Starting phenix.real_space_refine on Mon Jan 13 19:19:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b33_44124/01_2025/9b33_44124.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b33_44124/01_2025/9b33_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b33_44124/01_2025/9b33_44124.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b33_44124/01_2025/9b33_44124.map" model { file = "/net/cci-nas-00/data/ceres_data/9b33_44124/01_2025/9b33_44124.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b33_44124/01_2025/9b33_44124.cif" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.80, per 1000 atoms: 0.77 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: 0.87 Conformation dependent library (CDL) restraints added in 404.3 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: 0.34 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: 0.81 Time building geometry restraints manager: 1.01 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 237 or resid 1001 th \ rough 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: 0.780 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.720 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6344 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 3699 Z= 0.476 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.042 0.008 TRP E 182 HIS 0.008 0.002 HIS F 24 PHE 0.047 0.006 PHE F 130 TYR 0.042 0.005 TYR E 176 ARG 0.013 0.002 ARG F 60 *********************** 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 : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 ILE cc_start: 0.7824 (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: 0.7386 (m-30) cc_final: 0.7002 (m-30) REVERT: F 17 ILE cc_start: 0.8285 (pt) cc_final: 0.8038 (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: 0.7909 (p0) cc_final: 0.7700 (p0) REVERT: F 170 VAL cc_start: 0.6780 (p) cc_final: 0.6147 (t) outliers start: 2 outliers final: 0 residues processed: 175 average time/residue: 0.1713 time to fit residues: 35.7321 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 : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 0.0970 chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 ASN E 41 ASN ** E 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 166 GLN ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.166826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.142812 restraints weight = 7708.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.146760 restraints weight = 4845.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.149719 restraints weight = 3479.327| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3699 Z= 0.249 Angle : 1.028 16.424 5044 Z= 0.527 Chirality : 0.055 0.277 580 Planarity : 0.006 0.068 651 Dihedral : 11.255 54.648 500 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 1.28 % Allowed : 19.36 % Favored : 79.36 % Rotamer: Outliers : 0.49 % Allowed : 4.20 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.31), residues: 470 helix: None (None), residues: 0 sheet: -3.96 (0.33), residues: 166 loop : -3.75 (0.28), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 182 HIS 0.009 0.001 HIS F 180 PHE 0.031 0.003 PHE F 130 TYR 0.012 0.002 TYR F 54 ARG 0.005 0.001 ARG F 172 *********************** 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 152 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.323 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 40 TRP cc_start: 0.7494 (t60) cc_final: 0.7256 (t60) REVERT: E 51 HIS cc_start: 0.7566 (t-90) cc_final: 0.7053 (t70) REVERT: E 60 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7729 (mmm-85) REVERT: E 79 VAL cc_start: 0.8477 (p) cc_final: 0.8158 (p) REVERT: E 81 LEU cc_start: 0.8245 (mm) cc_final: 0.7952 (mm) REVERT: E 90 ARG cc_start: 0.7347 (mtp180) cc_final: 0.6770 (mmm-85) REVERT: E 138 LYS cc_start: 0.7451 (mtmt) cc_final: 0.6920 (mtmm) REVERT: E 140 LEU cc_start: 0.8440 (mt) cc_final: 0.8114 (mt) REVERT: E 174 