365 -0.033 1.21e-02 6.83e+03 7.54e+00 bond pdb=" CB ASN E 69 " pdb=" CG ASN E 69 " ideal model delta sigma weight residual 1.516 1.577 -0.061 2.50e-02 1.60e+03 5.92e+00 bond pdb=" CB ASN F 69 " pdb=" CG ASN F 69 " ideal model delta sigma weight residual 1.516 1.576 -0.060 2.50e-02 1.60e+03 5.69e+00 ... (remaining 3694 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 4956 4.68 - 9.37: 74 9.37 - 14.05: 11 14.05 - 18.73: 1 18.73 - 23.42: 2 Bond angle restraints: 5044 Sorted by residual: angle pdb=" N GLY E 48 " pdb=" CA GLY E 48 " pdb=" C GLY E 48 " ideal model delta sigma weight residual 113.18 136.60 -23.42 2.37e+00 1.78e-01 9.76e+01 angle pdb=" N GLY F 48 " pdb=" CA GLY F 48 " pdb=" C GLY F 48 " ideal model delta sigma weight residual 114.74 135.99 -21.25 2.54e+00 1.55e-01 7.00e+01 angle pdb=" C PRO E 68 " pdb=" N ASN E 69 " pdb=" CA ASN E 69 " ideal model delta sigma weight residual 122.74 133.62 -10.88 1.44e+00 4.82e-01 5.71e+01 angle pdb=" C PRO F 68 " pdb=" N ASN F 69 " pdb=" CA ASN F 69 " ideal model delta sigma weight residual 123.93 135.01 -11.08 1.54e+00 4.22e-01 5.18e+01 angle pdb=" N ALA F 207 " pdb=" CA ALA F 207 " pdb=" C ALA F 207 " ideal model delta sigma weight residual 107.28 117.92 -10.64 1.75e+00 3.27e-01 3.69e+01 ... (remaining 5039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 1985 15.13 - 30.26: 133 30.26 - 45.39: 48 45.39 - 60.52: 12 60.52 - 75.64: 4 Dihedral angle restraints: 2182 sinusoidal: 812 harmonic: 1370 Sorted by residual: dihedral pdb=" CA ALA E 207 " pdb=" C ALA E 207 " pdb=" N ASP E 208 " pdb=" CA ASP E 208 " ideal model delta harmonic sigma weight residual 180.00 115.63 64.37 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" CA SER F 185 " pdb=" C SER F 185 " pdb=" N ALA F 186 " pdb=" CA ALA F 186 " ideal model delta harmonic sigma weight residual -180.00 -118.77 -61.23 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA VAL E 47 " pdb=" C VAL E 47 " pdb=" N GLY E 48 " pdb=" CA GLY E 48 " ideal model delta harmonic sigma weight residual 180.00 120.27 59.73 0 5.00e+00 4.00e-02 1.43e+02 ... (remaining 2179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 422 0.069 - 0.138: 119 0.138 - 0.207: 28 0.207 - 0.276: 5 0.276 - 0.344: 6 Chirality restraints: 580 Sorted by residual: chirality pdb=" CB VAL F 187 " pdb=" CA VAL F 187 " pdb=" CG1 VAL F 187 " pdb=" CG2 VAL F 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CB VAL E 187 " pdb=" CA VAL E 187 " pdb=" CG1 VAL E 187 " pdb=" CG2 VAL E 187 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CB VAL E 159 " pdb=" CA VAL E 159 " pdb=" CG1 VAL E 159 " pdb=" CG2 VAL E 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 577 not shown) Planarity restraints: 651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 177 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO F 178 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO F 178 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 178 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 177 " -0.048 5.00e-02 4.00e+02 7.35e-02 8.65e+00 pdb=" N PRO E 178 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO E 178 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 178 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 130 " 0.017 2.00e-02 2.50e+03 2.17e-02 8.21e+00 pdb=" CG PHE E 130 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE E 130 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE E 130 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 130 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 130 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE E 130 " -0.014 2.00e-02 2.50e+03 ... (remaining 648 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 182 2.69 - 3.24: 3514 3.24 - 3.80: 5946 3.80 - 4.35: 7507 4.35 - 4.90: 12463 Nonbonded interactions: 29612 Sorted by model distance: nonbonded pdb=" OD2 