Starting phenix.real_space_refine on Fri Aug 2 16:48:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b33_44124/08_2024/9b33_44124.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b33_44124/08_2024/9b33_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b33_44124/08_2024/9b33_44124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b33_44124/08_2024/9b33_44124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b33_44124/08_2024/9b33_44124.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b33_44124/08_2024/9b33_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 Residue "E PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 158": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 2.79, 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 - 3.50 Amino acid : False - 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: 1.34 Conformation dependent library (CDL) restraints added in 625.9 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: 0.45 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: 0.85 Time building geometry restraints manager: 1.47 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: 100.29 - 107.55: 213 107.55 - 114.81: 2084 114.81 - 122.07: 1894 122.07 - 129.34: 811 129.34 - 136.60: 42 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: 0.690 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.350 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 0.378 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: 0.1673 time to fit residues: 35.0015 Evaluate side-chains 125 residues out of total 406 non-(ALA, GLY, PRO) need fitting. 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 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 fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 0.424 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 36 LYS cc_start: 0.7031 (mmtt) cc_final: 0.6811 (mttt) REVERT: E 39 LYS cc_start: 0.8807 (tttt) cc_final: 0.8414 (tptp) REVERT: E 40 TRP cc_start: 0.7757 (t60) cc_final: 0.7358 (t60) REVERT: E 51 HIS cc_start: 0.7678 (t-90) cc_final: 0.7040 (t70) REVERT: E 60 ARG cc_start: 0.7901 (mmm160) cc_final: 0.7486 (mmm-85) REVERT: E 79 VAL cc_start: 0.8738 (p) cc_final: 0.8353 (p) REVERT: E 81 LEU cc_start: 0.8367 (mm) cc_final: 0.8026 (mm) REVERT: E 85 LEU cc_start: 0.8752 (tt) cc_final: 0.8450 (tt) REVERT: E 90 ARG cc_start: 0.7313 (mtp180) cc_final: 0.6388 (mmm-85) REVERT: E 130 PHE cc_start: 0.7988 (m-10) cc_final: 0.7770 (m-10) REVERT: E 133 PHE cc_start: 0.6474 (m-80) cc_final: 0.6231 (m-10) REVERT: E 138 LYS cc_start: 0.7666 (mtmt) cc_final: 0.6933 (mtmm) REVERT: E 140 LEU cc_start: 0.8707 (mt) cc_final: 0.8404 (mt) REVERT: E 174 LEU cc_start: 0.8078 (mp) cc_final: 0.7802 (mp) REVERT: E 176 TYR cc_start: 0.8060 (t80) cc_final: 0.6880 (t80) REVERT: E 191 PHE cc_start: 0.7723 (p90) cc_final: 0.7478 (p90) REVERT: F 16 ASP cc_start: 0.7381 (m-30) cc_final: 0.7056 (m-30) REVERT: F 17 ILE cc_start: 0.8285 (pt) cc_final: 0.7951 (mm) REVERT: F 27 ILE cc_start: 0.6855 (tt) cc_final: 0.6583 (mt) REVERT: F 29 ILE cc_start: 0.8008 (mt) cc_final: 0.7745 (tp) REVERT: F 93 LEU cc_start: 0.8609 (mt) cc_final: 0.8368 (mp) REVERT: F 126 LEU cc_start: 0.8092 (tp) cc_final: 0.7400 (tp) REVERT: F 130 PHE cc_start: 0.7812 (m-80) cc_final: 0.7570 (m-80) REVERT: F 133 PHE cc_start: 0.7846 (m-80) cc_final: 0.7634 (m-10) REVERT: F 139 ASP cc_start: 0.8280 (p0) cc_final: 0.7877 (p0) REVERT: F 170 VAL cc_start: 0.6633 (p) cc_final: 0.6312 (t) REVERT: F 176 TYR cc_start: 0.8412 (t80) cc_final: 0.7270 (t80) REVERT: F 183 GLU cc_start: 0.6964 (tp30) cc_final: 0.6680 (tp30) REVERT: F 191 PHE cc_start: 0.8123 (p90) cc_final: 