LEU cc_start: 0.7646 (mp) cc_final: 0.7230 (mp) REVERT: E 176 TYR cc_start: 0.7826 (t80) cc_final: 0.6878 (t80) REVERT: F 16 ASP cc_start: 0.6631 (m-30) cc_final: 0.6326 (m-30) REVERT: F 27 ILE cc_start: 0.7663 (tt) cc_final: 0.7389 (mt) REVERT: F 93 LEU cc_start: 0.8602 (mt) cc_final: 0.8324 (mp) REVERT: F 126 LEU cc_start: 0.8194 (tp) cc_final: 0.7693 (tp) REVERT: F 176 TYR cc_start: 0.8377 (t80) cc_final: 0.7451 (t80) REVERT: F 213 PHE cc_start: 0.7944 (p90) cc_final: 0.7736 (p90) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.1654 time to fit residues: 30.0757 Evaluate side-chains 117 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 6 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS ** F 180 HIS ** 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 = 0.4223 r_free = 0.4223 target = 0.158490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.134081 restraints weight = 8015.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.137651 restraints weight = 5206.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.140274 restraints weight = 3857.421| |-----------------------------------------------------------------------------| r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3699 Z= 0.294 Angle : 1.003 16.235 5044 Z= 0.512 Chirality : 0.057 0.317 580 Planarity : 0.007 0.058 651 Dihedral : 11.039 58.224 500 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.85 % Allowed : 23.83 % Favored : 75.32 % 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 : 3.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.40 (0.32), residues: 470 helix: None (None), residues: 0 sheet: -3.80 (0.34), residues: 166 loop : -3.63 (0.29), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP F 182 HIS 0.005 0.002 HIS F 127 PHE 0.016 0.003 PHE F 111 TYR 0.012 0.002 TYR F 67 ARG 0.005 0.001 ARG F 172 *********************** 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 138 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.427 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 60 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7061 (mmm-85) REVERT: E 78 ASP cc_start: 0.8427 (m-30) cc_final: 0.8065 (p0) REVERT: E 103 THR cc_start: 0.7463 (m) cc_final: 0.6656 (m) REVERT: E 104 ASN cc_start: 0.7919 (m-40) cc_final: 0.7033 (p0) REVERT: E 154 LEU cc_start: 0.8680 (tp) cc_final: 0.8457 (tp) REVERT: E 176 TYR cc_start: 0.8214 (t80) cc_final: 0.7549 (t80) REVERT: F 93 LEU cc_start: 0.8804 (mt) cc_final: 0.8300 (mp) REVERT: F 126 LEU cc_start: 0.8299 (tp) cc_final: 0.8067 (tp) REVERT: F 176 TYR cc_start: 0.8465 (t80) cc_final: 0.7965 (t80) REVERT: F 208 ASP cc_start: 0.5111 (t70) cc_final: 0.4748 (t70) REVERT: F 210 ILE cc_start: 0.7719 (mt) cc_final: 0.7449 (mm) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1585 time to fit residues: 26.4406 Evaluate side-chains 119 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 13 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS F 127 HIS F 137 GLN F 180 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.162947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.138073 restraints weight = 7835.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.142079 restraints weight = 4942.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.145010 restraints weight = 3577.713| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3699 Z= 0.222 Angle : 0.907 13.494 5044 Z= 0.467 Chirality : 0.055 0.240 580 Planarity : 0.006 0.056 651 Dihedral : 10.225 50.439 500 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 1.06 % Allowed : 21.06 % Favored : 77.87 % Rotamer: Outliers : 0.25 % Allowed : 3.70 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -3.33 (0.37), residues: 158 loop : -3.63 (0.29), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 182 HIS 0.003 0.001 HIS F 180 PHE 0.017 0.002 PHE F 111 TYR 0.013 0.001 TYR E 54 ARG 0.004 0.001 ARG F 158 *********************** 