Starting phenix.real_space_refine on Tue Feb 11 06:15:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj0_25149/02_2025/7sj0_25149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj0_25149/02_2025/7sj0_25149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sj0_25149/02_2025/7sj0_25149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj0_25149/02_2025/7sj0_25149.map" model { file = "/net/cci-nas-00/data/ceres_data/7sj0_25149/02_2025/7sj0_25149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj0_25149/02_2025/7sj0_25149.cif" } resolution = 3.36 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 812 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2279 2.51 5 N 593 2.21 5 O 704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3590 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1806 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 10, 'TRANS': 213} Chain breaks: 4 Chain: "B" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 784 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 3.75, per 1000 atoms: 1.04 Number of scatterers: 3590 At special positions: 0 Unit cell: (99, 78.1, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 704 8.00 N 593 7.00 C 2279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 17 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 149 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 485.1 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 9 sheets defined 2.0% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'B' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 4.312A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 4.045A pdb=" N ARG A 78 " --> pdb=" O HIS A 69 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HIS A 69 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.702A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 155 removed outlier: 4.000A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.735A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.846A pdb=" N THR B 119 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 118 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA B 92 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY B 99 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 40 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.525A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 46 through 50 removed outlier: 3.640A pdb=" N GLN L 38 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER L 35 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY L 90 " --> pdb=" O SER L 35 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 228 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: 0.98 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1130 1.34 - 1.46: 942 1.46 - 1.58: 1584 1.58 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3676 Sorted by residual: bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.94e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 3671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 4795 1.51 - 3.02: 173 3.02 - 4.53: 22 4.53 - 6.04: 4 6.04 - 7.54: 2 Bond angle restraints: 4996 Sorted by residual: angle pdb=" CA THR A 33 " pdb=" CB THR A 33 " pdb=" CG2 THR A 33 " ideal model delta sigma weight residual 110.50 114.45 -3.95 1.70e+00 3.46e-01 5.39e+00 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 119.53 -5.13 2.30e+00 1.89e-01 4.98e+00 angle pdb=" CA LEU L 96 " pdb=" CB LEU L 96 " pdb=" CG LEU L 96 " ideal model delta sigma weight residual 116.30 123.84 -7.54 3.50e+00 8.16e-02 4.65e+00 angle pdb=" CB MET B 34 " pdb=" CG MET B 34 " pdb=" SD MET B 34 " ideal model delta sigma weight residual 112.70 118.84 -6.14 3.00e+00 1.11e-01 4.20e+00 angle pdb=" C PHE A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 122.68 125.62 -2.94 1.47e+00 4.63e-01 4.01e+00 ... (remaining 4991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 2034 17.30 - 34.60: 135 34.60 - 51.90: 33 51.90 - 69.20: 8 69.20 - 86.49: 3 Dihedral angle restraints: 2213 sinusoidal: 922 harmonic: 1291 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -135.37 49.37 1 1.00e+01 1.00e-02 3.35e+01 dihedral pdb=" CA ASN A 99 " pdb=" C ASN A 99 " pdb=" N ILE A 100 " pdb=" CA ILE A 100 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA THR A 167 " pdb=" C THR A 167 " pdb=" N PHE A 168 " pdb=" CA PHE A 168 " ideal model delta harmonic sigma weight residual -180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 2210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 503 0.082 - 0.164: 60 0.164 - 0.246: 0 