0.7893 (p90) REVERT: F 213 PHE cc_start: 0.8352 (p90) cc_final: 0.8152 (p90) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.1606 time to fit residues: 29.1561 Evaluate side-chains 122 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 41 ASN F 51 HIS F 127 HIS ** F 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3699 Z= 0.249 Angle : 0.956 16.016 5044 Z= 0.490 Chirality : 0.055 0.319 580 Planarity : 0.006 0.057 651 Dihedral : 10.761 56.403 500 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.85 % Allowed : 22.55 % Favored : 76.60 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % 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: -5.30 (0.32), residues: 470 helix: None (None), residues: 0 sheet: -3.72 (0.34), residues: 166 loop : -3.57 (0.29), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP F 40 HIS 0.005 0.001 HIS F 127 PHE 0.019 0.003 PHE F 111 TYR 0.012 0.002 TYR F 12 ARG 0.004 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 140 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 39 LYS cc_start: 0.8943 (tttt) cc_final: 0.8738 (tmtt) REVERT: E 51 HIS cc_start: 0.6938 (t-90) cc_final: 0.6626 (m-70) REVERT: E 60 ARG cc_start: 0.7697 (mmm160) cc_final: 0.6915 (mmm-85) REVERT: E 75 VAL cc_start: 0.8361 (p) cc_final: 0.8109 (p) REVERT: E 78 ASP cc_start: 0.8962 (m-30) cc_final: 0.8447 (p0) REVERT: E 104 ASN cc_start: 0.7616 (m-40) cc_final: 0.6414 (p0) REVERT: E 140 LEU cc_start: 0.8825 (mt) cc_final: 0.8542 (mt) REVERT: E 176 TYR cc_start: 0.8335 (t80) cc_final: 0.7361 (t80) REVERT: F 17 ILE cc_start: 0.8184 (pt) cc_final: 0.7770 (mm) REVERT: F 93 LEU cc_start: 0.8803 (mt) cc_final: 0.8532 (mp) REVERT: F 106 ILE cc_start: 0.8971 (mm) cc_final: 0.8749 (mt) REVERT: F 126 LEU cc_start: 0.8145 (tp) cc_final: 0.7712 (tp) REVERT: F 133 PHE cc_start: 0.7795 (m-80) cc_final: 0.7215 (m-80) REVERT: F 176 TYR cc_start: 0.8537 (t80) cc_final: 0.7754 (t80) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1769 time to fit residues: 29.5915 Evaluate side-chains 113 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 0.0370 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- 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** E 51 HIS F 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.6855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3699 Z= 0.352 Angle : 1.008 12.978 5044 Z= 0.522 Chirality : 0.056 0.239 580 Planarity : 0.007 0.062 651 Dihedral : 10.876 53.095 500 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 1.06 % Allowed : 25.11 % Favored : 73.83 % 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 : 3.56 % 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: -5.48 (0.32), residues: 470 helix: None (None), residues: 0 sheet: -3.63 (0.35), residues: 162 loop : -3.86 (0.29), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 182 HIS 0.005 0.001 HIS E 24 PHE 0.025 0.003 PHE F 130 TYR 0.011 0.002 TYR F 12 ARG 0.005 0.001 ARG F 90 *********************** 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 138 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.440 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 4 ILE cc_start: 0.8642 (pt) cc_final: 0.8344 (pt) REVERT: E 39 LYS cc_start: 0.8846 (tttt) cc_final: 0.8479 (tptp) REVERT: E 40 TRP cc_start: 0.8145 (t60) cc_final: 0.7814 (t60) REVERT: E 51 HIS cc_start: 0.7384 (t70) cc_final: 0.7144 (t-170) REVERT: E 60 ARG cc_start: 0.7681 (mmm160) cc_final: 0.6959 (mmm-85) REVERT: E 78 ASP cc_start: 0.8929 (m-30) cc_final: 0.8459 (p0) REVERT: E 104 ASN cc_start: 0.7619 (m-40) cc_final: 0.7016 (p0) REVERT: E 130 PHE cc_start: 0.7984 (m-10) cc_final: 0.7779 (m-10) REVERT: E 154 LEU cc_start: 0.8686 (tp) cc_final: 0.8439 (tp) REVERT: E 175 PHE cc_start: 0.8438 (t80) cc_final: 0.8214 (t80) REVERT: E 176 TYR cc_start: 0.8642 (t80) cc_final: 0.8044 (t80) REVERT: E 213 PHE cc_start: 0.8581 (p90) cc_final: 0.7965 (p90) REVERT: F 29 ILE cc_start: 0.8447 (mt) cc_final: 0.8237 (mm) REVERT: F 93 LEU cc_start: 0.8909 (mt) cc_final: 0.8648 (mp) REVERT: F 106 ILE cc_start: 0.8951 (mm) cc_final: 0.8702 (mt) REVERT: F 126 LEU cc_start: 0.8482 (tp) cc_final: 0.8131 (tp) REVERT: F 133 PHE cc_start: 0.7878 (m-80) cc_final: 0.7237 (m-80) REVERT: F 136 ASP cc_start: 0.8152 (t70) cc_final: 0.7951 (t0) REVERT: F 174 LEU cc_start: 0.8736 (mp) cc_final: 0.8386 (mp) REVERT: F 175 PHE cc_start: 0.8265 (t80) cc_final: 0.7666 (t80) REVERT: F 197 PHE cc_start: 0.8558 (p90) cc_final: 0.8291 (p90) REVERT: F 200 LYS cc_start: 0.6830 (tttp) cc_final: 0.6625 (tmmt) REVERT: F 208 ASP cc_start: 0.5117 (t70) cc_final: 0.4510 (t70) REVERT: F 210 ILE cc_start: 0.7570 (mt) cc_final: 0.7351 (mp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1702 time to fit residues: 28.2623 Evaluate side-chains 124 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.7229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3699 Z= 0.248 Angle : 0.915 12.321 5044 Z= 0.474 Chirality : 0.054 0.293 580 Planarity : 0.006 0.056 651 Dihedral : 10.377 46.950 500 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 1.06 % Allowed : 21.70 % Favored : 77.23 % 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 (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: -5.18 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -3.26 (0.37), residues: 154 loop : -3.77 (0.29), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP F 40 HIS 0.006 0.001 HIS F 180 PHE 0.019 0.003 PHE E 111 TYR 0.014 0.002 TYR E 54 ARG 0.004 0.001 ARG F 172 *********************** 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 133 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ASP cc_start: 0.8521 (p0) cc_final: 0.8284 (p0) REVERT: E 25 ILE cc_start: 0.8203 (tt) cc_final: 0.7872 (tt) REVERT: E 39 LYS cc_start: 0.8856 (tttt) cc_final: 0.8523 (tptp) REVERT: E 40 TRP cc_start: 0.7975 (t60) cc_final: 0.7639 (t60) REVERT: E 60 ARG cc_start: 0.7660 (mmm160) cc_final: 0.6834 (mmm-85) REVERT: E 78 ASP cc_start: 0.8871 (m-30) cc_final: 0.8383 (p0) REVERT: E 130 PHE cc_start: 0.8116 (m-10) cc_final: 0.7910 (m-10) REVERT: E 140 LEU cc_start: 0.8898 (mt) cc_final: 0.8689 (mt) REVERT: E 176 TYR cc_start: 0.8297 (t80) cc_final: 0.7541 (t80) REVERT: F 7 VAL cc_start: 0.7254 (t) cc_final: 0.7050 (t) REVERT: F 29 ILE cc_start: 0.8478 (mt) cc_final: 0.8213 (mm) REVERT: F 93 LEU cc_start: 0.8903 (mt) cc_final: 0.8664 (mp) REVERT: F 106 ILE cc_start: 0.8950 (mm) cc_final: 0.8725 (mt) REVERT: F 126 LEU cc_start: 0.8505 (tp) cc_final: 0.8183 (tp) REVERT: F 136 ASP cc_start: 0.8347 (t70) cc_final: 0.7768 (t0) REVERT: F 175 PHE cc_start: 0.8222 (t80) cc_final: 0.7551 (t80) REVERT: F 210 ILE cc_start: 0.7759 (mt) cc_final: 0.7282 (mm) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1581 time to fit residues: 25.3933 Evaluate side-chains 114 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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** E 124 ASN E 166 GLN F 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.7921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3699 Z= 0.277 Angle : 0.924 13.259 5044 Z= 0.478 Chirality : 0.055 0.258 580 Planarity : 0.006 0.051 651 Dihedral : 10.212 45.405 500 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 1.06 % Allowed : 24.68 % Favored : 74.26 % Rotamer: Outliers : 0.25 % Allowed : 3.21 % 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: -5.14 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -3.10 (0.38), residues: 154 loop : -3.83 (0.29), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 182 HIS 0.005 0.002 HIS F 127 PHE 0.017 0.003 PHE F 191 TYR 0.013 0.002 TYR E 54 ARG 0.004 0.000 ARG E 228 *********************** 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 136 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 0.428 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: 0.8645 (p0) cc_final: 0.8442 (p0) REVERT: E 78 ASP cc_start: 0.8841 (m-30) cc_final: 0.8340 (p0) REVERT: E 104 ASN cc_start: 0.7698 (m-40) cc_final: 0.6374 (p0) REVERT: E 130 PHE cc_start: 0.8134 (m-10) cc_final: 0.7722 (m-10) REVERT: E 140 LEU cc_start: 0.8916 (mt) cc_final: 0.8633 (mt) REVERT: E 174 LEU cc_start: 0.8365 (mt) cc_final: 0.8121 (mt) REVERT: E 175 PHE cc_start: 0.8239 (t80) cc_final: 0.7817 (t80) REVERT: E 176 TYR cc_start: 0.8546 (t80) cc_final: 0.7507 (t80) REVERT: E 191 PHE cc_start: 0.7824 (p90) cc_final: 0.7554 (p90) REVERT: E 208 ASP cc_start: 0.6014 (t0) cc_final: 0.5800 (t0) REVERT: E 213 PHE cc_start: 0.8554 (p90) cc_final: 0.8190 (p90) REVERT: F 7 VAL cc_start: 0.7530 (t) cc_final: 0.7326 (t) REVERT: F 29 ILE cc_start: 0.8389 (mt) cc_final: 0.8126 (mm) REVERT: F 42 MET cc_start: 0.3704 (mmm) cc_final: 0.3414 (mmm) REVERT: F 93 LEU cc_start: 0.8898 (mt) cc_final: 0.8432 (mp) REVERT: F 126 LEU cc_start: 0.8500 (tp) cc_final: 0.8298 (tp) REVERT: F 135 LYS cc_start: 0.9208 (tttm) cc_final: 0.8561 (tppt) REVERT: F 172 ARG cc_start: 0.7799 (mmm-85) cc_final: 0.7016 (mmm-85) REVERT: F 175 PHE cc_start: 0.8297 (t80) cc_final: 0.7681 (t80) REVERT: F 208 ASP cc_start: 0.5237 (t70) cc_final: 0.4938 (t0) outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.1714 time to fit residues: 27.9502 Evaluate side-chains 108 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.2980 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.8215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3699 Z= 0.231 Angle : 0.893 13.027 5044 Z= 0.462 Chirality : 0.055 0.277 580 Planarity : 0.006 0.048 651 Dihedral : 9.951 43.855 500 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 1.06 % Allowed : 21.49 % Favored : 77.45 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: -5.02 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -2.83 (0.41), residues: 146 loop : -3.85 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 40 HIS 0.003 0.001 HIS F 180 PHE 0.021 0.003 PHE E 195 TYR 0.014 0.002 TYR E 54 ARG 0.002 0.000 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 132 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 THR cc_start: 0.8955 (m) cc_final: 0.8716 (p) REVERT: E 40 TRP cc_start: 0.7861 (t60) cc_final: 0.7197 (t60) REVERT: E 67 TYR cc_start: 0.6821 (m-80) cc_final: 0.6139 (m-80) REVERT: E 78 ASP cc_start: 0.8727 (m-30) cc_final: 0.8278 (p0) REVERT: E 130 PHE cc_start: 0.8064 (m-10) cc_final: 0.7458 (m-10) REVERT: E 137 GLN cc_start: 0.8518 (tt0) cc_final: 0.8237 (tt0) REVERT: E 139 ASP cc_start: 0.6782 (p0) cc_final: 0.6516 (p0) REVERT: E 140 LEU cc_start: 0.8907 (mt) cc_final: 0.8625 (mt) REVERT: E 176 TYR cc_start: 0.8303 (t80) cc_final: 0.7412 (t80) REVERT: F 29 ILE cc_start: 0.8437 (mt) cc_final: 0.8117 (mm) REVERT: F 42 MET cc_start: 0.4195 (mmm) cc_final: 0.3533 (mmm) REVERT: F 135 LYS cc_start: 0.9256 (tttm) cc_final: 0.8630 (tppt) REVERT: F 175 PHE cc_start: 0.8211 (t80) cc_final: 0.7553 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1582 time to fit residues: 25.2120 Evaluate side-chains 102 