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 133 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 ILE cc_start: 0.8076 (tt) cc_final: 0.7861 (tt) REVERT: E 40 TRP cc_start: 0.7726 (t60) cc_final: 0.7260 (t60) REVERT: E 51 HIS cc_start: 0.8138 (t70) cc_final: 0.7744 (t-170) REVERT: E 55 ASN cc_start: 0.8347 (p0) cc_final: 0.8068 (p0) REVERT: E 60 ARG cc_start: 0.7796 (mmm160) cc_final: 0.7210 (mmm-85) REVERT: E 78 ASP cc_start: 0.8501 (m-30) cc_final: 0.8051 (p0) REVERT: E 103 THR cc_start: 0.7666 (m) cc_final: 0.6867 (m) REVERT: E 104 ASN cc_start: 0.7971 (m-40) cc_final: 0.6714 (p0) REVERT: E 128 PHE cc_start: 0.8587 (p90) cc_final: 0.8234 (p90) REVERT: E 140 LEU cc_start: 0.8291 (mm) cc_final: 0.7814 (mt) REVERT: E 154 LEU cc_start: 0.8617 (tp) cc_final: 0.8335 (tp) REVERT: F 7 VAL cc_start: 0.7349 (t) cc_final: 0.7038 (t) REVERT: F 93 LEU cc_start: 0.8565 (mt) cc_final: 0.8337 (mt) REVERT: F 126 LEU cc_start: 0.8286 (tp) cc_final: 0.7975 (tp) REVERT: F 136 ASP cc_start: 0.7596 (t70) cc_final: 0.7352 (t0) REVERT: F 176 TYR cc_start: 0.8518 (t80) cc_final: 0.8223 (t80) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.1478 time to fit residues: 23.9514 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 chunk 44 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.152194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.127882 restraints weight = 7973.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.131526 restraints weight = 5129.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.134054 restraints weight = 3756.109| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.7251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3699 Z= 0.360 Angle : 0.999 12.420 5044 Z= 0.519 Chirality : 0.057 0.274 580 Planarity : 0.007 0.054 651 Dihedral : 10.686 51.065 500 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 1.28 % Allowed : 23.83 % Favored : 74.89 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -3.33 (0.37), residues: 152 loop : -3.76 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP F 182 HIS 0.006 0.002 HIS E 24 PHE 0.017 0.003 PHE E 128 TYR 0.014 0.002 TYR F 176 ARG 0.005 0.001 ARG F 90 *********************** 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 132 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.442 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 40 TRP cc_start: 0.8087 (t60) cc_final: 0.7868 (t60) REVERT: E 51 HIS cc_start: 0.8226 (t70) cc_final: 0.7894 (t-170) REVERT: E 55 ASN cc_start: 0.8315 (p0) cc_final: 0.7964 (p0) REVERT: E 78 ASP cc_start: 0.8346 (m-30) cc_final: 0.8011 (p0) REVERT: E 104 ASN cc_start: 0.7580 (m-40) cc_final: 0.7187 (p0) REVERT: E 176 TYR cc_start: 0.8399 (t80) cc_final: 0.7569 (t80) REVERT: E 213 PHE cc_start: 0.8567 (p90) cc_final: 0.8251 (p90) REVERT: F 93 LEU cc_start: 0.8712 (mt) cc_final: 0.8308 (mt) REVERT: F 103 THR cc_start: 0.7593 (m) cc_final: 0.7164 (m) REVERT: F 126 LEU cc_start: 0.8383 (tp) cc_final: 0.8155 (tp) REVERT: F 133 PHE cc_start: 0.7649 (m-80) cc_final: 0.7380 (m-10) REVERT: F 136 ASP cc_start: 0.7804 (t70) cc_final: 0.7527 (t0) REVERT: F 140 LEU cc_start: 0.8798 (mt) cc_final: 0.8517 (mp) REVERT: F 176 TYR cc_start: 0.7992 (t80) cc_final: 0.7777 (t80) REVERT: F 208 ASP cc_start: 0.4781 (t70) cc_final: 0.4209 (t70) REVERT: F 210 ILE cc_start: 0.8116 (mt) cc_final: 0.7799 (mp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1670 time to fit residues: 26.9006 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 : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 38 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 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 = 0.4151 r_free = 0.4151 target = 0.151450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.127318 restraints weight = 8058.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.130876 restraints weight = 5220.