0.246 - 0.328: 1 0.328 - 0.410: 1 Chirality restraints: 565 Sorted by residual: chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 ... (remaining 562 not shown) Planarity restraints: 637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG L 55 " 0.020 5.00e-02 4.00e+02 3.04e-02 1.48e+00 pdb=" N PRO L 56 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO L 56 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO L 56 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 99 " -0.006 2.00e-02 2.50e+03 1.21e-02 1.46e+00 pdb=" C ASN A 99 " 0.021 2.00e-02 2.50e+03 pdb=" O ASN A 99 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 100 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.010 2.00e-02 2.50e+03 9.87e-03 1.22e+00 pdb=" CG ASN A 61 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " -0.011 2.00e-02 2.50e+03 ... (remaining 634 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 512 2.76 - 3.30: 3344 3.30 - 3.83: 4986 3.83 - 4.37: 5454 4.37 - 4.90: 10160 Nonbonded interactions: 24456 Sorted by model distance: nonbonded pdb=" OG SER L 68 " pdb=" OG SER L 71 " model vdw 2.225 3.040 nonbonded pdb=" O GLY L 30 " pdb=" NZ LYS L 67 " model vdw 2.273 3.120 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.300 3.040 nonbonded pdb=" NZ LYS A 129 " pdb=" O PHE A 168 " model vdw 2.337 3.120 nonbonded pdb=" OG1 THR A 124 " pdb=" O7 NAG A1301 " model vdw 2.337 3.040 ... (remaining 24451 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.950 Find NCS groups from input model: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3676 Z= 0.209 Angle : 0.656 7.544 4996 Z= 0.331 Chirality : 0.052 0.410 565 Planarity : 0.004 0.030 632 Dihedral : 12.810 86.494 1377 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.98 (0.38), residues: 438 helix: None (None), residues: 0 sheet: -0.01 (0.42), residues: 141 loop : -2.13 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 108 HIS 0.001 0.000 HIS A 69 PHE 0.012 0.001 PHE A 238 TYR 0.010 0.001 TYR B 27 ARG 0.007 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.387 Fit side-chains REVERT: A 69 HIS cc_start: 0.7608 (t-90) cc_final: 0.7232 (t-90) REVERT: A 128 ILE cc_start: 0.8539 (mp) cc_final: 0.8327 (mp) REVERT: A 144 TYR cc_start: 0.8296 (p90) cc_final: 0.8091 (p90) REVERT: A 202 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8367 (mtpt) REVERT: B 64 PHE cc_start: 0.8333 (m-10) cc_final: 0.8057 (m-10) REVERT: B 107 ASN cc_start: 0.7869 (p0) cc_final: 0.7609 (p0) REVERT: L 76 ILE cc_start: 0.8006 (tp) cc_final: 0.7749 (tt) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1712 time to fit residues: 21.7576 Evaluate side-chains 94 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.0040 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 99 ASN A 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.085804 restraints weight = 8830.650| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.20 r_work: 0.3199 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3676 Z= 0.291 Angle : 0.707 8.792 4996 Z= 0.369 Chirality : 0.055 0.543 565 Planarity : 0.005 0.033 632 Dihedral : 7.729 58.372 587 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.31 % Allowed : 11.83 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.74 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.45 (0.42), residues: 144 loop : -2.17 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 108 HIS 0.003 0.001 HIS B 35 PHE 0.018 0.002 PHE A 86 TYR 0.015 0.002 TYR B 27 ARG 0.008 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.390 Fit side-chains REVERT: A 128 ILE cc_start: 0.8686 (mp) cc_final: 0.8405 (mp) REVERT: A 172 SER cc_start: 0.7887 (t) cc_final: 0.7141 (m) REVERT: A 202 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8581 (mtpt) REVERT: B 62 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8307 (tm-30) REVERT: B 107 ASN cc_start: 0.8379 (p0) cc_final: 0.8118 (p0) REVERT: L 55 ARG cc_start: 0.7862 (ptm160) cc_final: 0.7562 (ptm160) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 0.1837 time to fit residues: 22.0962 Evaluate side-chains 96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 250 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 13 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.0170 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN L 32 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.105078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.087897 restraints weight = 8867.049| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.26 r_work: 0.3226 