ASP E 10 " pdb="ZN ZN E1001 " model vdw 2.141 2.230 nonbonded pdb=" OD2 ASP F 19 " pdb="ZN ZN F1001 " model vdw 2.153 2.230 nonbonded pdb=" OE1 GLU F 8 " pdb="ZN ZN F1001 " model vdw 2.172 2.230 nonbonded pdb=" OG1 THR F 97 " pdb=" O TYR F 100 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASP F 10 " pdb="ZN ZN F1001 " model vdw 2.255 2.230 ... (remaining 29607 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 'E' selection = (chain 'F' and (resid 1 through 144 or (resid 145 through 146 and (name N or nam \ e CA or name C or name O or name CB )) or resid 147 through 1002)) } 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 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 : 0.007 0.099 3700 Z= 0.386 Angle : 1.560 23.418 5044 Z= 0.849 Chirality : 0.076 0.344 580 Planarity : 0.010 0.088 651 Dihedral : 13.121 75.644 1298 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 1.49 % Allowed : 23.19 % Favored : 75.32 % Rotamer: Outliers : 0.49 % Allowed : 4.94 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 3.78 % 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: -6.09 (0.29), residues: 470 helix: None (None), residues: 0 sheet: -4.52 (0.35), residues: 138 loop : -4.12 (0.25), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG F 60 TYR 0.042 0.005 TYR E 176 PHE 0.047 0.006 PHE F 130 TRP 0.042 0.008 TRP E 182 HIS 0.008 0.002 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00713 / 0.39 ( 3699) covalent geometry : angle 1.55983 / 0.85 ( 5044) hydrogen bonds : bond 0.30435 / 21.29 ( 51) hydrogen bonds : angle 14.50618 / 10.33 ( 123) metal coordination : bond 0.02331 / 1.23 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 ILE cc_start: 0.7825 (pt) cc_final: 0.7491 (mp) REVERT: E 39 LYS cc_start: 0.8846 (tttt) cc_final: 0.8333 (tptp) REVERT: E 40 TRP cc_start: 0.8120 (t60) cc_final: 0.7913 (t60) REVERT: E 53 ILE cc_start: 0.7885 (pp) cc_final: 0.7357 (pt) REVERT: E 60 ARG cc_start: 0.7374 (mmm160) cc_final: 0.6917 (mmm-85) REVERT: E 133 PHE cc_start: 0.6780 (m-80) cc_final: 0.6445 (m-10) REVERT: E 213 PHE cc_start: 0.7632 (p90) cc_final: 0.7422 (p90) REVERT: F 16 ASP cc_start: 0.7385 (m-30) cc_final: 0.7002 (m-30) REVERT: F 17 ILE cc_start: 0.8285 (pt) cc_final: 0.8039 (mm) REVERT: F 93 LEU cc_start: 0.8459 (mt) cc_final: 0.8083 (mp) REVERT: F 100 TYR cc_start: 0.7322 (m-10) cc_final: 0.6877 (m-80) REVERT: F 106 ILE cc_start: 0.8591 (mm) cc_final: 0.8248 (mt) REVERT: F 139 ASP cc_start: 0.7908 (p0) cc_final: 0.7701 (p0) REVERT: F 170 VAL cc_start: 0.6780 (p) cc_final: 0.6148 (t) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.0660 time to fit residues: 14.0710 Evaluate side-chains 125 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 14 ASN E 41 ASN ** E 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 ASN F 166 GLN ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.165171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.140434 restraints weight = 7751.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.144370 restraints weight = 4884.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.147289 restraints weight = 3540.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.149371 restraints weight = 2775.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.150868 restraints weight = 2306.307| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3700 Z= 0.187 Angle : 1.041 16.446 5044 Z= 0.534 Chirality : 0.055 0.291 580 Planarity : 0.006 0.068 651 Dihedral : 11.398 55.142 500 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 1.28 % Allowed : 19.15 % Favored : 79.57 % Rotamer: Outliers : 0.49 % Allowed : 4.44 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.00 % 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: -5.62 (0.31), residues: 470 helix: None (None), residues: 0 sheet: -3.98 (0.33), residues: 166 loop : -3.77 (0.28), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 172 TYR 0.013 0.002 TYR F 67 PHE 0.032 0.003 PHE F 130 TRP 0.030 0.003 TRP F 182 HIS 0.008 0.001 HIS F 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 ( 3699) covalent geometry : angle 1.04059 / 0.53 ( 5044) hydrogen bonds : bond 0.04831 / 3.35 ( 51) hydrogen bonds : angle 9.05109 / 6.34 ( 123) metal coordination : bond 0.00213 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.7529 (t-90) cc_final: 0.7148 (t70) REVERT: E 60 ARG cc_start: 0.7902 (mmm160) cc_final: 0.7693 (mmm-85) REVERT: E 90 ARG cc_start: 0.7458 (mtp180) cc_final: 0.6787 (mmm-85) REVERT: E 138 LYS cc_start: 0.7582 (mtmt) cc_final: 0.7015 (mtmm) REVERT: E 140 LEU cc_start: 0.8505 (mt) cc_final: 0.8168 (mt) REVERT: E 174 LEU cc_start: 0.7708 (mp) cc_final: 0.7350 (mp) REVERT: E 176 TYR cc_start: 0.7972 (t80) cc_final: 0.7016 (t80) REVERT: F 16 ASP cc_start: 0.6736 (m-30) cc_final: 0.6448 (m-30) REVERT: F 27 ILE cc_start: 0.7704 (tt) cc_final: 0.7394 (mt) REVERT: F 79 VAL cc_start: 0.7949 (t) cc_final: 0.7666 (t) REVERT: F 93 LEU cc_start: 0.8619 (mt) cc_final: 0.8324 (mp) REVERT: F 126 LEU cc_start: 0.8244 (tp) cc_final: 0.7878 (tp) REVERT: F 130 PHE cc_start: 0.7612 (m-80) cc_final: 0.7402 (m-80) REVERT: F 139 ASP cc_start: 0.7875 (p0) cc_final: 0.7663 (p0) REVERT: F 176 TYR cc_start: 0.8407 (t80) cc_final: 0.7549 (t80) outliers start: 2 outliers final: 0 residues processed: 150 average time/residue: 0.0600 time to fit residues: 11.0268 Evaluate side-chains 124 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 41 ASN E 51 HIS F 51 HIS F 180 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.165169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.139816 restraints weight = 7786.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.143543 restraints weight = 5123.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.146296 restraints weight = 3787.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.148383 restraints weight = 3027.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.149854 restraints weight = 2538.126| |-----------------------------------------------------------------------------| r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3700 Z= 0.160 Angle : 0.944 15.069 5044 Z= 0.482 Chirality : 0.056 0.311 580 Planarity : 0.006 0.065 651 Dihedral : 10.629 55.205 500 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 1.28 % Allowed : 22.13 % Favored : 76.60 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.78 % 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: -5.35 (0.32), residues: 470 helix: None (None), residues: 0 sheet: -3.72 (0.34), residues: 164 loop : -3.64 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 172 TYR 0.013 0.002 TYR E 54 PHE 0.022 0.003 PHE E 130 TRP 0.025 0.003 TRP F 40 HIS 0.002 0.001 HIS F 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 3699) covalent geometry : angle 0.94405 / 0.48 ( 5044) hydrogen bonds : bond 0.03923 / 2.83 ( 51) hydrogen bonds : angle 8.52371 / 6.02 ( 123) metal coordination : bond 0.00168 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 ILE cc_start: 0.8806 (pt) cc_final: 0.8436 (pt) REVERT: E 60 ARG cc_start: 0.7836 (mmm160) cc_final: 0.7277 (mmm-85) REVERT: E 78 ASP cc_start: 0.8327 (m-30) cc_final: 0.8002 (p0) REVERT: E 90 ARG cc_start: 0.7438 (mtp180) cc_final: 0.6966 (mmm-85) REVERT: E 104 ASN cc_start: 0.7798 (m-40) cc_final: 0.6925 (p0) REVERT: E 140 LEU cc_start: 0.8596 (mt) cc_final: 0.8335 (mt) REVERT: E 174 LEU cc_start: 0.7748 (mp) cc_final: 0.7521 (mp) REVERT: E 176 TYR cc_start: 0.7828 (t80) cc_final: 0.7074 (t80) REVERT: E 197 PHE cc_start: 0.8785 (p90) cc_final: 0.8501 (p90) REVERT: F 16 ASP cc_start: 0.7515 (m-30) cc_final: 0.7296 (m-30) REVERT: F 67 TYR cc_start: 0.5662 (m-80) cc_final: 0.5199 (m-80) REVERT: F 126 LEU cc_start: 0.8234 (tp) cc_final: 0.7912 (tp) REVERT: F 176 TYR cc_start: 0.8550 (t80) cc_final: 0.7951 (t80) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0663 time to fit residues: 11.1894 Evaluate side-chains 110 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 0.0040 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 41 ASN ** E 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.164206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.139561 restraints weight = 7697.