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.133397 restraints weight = 3847.851| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.8037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 3699 Z= 0.341 Angle : 0.971 12.426 5044 Z= 0.503 Chirality : 0.056 0.250 580 Planarity : 0.007 0.058 651 Dihedral : 10.509 46.983 500 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 23.57 Ramachandran Plot: Outliers : 1.06 % Allowed : 24.26 % Favored : 74.68 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.26 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -3.27 (0.38), residues: 156 loop : -3.85 (0.29), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP F 40 HIS 0.004 0.001 HIS E 127 PHE 0.017 0.003 PHE F 191 TYR 0.014 0.002 TYR E 54 ARG 0.005 0.001 ARG F 158 *********************** 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 127 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.8267 (t70) cc_final: 0.7904 (t-170) REVERT: E 78 ASP cc_start: 0.8268 (m-30) cc_final: 0.7978 (p0) REVERT: E 104 ASN cc_start: 0.7747 (m-40) cc_final: 0.7091 (p0) REVERT: E 137 GLN cc_start: 0.8679 (tt0) cc_final: 0.8388 (tm-30) REVERT: E 140 LEU cc_start: 0.8595 (mm) cc_final: 0.7737 (mt) REVERT: E 174 LEU cc_start: 0.8256 (mt) cc_final: 0.8033 (mt) REVERT: E 213 PHE cc_start: 0.8442 (p90) cc_final: 0.8216 (p90) REVERT: F 126 LEU cc_start: 0.8483 (tp) cc_final: 0.8248 (tp) REVERT: F 130 PHE cc_start: 0.7063 (m-80) cc_final: 0.5724 (m-80) REVERT: F 136 ASP cc_start: 0.7740 (t70) cc_final: 0.7481 (t0) REVERT: F 137 GLN cc_start: 0.8654 (mt0) cc_final: 0.8220 (tt0) REVERT: F 140 LEU cc_start: 0.8908 (mt) cc_final: 0.8685 (mp) REVERT: F 175 PHE cc_start: 0.8549 (t80) cc_final: 0.8136 (t80) REVERT: F 208 ASP cc_start: 0.4935 (t70) cc_final: 0.4190 (t70) REVERT: F 215 SER cc_start: 0.8507 (t) cc_final: 0.8271 (t) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1684 time to fit residues: 25.9728 Evaluate side-chains 112 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 0.0000 chunk 40 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.148874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.124095 restraints weight = 7906.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.127842 restraints weight = 5073.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.130586 restraints weight = 3680.985| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.8239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3699 Z= 0.249 Angle : 0.923 12.289 5044 Z= 0.479 Chirality : 0.055 0.233 580 Planarity : 0.006 0.053 651 Dihedral : 9.970 44.348 500 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 1.28 % Allowed : 23.19 % Favored : 75.53 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.78 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -3.03 (0.40), residues: 154 loop : -3.83 (0.29), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP F 182 HIS 0.004 0.001 HIS F 180 PHE 0.021 0.003 PHE E 111 TYR 0.019 0.002 TYR F 176 ARG 0.004 0.001 ARG F 158 *********************** 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 124 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 40 TRP cc_start: 0.7660 (t60) cc_final: 0.7322 (t60) REVERT: E 51 HIS cc_start: 0.8416 (t70) cc_final: 0.7818 (t-170) REVERT: E 55 ASN cc_start: 0.8399 (p0) cc_final: 0.8043 (p0) REVERT: E 78 ASP cc_start: 0.8446 (m-30) cc_final: 0.8073 (p0) REVERT: E 104 ASN cc_start: 0.7275 (m-40) cc_final: 0.6626 (p0) REVERT: E 137 GLN cc_start: 0.8683 (tt0) cc_final: 0.8397 (tm-30) REVERT: E 140 LEU cc_start: 0.8527 (mm) cc_final: 0.7508 (mt) REVERT: E 141 ILE cc_start: 0.8580 (mt) cc_final: 0.8238 (tt) REVERT: E 181 ILE cc_start: 0.5899 (mm) cc_final: 0.5667 (mm) REVERT: E 192 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7945 (tm-30) REVERT: F 136 ASP cc_start: 0.7821 (t70) cc_final: 0.7498 (t0) REVERT: F 137 GLN cc_start: 0.8684 (mt0) cc_final: 0.8446 (tt0) REVERT: F 140 LEU cc_start: 0.8978 (mt) cc_final: 0.8708 (mp) REVERT: F 175 PHE cc_start: 0.8337 (t80) cc_final: 0.7793 (t80) REVERT: F 208 ASP cc_start: 0.4502 (t70) cc_final: 0.3811 (t70) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1659 time to fit residues: 25.0189 Evaluate side-chains 101 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.148970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.125767 restraints weight = 7637.