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3676 Z= 0.172 Angle : 0.631 8.152 4996 Z= 0.328 Chirality : 0.051 0.450 565 Planarity : 0.005 0.035 632 Dihedral : 7.522 59.749 587 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.31 % Allowed : 14.14 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.49 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.59 (0.41), residues: 152 loop : -2.04 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.001 0.000 HIS B 35 PHE 0.009 0.001 PHE A 92 TYR 0.008 0.001 TYR B 27 ARG 0.008 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.379 Fit side-chains REVERT: A 34 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7522 (tpt90) REVERT: A 128 ILE cc_start: 0.8646 (mp) cc_final: 0.8388 (mp) REVERT: A 202 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8494 (mtpt) REVERT: B 31 GLU cc_start: 0.8368 (pm20) cc_final: 0.8137 (pm20) REVERT: B 62 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 107 ASN cc_start: 0.8449 (p0) cc_final: 0.8144 (p0) REVERT: L 54 LYS cc_start: 0.8462 (ttmm) cc_final: 0.8075 (tppt) outliers start: 9 outliers final: 5 residues processed: 103 average time/residue: 0.1795 time to fit residues: 22.0180 Evaluate side-chains 96 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.0060 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 146 HIS A 218 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086144 restraints weight = 8745.686| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.17 r_work: 0.3195 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3676 Z= 0.236 Angle : 0.651 8.196 4996 Z= 0.337 Chirality : 0.052 0.497 565 Planarity : 0.004 0.032 632 Dihedral : 7.463 59.923 587 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.60 % Allowed : 13.88 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.33 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.61 (0.40), residues: 167 loop : -2.01 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS B 35 PHE 0.014 0.002 PHE A 86 TYR 0.012 0.001 TYR B 27 ARG 0.005 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.386 Fit side-chains REVERT: A 100 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8676 (pt) REVERT: A 128 ILE cc_start: 0.8673 (mp) cc_final: 0.8438 (mp) REVERT: A 195 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8795 (ttpp) REVERT: A 202 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8488 (mtpt) REVERT: B 81 MET cc_start: 0.8898 (tmm) cc_final: 0.8652 (ttm) REVERT: B 107 ASN cc_start: 0.8544 (p0) cc_final: 0.8254 (p0) REVERT: L 93 ASP cc_start: 0.9321 (t0) cc_final: 0.9044 (t0) outliers start: 14 outliers final: 9 residues processed: 103 average time/residue: 0.1872 time to fit residues: 23.0636 Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.102093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.084957 restraints weight = 8989.357| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 4.28 r_work: 0.3171 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3676 Z= 0.278 Angle : 0.692 7.498 4996 Z= 0.362 Chirality : 0.053 0.522 565 Planarity : 0.005 0.047 632 Dihedral : 7.343 59.680 587 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.86 % Allowed : 15.68 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.41 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.60 (0.39), residues: 166 loop : -2.09 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 112 HIS 0.004 0.001 HIS B 35 PHE 0.016 0.002 PHE A 86 TYR 0.012 0.002 TYR B 95 ARG 0.009 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.360 Fit side-chains REVERT: A 128 ILE cc_start: 0.8706 (mp) cc_final: 0.8446 (mp) REVERT: A 202 LYS cc_start: 0.8932 (mtpt) cc_final: 0.8543 (mtpt) REVERT: B 81 MET cc_start: 0.8886 (tmm) cc_final: 0.8600 (ttm) REVERT: B 107 ASN cc_start: 0.8635 (p0) cc_final: 0.8386 (p0) REVERT: L 93 ASP cc_start: 0.9325 (t0) cc_final: 0.9052 (t0) outliers start: 15 outliers final: 11 residues processed: 102 average time/residue: 0.1844 time to fit residues: 22.4470 Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.0970 chunk 8 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084343 restraints weight = 8959.900| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 4.26 r_work: 0.3160 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3676 Z= 0.306 Angle : 0.712 7.590 4996 Z= 0.374 Chirality : 0.053 0.533 565 Planarity : 0.005 0.050 632 Dihedral : 7.385 59.166 587 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.60 % Allowed : 16.45 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.51 