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.143434 restraints weight = 5024.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.146286 restraints weight = 3690.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.148195 restraints weight = 2925.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.149716 restraints weight = 2470.274| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.5999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3700 Z= 0.161 Angle : 0.898 13.509 5044 Z= 0.465 Chirality : 0.054 0.262 580 Planarity : 0.006 0.052 651 Dihedral : 10.206 51.107 500 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 1.28 % Allowed : 21.06 % Favored : 77.66 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.56 % 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: -5.17 (0.32), residues: 470 helix: None (None), residues: 0 sheet: -3.49 (0.36), residues: 156 loop : -3.60 (0.29), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 158 TYR 0.009 0.001 TYR E 54 PHE 0.030 0.003 PHE F 130 TRP 0.023 0.002 TRP F 40 HIS 0.003 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 3699) covalent geometry : angle 0.89837 / 0.47 ( 5044) hydrogen bonds : bond 0.03396 / 2.45 ( 51) hydrogen bonds : angle 8.62151 / 6.01 ( 123) metal coordination : bond 0.00184 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 ILE cc_start: 0.8793 (pt) cc_final: 0.8584 (pt) REVERT: E 53 ILE cc_start: 0.8641 (mt) cc_final: 0.8334 (mt) REVERT: E 60 ARG cc_start: 0.7841 (mmm160) cc_final: 0.7296 (mmm-85) REVERT: E 78 ASP cc_start: 0.8149 (m-30) cc_final: 0.7858 (p0) REVERT: E 90 ARG cc_start: 0.7517 (mtp180) cc_final: 0.6714 (mmm-85) REVERT: E 104 ASN cc_start: 0.7991 (m-40) cc_final: 0.7100 (p0) REVERT: E 140 LEU cc_start: 0.8345 (mt) cc_final: 0.8075 (mt) REVERT: E 192 GLU cc_start: 0.7840 (tp30) cc_final: 0.7493 (tp30) REVERT: F 7 VAL cc_start: 0.7520 (t) cc_final: 0.7253 (t) REVERT: F 42 MET cc_start: 0.1580 (mmp) cc_final: 0.0936 (mmp) REVERT: F 107 LEU cc_start: 0.8527 (mm) cc_final: 0.8224 (mm) REVERT: F 126 LEU cc_start: 0.8232 (tp) cc_final: 0.7975 (tp) REVERT: F 176 TYR cc_start: 0.8541 (t80) cc_final: 0.8196 (t80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0682 time to fit residues: 10.9003 Evaluate side-chains 109 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.0010 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 41 ASN F 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.160106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.135558 restraints weight = 7832.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.139340 restraints weight = 5023.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.142197 restraints weight = 3690.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.143684 restraints weight = 2907.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.145430 restraints weight = 2496.592| |-----------------------------------------------------------------------------| r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3700 Z= 0.181 Angle : 0.891 12.645 5044 Z= 0.464 Chirality : 0.054 0.290 580 Planarity : 0.006 0.049 651 Dihedral : 10.081 49.875 500 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 1.06 % Allowed : 21.49 % Favored : 77.45 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.56 % 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: -5.17 (0.32), residues: 470 