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.129303 restraints weight = 4933.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.131908 restraints weight = 3596.143| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.8517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3699 Z= 0.256 Angle : 0.929 12.808 5044 Z= 0.480 Chirality : 0.055 0.193 580 Planarity : 0.006 0.051 651 Dihedral : 9.853 44.464 500 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 1.28 % Allowed : 21.28 % Favored : 77.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -2.94 (0.41), residues: 154 loop : -3.81 (0.29), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP F 40 HIS 0.004 0.001 HIS E 24 PHE 0.019 0.003 PHE F 191 TYR 0.016 0.002 TYR F 176 ARG 0.002 0.000 ARG F 158 *********************** 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 119 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ASP cc_start: 0.8392 (p0) cc_final: 0.8180 (p0) REVERT: E 51 HIS cc_start: 0.8374 (t70) cc_final: 0.7980 (t-170) REVERT: E 78 ASP cc_start: 0.8308 (m-30) cc_final: 0.7966 (p0) REVERT: E 104 ASN cc_start: 0.7472 (m-40) cc_final: 0.6949 (p0) REVERT: E 140 LEU cc_start: 0.8500 (mm) cc_final: 0.7747 (mt) REVERT: E 141 ILE cc_start: 0.8544 (mt) cc_final: 0.8229 (tt) REVERT: F 136 ASP cc_start: 0.7686 (t70) cc_final: 0.7379 (t0) REVERT: F 140 LEU cc_start: 0.8942 (mt) cc_final: 0.8665 (mp) REVERT: F 175 PHE cc_start: 0.8372 (t80) cc_final: 0.7831 (t80) REVERT: F 208 ASP cc_start: 0.4609 (t70) cc_final: 0.3842 (t70) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1660 time to fit residues: 24.0215 Evaluate side-chains 103 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.0170 chunk 24 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 HIS E 137 GLN ** F 124 ASN ** 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 = 0.4105 r_free = 0.4105 target = 0.150350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.126336 restraints weight = 7721.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.130117 restraints weight = 4882.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.132873 restraints weight = 3520.849| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.8811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3699 Z= 0.247 Angle : 0.928 12.197 5044 Z= 0.480 Chirality : 0.056 0.303 580 Planarity : 0.006 0.052 651 Dihedral : 9.672 44.438 500 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 1.06 % Allowed : 24.68 % Favored : 74.26 % 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 : 3.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.93 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -2.64 (0.44), residues: 140 loop : -3.85 (0.27), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 182 HIS 0.004 0.001 HIS E 24 PHE 0.024 0.003 PHE E 195 TYR 0.013 0.002 TYR F 77 ARG 0.008 0.001 ARG F 172 *********************** 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 131 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.449 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 51 HIS cc_start: 0.8465 (t70) cc_final: 0.7928 (t-170) REVERT: E 78 ASP cc_start: 0.8439 (m-30) cc_final: 0.8050 (p0) REVERT: E 104 ASN cc_start: 0.7045 (m-40) cc_final: 0.6403 (p0) REVERT: E 128 PHE cc_start: 0.8478 (p90) cc_final: 0.8128 (p90) REVERT: E 137 GLN cc_start: 0.8225 (tm130) cc_final: 0.7556 (tm-30) REVERT: E 140 LEU cc_start: 0.8402 (mm) cc_final: 0.8033 (mt) REVERT: F 126 LEU cc_start: 0.8624 (tp) cc_final: 0.8374 (tp) REVERT: F 135 LYS cc_start: 0.9177 (tttm) cc_final: 0.8557 (tppt) REVERT: F 140 