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 42 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.8568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3699 Z= 0.225 Angle : 0.912 13.803 5044 Z= 0.470 Chirality : 0.055 0.319 580 Planarity : 0.006 0.048 651 Dihedral : 9.514 42.461 500 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 1.06 % Allowed : 21.91 % Favored : 77.02 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.11 % 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: -4.83 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -2.68 (0.43), residues: 136 loop : -3.72 (0.29), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 40 HIS 0.005 0.001 HIS E 180 PHE 0.019 0.003 PHE F 128 TYR 0.015 0.001 TYR E 54 ARG 0.003 0.001 ARG F 172 *********************** 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 132 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 3 THR cc_start: 0.8886 (m) cc_final: 0.8647 (p) REVERT: E 40 TRP cc_start: 0.7734 (t60) cc_final: 0.7242 (t60) REVERT: E 51 HIS cc_start: 0.8325 (t70) cc_final: 0.7989 (t70) REVERT: E 67 TYR cc_start: 0.7026 (m-80) cc_final: 0.6288 (m-80) REVERT: E 78 ASP cc_start: 0.8664 (m-30) cc_final: 0.8156 (p0) REVERT: E 130 PHE cc_start: 0.7964 (m-10) cc_final: 0.7526 (m-10) REVERT: E 137 GLN cc_start: 0.8481 (tt0) cc_final: 0.8238 (tt0) REVERT: E 140 LEU cc_start: 0.8890 (mt) cc_final: 0.8610 (mt) REVERT: E 176 TYR cc_start: 0.8418 (t80) cc_final: 0.7517 (t80) REVERT: F 29 ILE cc_start: 0.8414 (mt) cc_final: 0.8129 (mm) REVERT: F 40 TRP cc_start: 0.4994 (t60) cc_final: 0.4741 (t60) REVERT: F 93 LEU cc_start: 0.8421 (mt) cc_final: 0.8123 (mp) REVERT: F 172 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.7051 (mmm-85) REVERT: F 175 PHE cc_start: 0.8261 (t80) cc_final: 0.7587 (t80) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1695 time to fit residues: 27.1070 Evaluate side-chains 113 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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** E 121 HIS F 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.8850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3699 Z= 0.310 Angle : 0.940 12.634 5044 Z= 0.486 Chirality : 0.055 0.287 580 Planarity : 0.006 0.047 651 Dihedral : 9.964 47.580 500 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 22.03 Ramachandran Plot: Outliers : 0.85 % Allowed : 24.04 % Favored : 75.11 % 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 : 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: -5.01 (0.33), residues: 470 helix: None (None), residues: 0 sheet: -2.65 (0.43), residues: 146 loop : -3.94 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 40 HIS 0.005 0.002 HIS F 127 PHE 0.025 0.003 PHE E 195 TYR 0.023 0.002 TYR E 176 ARG 0.006 0.001 ARG E 158 *********************** 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 124 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 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: 0.8715 (p0) cc_final: 0.8374 (p0) REVERT: E 40 TRP cc_start: 0.8091 (t60) cc_final: 0.7484 (t60) REVERT: E 51 HIS cc_start: 0.8502 (t70) cc_final: 0.7887 (t-90) REVERT: E 67 TYR cc_start: 0.7087 (m-80) cc_final: 0.6525 (m-80) REVERT: E 78 ASP cc_start: 0.8669 (m-30) cc_final: 0.8229 (p0) REVERT: E 90 ARG cc_start: 0.7532 (mtp180) cc_final: 0.6757 (tpt-90) REVERT: E 130 PHE cc_start: 0.8094 (m-10) cc_final: 0.7758 (m-10) REVERT: E 137 GLN cc_start: 0.8553 (tt0) cc_final: 0.8197 (tt0) REVERT: E 192 GLU cc_start: 0.7460 (tt0) cc_final: 0.7100 (tt0) REVERT: F 9 LEU cc_start: 0.8110 (mp) cc_final: 0.7852 (mp) REVERT: F 29 ILE cc_start: 0.8404 (mt) cc_final: 0.8129 (mm) REVERT: F 