helix: None (None), residues: 0 sheet: -3.35 (0.37), residues: 154 loop : -3.70 (0.28), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 172 TYR 0.012 0.002 TYR E 54 PHE 0.017 0.003 PHE F 233 TRP 0.025 0.002 TRP E 182 HIS 0.003 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 3699) covalent geometry : angle 0.89072 / 0.46 ( 5044) hydrogen bonds : bond 0.03320 / 2.31 ( 51) hydrogen bonds : angle 8.55873 / 6.01 ( 123) metal coordination : bond 0.00278 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 ARG cc_start: 0.7654 (mmm160) cc_final: 0.7142 (mmm-85) REVERT: E 78 ASP cc_start: 0.8166 (m-30) cc_final: 0.7844 (p0) REVERT: E 104 ASN cc_start: 0.8050 (m-40) cc_final: 0.7127 (p0) REVERT: E 140 LEU cc_start: 0.8392 (mt) cc_final: 0.8079 (mt) REVERT: E 154 LEU cc_start: 0.8577 (tp) cc_final: 0.8341 (tp) REVERT: E 176 TYR cc_start: 0.8219 (t80) cc_final: 0.7887 (t80) REVERT: E 197 PHE cc_start: 0.8963 (p90) cc_final: 0.8573 (p90) REVERT: F 7 VAL cc_start: 0.7666 (t) cc_final: 0.7374 (t) REVERT: F 103 THR cc_start: 0.7187 (m) cc_final: 0.6949 (m) REVERT: F 107 LEU cc_start: 0.8657 (mm) cc_final: 0.8332 (mm) REVERT: F 174 LEU cc_start: 0.8857 (mp) cc_final: 0.8566 (mp) REVERT: F 176 TYR cc_start: 0.8643 (t80) cc_final: 0.8421 (t80) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0594 time to fit residues: 9.5971 Evaluate side-chains 113 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 41 ASN E 124 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.151101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.126927 restraints weight = 7892.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.130704 restraints weight = 4923.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.133346 restraints weight = 3568.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.135220 restraints weight = 2822.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.136580 restraints weight = 2363.848| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.7688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 3700 Z= 0.243 Angle : 0.973 11.917 5044 Z= 0.505 Chirality : 0.057 0.268 580 Planarity : 0.006 0.049 651 Dihedral : 10.264 48.993 500 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.85 % Allowed : 24.04 % Favored : 75.11 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.56 % 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: -5.24 (0.32), residues: 470 helix: None (None), residues: 0 sheet: -3.33 (0.37), residues: 154 loop : -3.79 (0.28), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 90 TYR 0.016 0.002 TYR E 54 PHE 0.017 0.003 PHE F 213 TRP 0.039 0.003 TRP F 40 HIS 0.005 0.002 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 ( 3699) covalent geometry : angle 0.97263 / 0.50 ( 5044) hydrogen bonds : bond 0.03682 / 2.44 ( 51) hydrogen bonds : angle 9.11914 / 6.34 ( 123) metal coordination : bond 0.00353 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.143 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: E 25 ILE cc_start: 0.8165 (tt) cc_final: 0.7861 (tt) REVERT: E 40 TRP cc_start: 0.7788 (t60) cc_final: 0.6972 (t60) REVERT: E 60 ARG cc_start: 0.7823 (mmm160) cc_final: 0.7140 (mmm-85) REVERT: E 67 TYR cc_start: 0.6579 (m-80) cc_final: 0.5990 (m-80) REVERT: E 78 ASP cc_start: 0.8169 (m-30) cc_final: 0.7864 (p0) REVERT: E 93 LEU cc_start: 0.7778 (mt) cc_final: 0.7576 (mm) REVERT: E 104 ASN cc_start: 0.7787 (m-40) cc_final: 0.6970 (p0) REVERT: E 128 PHE cc_start: 0.8788 (p90) cc_final: 0.8551 (p90) REVERT: E 140 LEU cc_start: 0.8499 (mt) cc_final: 0.8210 (mt) REVERT: E 154 LEU cc_start: 0.8732 (tp) cc_final: 0.8527 (tp) REVERT: E 166 GLN cc_start: 0.7020 (mp10) cc_final: 0.6297 (mp10) REVERT: E 198 LEU cc_start: 0.8760 (tp) cc_final: 0.8518 (tp) REVERT: E 213 PHE cc_start: 0.8573 (p90) cc_final: 0.8139 (p90) REVERT: F 7 VAL cc_start: 0.7917 (t) cc_final: 0.7680 (t) REVERT: F 136 ASP cc_start: 0.7786 (t70) cc_final: 0.7407 (t0) REVERT: F 175 PHE cc_start: 0.8405 (t80) cc_final: 0.7925 (t80) REVERT: F 213 PHE cc_start: 0.8760 (p90) cc_final: 0.8427 (p90) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0544 time to fit residues: 8.9544 Evaluate side-chains 114 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 41 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.156957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.133660 restraints weight = 7874.