LEU cc_start: 0.8898 (mt) cc_final: 0.8612 (mp) REVERT: F 175 PHE cc_start: 0.8473 (t80) cc_final: 0.7911 (t80) REVERT: F 208 ASP cc_start: 0.4529 (t70) cc_final: 0.3704 (t70) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1504 time to fit residues: 24.2177 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 : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 0.0000 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 45 optimal weight: 0.2980 chunk 16 optimal weight: 0.0040 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.153021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.127920 restraints weight = 7656.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.131789 restraints weight = 4885.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.134534 restraints weight = 3536.341| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.9061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3699 Z= 0.229 Angle : 0.921 12.862 5044 Z= 0.472 Chirality : 0.056 0.301 580 Planarity : 0.006 0.052 651 Dihedral : 9.326 44.821 500 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 1.28 % Allowed : 22.98 % Favored : 75.74 % 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 : 2.89 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -2.26 (0.48), residues: 120 loop : -3.81 (0.26), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 182 HIS 0.003 0.001 HIS F 180 PHE 0.021 0.003 PHE F 128 TYR 0.022 0.002 TYR F 77 ARG 0.005 0.001 ARG F 172 ********************** 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 129 residues out of total 406 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 HIS cc_start: 0.8410 (t70) cc_final: 0.7682 (t-170) REVERT: E 61 LEU cc_start: 0.8383 (tp) cc_final: 0.8101 (tt) REVERT: E 78 ASP cc_start: 0.8353 (m-30) cc_final: 0.7905 (p0) REVERT: E 104 ASN cc_start: 0.7530 (m-40) cc_final: 0.6451 (p0) REVERT: E 140 LEU cc_start: 0.8525 (mm) cc_final: 0.7948 (mt) REVERT: E 154 LEU cc_start: 0.8364 (tp) cc_final: 0.8119 (tp) REVERT: E 155 GLU cc_start: 0.7517 (tt0) cc_final: 0.6868 (tt0) REVERT: F 7 VAL cc_start: 0.7881 (t) cc_final: 0.7657 (t) REVERT: F 93 LEU cc_start: 0.8739 (mt) cc_final: 0.8439 (mp) REVERT: F 126 LEU cc_start: 0.8543 (tp) cc_final: 0.8293 (tp) REVERT: F 135 LYS cc_start: 0.9156 (tttm) cc_final: 0.8578 (tppt) REVERT: F 140 LEU cc_start: 0.8823 (mt) cc_final: 0.8617 (mp) REVERT: F 175 PHE cc_start: 0.8383 (t80) cc_final: 0.7905 (t80) REVERT: F 208 ASP cc_start: 0.4438 (t70) cc_final: 0.3647 (t70) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1613 time to fit residues: 25.9396 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 : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 8 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 180 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.150861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.126211 restraints weight = 7699.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.129997 restraints weight = 4885.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.132718 restraints weight = 3541.090| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.9298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3699 Z= 0.258 Angle : 0.921 12.084 5044 Z= 0.477 Chirality : 0.056 0.292 580 Planarity : 0.006 0.056 651 Dihedral : 9.484 44.720 500 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 1.06 % Allowed : 22.55 % Favored : 76.38 % 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 : 2.89 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.71 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -2.30 (0.47), residues: 136 loop : -3.79 (0.27), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 182 HIS 0.010 0.001 HIS E 127 PHE 0.023 0.003 PHE E 128 TYR 0.018 0.002 TYR F 77 ARG 0.004 0.001 ARG F 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1737.88 seconds wall clock time: 31 minutes 49.49 seconds (1909.49 seconds total)