40 TRP cc_start: 0.4939 (t60) cc_final: 0.4737 (t60) REVERT: F 93 LEU cc_start: 0.8639 (mt) cc_final: 0.8171 (mp) REVERT: F 197 PHE cc_start: 0.8445 (p90) cc_final: 0.8074 (p90) REVERT: F 208 ASP cc_start: 0.5332 (t70) cc_final: 0.5070 (t0) REVERT: F 210 ILE cc_start: 0.7785 (mt) cc_final: 0.7407 (mp) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1657 time to fit residues: 24.8307 Evaluate side-chains 115 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 45 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.9102 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= 0.220 Angle : 0.885 13.580 5044 Z= 0.458 Chirality : 0.053 0.298 580 Planarity : 0.005 0.044 651 Dihedral : 9.392 44.534 500 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 1.06 % Allowed : 20.85 % Favored : 78.09 % 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: -4.77 (0.34), residues: 470 helix: None (None), residues: 0 sheet: -2.47 (0.45), residues: 136 loop : -3.76 (0.28), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 109 HIS 0.003 0.001 HIS E 24 PHE 0.023 0.003 PHE E 111 TYR 0.017 0.002 TYR F 176 ARG 0.002 0.000 ARG F 90 ********************** 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 125 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ASP cc_start: 0.8743 (p0) cc_final: 0.8417 (p0) REVERT: E 40 TRP cc_start: 0.7697 (t60) cc_final: 0.7415 (t60) REVERT: E 78 ASP cc_start: 0.8655 (m-30) cc_final: 0.8181 (p0) REVERT: E 90 ARG cc_start: 0.7679 (mtp180) cc_final: 0.7016 (tpt-90) REVERT: E 109 TRP cc_start: 0.8683 (t60) cc_final: 0.8458 (t60) REVERT: E 130 PHE cc_start: 0.8128 (m-10) cc_final: 0.7700 (m-10) REVERT: E 137 GLN cc_start: 0.8440 (tt0) cc_final: 0.8163 (tm-30) REVERT: E 140 LEU cc_start: 0.8502 (mt) cc_final: 0.7524 (mt) REVERT: E 174 LEU cc_start: 0.8075 (mt) cc_final: 0.7734 (mt) REVERT: E 192 GLU cc_start: 0.7322 (tt0) cc_final: 0.6835 (tm-30) REVERT: F 9 LEU cc_start: 0.7896 (mp) cc_final: 0.7692 (mp) REVERT: F 29 ILE cc_start: 0.8338 (mt) cc_final: 0.8039 (mm) REVERT: F 93 LEU cc_start: 0.8575 (mt) cc_final: 0.8079 (mp) REVERT: F 172 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.7122 (mmm-85) REVERT: F 197 PHE cc_start: 0.8376 (p90) cc_final: 0.8039 (p90) REVERT: F 200 LYS cc_start: 0.6617 (tmmt) cc_final: 0.6389 (tmtt) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1594 time to fit residues: 24.1969 Evaluate side-chains 112 residues out of total 406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 ASN E 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.156581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.132878 restraints weight = 7923.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.136481 restraints weight = 5141.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.139058 restraints weight = 3800.704| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.9370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3699 Z= 0.234 Angle : 0.889 12.691 5044 Z= 0.452 Chirality : 0.054 0.286 580 Planarity : 0.005 0.049 651 Dihedral : 9.207 45.254 500 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.85 % Allowed : 22.13 % 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 : 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: -4.64 (0.35), residues: 470 helix: None (None), residues: 0 sheet: -2.28 (0.50), residues: 122 loop : -3.70 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 109 HIS 0.003 0.001 HIS E 24 PHE 0.021 0.003 PHE E 195 TYR 0.019 0.002 TYR F 176 ARG 0.003 0.000 ARG E 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1480.70 seconds wall clock time: 27 minutes 13.10 seconds (1633.10 seconds total)