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.137589 restraints weight = 4821.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.140325 restraints weight = 3447.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.142312 restraints weight = 2688.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.143580 restraints weight = 2224.585| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.8030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3700 Z= 0.160 Angle : 0.877 12.351 5044 Z= 0.456 Chirality : 0.054 0.279 580 Planarity : 0.006 0.056 651 Dihedral : 9.707 44.799 500 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.85 % Allowed : 21.91 % Favored : 77.23 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.33 % 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: -5.09 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -3.07 (0.39), residues: 154 loop : -3.78 (0.28), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 172 TYR 0.015 0.002 TYR E 54 PHE 0.017 0.003 PHE E 212 TRP 0.015 0.001 TRP E 182 HIS 0.005 0.001 HIS F 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 ( 3699) covalent geometry : angle 0.87743 / 0.46 ( 5044) hydrogen bonds : bond 0.03286 / 2.17 ( 51) hydrogen bonds : angle 8.89103 / 6.19 ( 123) metal coordination : bond 0.00209 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.141 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: E 2 ASP cc_start: 0.8484 (p0) cc_final: 0.8265 (p0) REVERT: E 78 ASP cc_start: 0.8060 (m-30) cc_final: 0.7688 (p0) REVERT: E 104 ASN cc_start: 0.7550 (m-40) cc_final: 0.6864 (p0) REVERT: E 128 PHE cc_start: 0.8778 (p90) cc_final: 0.8538 (p90) REVERT: F 7 VAL cc_start: 0.7987 (t) cc_final: 0.7773 (t) REVERT: F 42 MET cc_start: 0.4321 (mmm) cc_final: 0.3494 (mmm) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0557 time to fit residues: 8.8243 Evaluate side-chains 98 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 4.9990 chunk 45 optimal weight: 0.0870 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 41 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.153741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.130056 restraints weight = 7879.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.133838 restraints weight = 4951.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.136525 restraints weight = 3556.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.138559 restraints weight = 2788.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.139831 restraints weight = 2304.690| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.8376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3700 Z= 0.190 Angle : 0.913 12.950 5044 Z= 0.472 Chirality : 0.055 0.352 580 Planarity : 0.006 0.057 651 Dihedral : 9.672 44.649 500 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 1.28 % Allowed : 23.19 % Favored : 75.53 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.89 % 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: -5.02 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -2.93 (0.40), residues: 154 loop : -3.79 (0.29), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 228 TYR 0.015 0.002 TYR E 176 PHE 0.019 0.003 PHE E 191 TRP 0.016 0.002 TRP E 109 HIS 0.006 0.002 HIS F 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.19 ( 3699) covalent geometry : angle 0.91253 / 0.47 ( 5044) hydrogen bonds : bond 0.03145 / 2.04 ( 51) hydrogen bonds : angle 9.06625 / 6.31 ( 123) metal coordination : bond 0.00209 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ASP cc_start: 0.8457 (p0) cc_final: 0.8214 (p0) REVERT: E 14 ASN cc_start: 0.6642 (m-40) cc_final: 0.6126 (m-40) REVERT: E 54 TYR cc_start: 0.8256 (t80) cc_final: 0.7666 (t80) REVERT: E 78 ASP cc_start: 0.8094 (m-30) cc_final: 0.7770 (p0) REVERT: E 104 ASN cc_start: 0.7537 (m-40) cc_final: 0.7045 (p0) REVERT: E 130 PHE cc_start: 0.7352 (m-10) cc_final: 0.6858 (m-10) REVERT: E 140 LEU cc_start: 0.8635 (mt) cc_final: 0.8217 (mt) REVERT: E 175 PHE cc_start: 0.8023 (t80) cc_final: 0.7467 (t80) REVERT: F 40 TRP cc_start: 0.5059 (t60) cc_final: 0.4640 (t60) REVERT: F 126 LEU cc_start: 0.8629 (tp) cc_final: 0.8416 (tp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0470 time to fit residues: 7.6941 Evaluate side-chains 111 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 44 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 121 HIS ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.156518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.133070 restraints weight = 7758.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.136945 restraints weight = 4863.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.139696 restraints weight = 3496.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.141506 restraints weight = 2727.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.142991 restraints weight = 2276.885| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.8774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3700 Z= 0.167 Angle : 0.894 12.314 5044 Z= 0.463 Chirality : 0.056 0.310 580 Planarity : 0.005 0.052 651 Dihedral : 9.493 42.890 500 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 1.06 % Allowed : 21.91 % Favored : 77.02 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.11 % 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: -4.89 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -2.71 (0.42), residues: 150 loop : -3.78 (0.28), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E 158 TYR 0.012 0.001 TYR F 176 PHE 0.020 0.003 PHE E 195 TRP 0.022 0.002 TRP F 40 HIS 0.004 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 3699) covalent geometry : angle 0.89363 / 0.46 ( 5044) hydrogen bonds : bond 0.03126 / 2.05 ( 51) hydrogen bonds : angle 8.97826 / 6.36 ( 123) metal coordination : bond 0.00179 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.085 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: E 14 ASN cc_start: 0.6542 (m-40) cc_final: 0.6100 (m-40) REVERT: E 51 HIS cc_start: 0.8264 (t70) cc_final: 0.8018 (t70) REVERT: E 54 TYR cc_start: 0.8127 (t80) cc_final: 0.7450 (t80) REVERT: E 78 ASP cc_start: 0.8023 (m-30) cc_final: 0.7719 (p0) REVERT: E 104 ASN cc_start: 0.7701 (m-40) cc_final: 0.6737 (p0) REVERT: E 111 PHE cc_start: 0.8086 (t80) cc_final: 0.7821 (t80) REVERT: E 128 PHE cc_start: 0.8674 (p90) cc_final: 0.7879 (p90) REVERT: E 140 LEU cc_start: 0.8664 (mt) cc_final: 0.8222 (mt) REVERT: E 154 LEU cc_start: 0.8537 (tp) cc_final: 0.8331 (tp) REVERT: F 40 TRP cc_start: 0.5207 (t60) cc_final: 0.4752 (t60) REVERT: F 93 LEU cc_start: 0.8639 (mp) cc_final: 0.8066 (mp) REVERT: F 126 LEU cc_start: 0.8718 (tp) cc_final: 0.8464 (tp) REVERT: F 172 ARG cc_start: 0.7462 (mmm-85) cc_final: 0.6870 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0545 time to fit residues: 8.6427 Evaluate side-chains 107 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 9 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.0470 chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.159549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.135390 restraints weight = 7928.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.139391 restraints weight = 5031.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.142128 restraints weight = 3624.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.144126 restraints weight = 2847.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.145483 restraints weight = 2371.497| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.9103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3700 Z= 0.157 Angle : 0.906 13.698 5044 Z= 0.463 Chirality : 0.057 0.330 580 Planarity : 0.005 0.049 651 Dihedral : 9.200 42.336 500 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 1.06 % Allowed : 21.06 % Favored : 77.87 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.67 % 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: -4.77 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -2.41 (0.44), residues: 146 loop : -3.82 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 90 TYR 0.009 0.001 TYR E 176 PHE 0.018 0.003 PHE E 212 TRP 0.024 0.002 TRP F 40 HIS 0.003 0.001 HIS E 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 3699) covalent geometry : angle 0.90589 / 0.46 ( 5044) hydrogen bonds : bond 0.03092 / 2.06 ( 51) hydrogen bonds : angle 8.93246 / 6.31 ( 123) metal coordination : bond 0.00119 / 0.06 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 940 Ramachandran restraints generated. 470 Oldfield, 0 Emsley, 470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 54 TYR cc_start: 0.8129 (t80) cc_final: 0.7611 (t80) REVERT: E 78 ASP cc_start: 0.7844 (m-30) cc_final: 0.7624 (p0) REVERT: E 104 ASN cc_start: 0.7730 (m-40) cc_final: 0.6773 (p0) REVERT: E 128 PHE cc_start: 0.8417 (p90) cc_final: 0.7766 (p90) REVERT: E 140 LEU cc_start: 0.8322 (mt) cc_final: 0.7707 (mt) REVERT: E 154 LEU cc_start: 0.8551 (tp) cc_final: 0.8318 (tp) REVERT: E 198 LEU cc_start: 0.8602 (tp) cc_final: 0.8378 (tp) REVERT: F 7 VAL cc_start: 0.7964 (t) cc_final: 0.7727 (t) REVERT: F 40 TRP cc_start: 0.5113 (t60) cc_final: 0.4685 (t60) REVERT: F 93 LEU cc_start: 0.8569 (mp) cc_final: 0.7857 (mp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0606 time to fit residues: 9.6628 Evaluate side-chains 105 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 0.0570 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 38 optimal weight: 0.0070 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 43 GLN F 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.160862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.136531 restraints weight = 7669.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.140424 restraints weight = 4854.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.143303 restraints weight = 3525.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.145223 restraints weight = 2757.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.146854 restraints weight = 2301.585| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.9321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3700 Z= 0.149 Angle : 0.876 12.231 5044 Z= 0.445 Chirality : 0.055 0.317 580 Planarity : 0.005 0.048 651 Dihedral : 9.002 42.229 500 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 1.06 % Allowed : 22.77 % Favored : 76.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.67 % 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: -4.60 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -2.04 (0.50), residues: 116 loop : -3.75 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 172 TYR 0.007 0.001 TYR E 67 PHE 0.021 0.003 PHE E 195 TRP 0.028 0.003 TRP E 109 HIS 0.003 0.001 HIS E 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 3699) covalent geometry : angle 0.87635 / 0.44 ( 5044) hydrogen bonds : bond 0.03154 / 2.14 ( 51) hydrogen bonds : angle 8.81142 / 6.24 ( 123) metal coordination : bond 0.00084 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 840.85 seconds wall clock time: 15 minutes 4.61 seconds (904.61 seconds total)