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.52 (0.39), residues: 167 loop : -2.16 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 104 HIS 0.004 0.001 HIS B 35 PHE 0.016 0.002 PHE A 86 TYR 0.012 0.002 TYR B 95 ARG 0.011 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.380 Fit side-chains REVERT: A 128 ILE cc_start: 0.8695 (mp) cc_final: 0.8424 (mp) REVERT: A 202 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8539 (mtpt) REVERT: B 81 MET cc_start: 0.8858 (tmm) cc_final: 0.8593 (ttm) REVERT: L 93 ASP cc_start: 0.9283 (t0) cc_final: 0.9045 (t0) outliers start: 14 outliers final: 11 residues processed: 101 average time/residue: 0.1772 time to fit residues: 21.3214 Evaluate side-chains 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain L residue 23 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 42 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.083849 restraints weight = 8879.257| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 4.24 r_work: 0.3152 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3676 Z= 0.325 Angle : 0.733 7.783 4996 Z= 0.384 Chirality : 0.054 0.541 565 Planarity : 0.005 0.053 632 Dihedral : 7.459 59.266 587 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.63 % Allowed : 15.94 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.57 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.48 (0.39), residues: 173 loop : -2.26 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 112 HIS 0.004 0.001 HIS B 35 PHE 0.016 0.002 PHE A 86 TYR 0.013 0.002 TYR B 95 ARG 0.012 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8754 (pt) REVERT: A 128 ILE cc_start: 0.8691 (mp) cc_final: 0.8416 (mp) REVERT: A 138 ASP cc_start: 0.8920 (m-30) cc_final: 0.8716 (m-30) REVERT: A 202 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8537 (mtpt) REVERT: B 34 MET cc_start: 0.8696 (tpp) cc_final: 0.8320 (mmm) REVERT: B 81 MET cc_start: 0.8871 (tmm) cc_final: 0.8480 (ttm) REVERT: L 93 ASP cc_start: 0.9270 (t0) cc_final: 0.9047 (t0) outliers start: 18 outliers final: 12 residues processed: 103 average time/residue: 0.1849 time to fit residues: 22.7803 Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 chunk 33 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084207 restraints weight = 8951.186| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 4.21 r_work: 0.3159 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3676 Z= 0.295 Angle : 0.729 8.233 4996 Z= 0.381 Chirality : 0.053 0.522 565 Planarity : 0.005 0.058 632 Dihedral : 7.381 59.184 587 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.60 % Allowed : 17.48 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.54 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.56 (0.40), residues: 173 loop : -2.29 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 104 HIS 0.003 0.001 HIS B 35 PHE 0.014 0.002 PHE A 86 TYR 0.012 0.001 TYR B 95 ARG 0.013 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8684 (mp) cc_final: 0.8413 (mp) REVERT: A 202 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8550 (mtpt) REVERT: B 81 MET cc_start: 0.8872 (tmm) cc_final: 0.8479 (ttm) outliers start: 14 outliers final: 12 residues processed: 99 average time/residue: 0.2176 time to fit residues: 25.8152 Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 26 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.101819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084603 restraints weight = 8713.843| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.26 r_work: 0.3171 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3676 Z= 0.248 Angle : 0.727 8.152 4996 Z= 0.378 Chirality : 0.052 0.501 565 Planarity : 0.005 0.060 632 Dihedral : 7.247 59.238 587 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.34 % Allowed : 18.51 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.47 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.64 (0.40), residues: 173 loop : -2.27 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 104 HIS 0.003 0.001 HIS B 35 PHE 0.014 0.002 PHE B 102 TYR 0.011 0.001 TYR B 95 ARG 0.014 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8701 (mp) cc_final: 0.8435 (mp) REVERT: A 187 LYS cc_start: 0.6929 (mmmt) cc_final: 0.6701 (mmmt) REVERT: A 202 LYS cc_start: 0.8929 (mtpt) cc_final: 0.8534 (mtpt) REVERT: B 81 MET cc_start: 0.8881 (tmm) cc_final: 0.8607 (ttm) REVERT: L 33 TYR cc_start: 0.8027 (m-80) cc_final: 0.6918 (m-80) outliers start: 13 outliers final: 12 residues processed: 100 average time/residue: 0.1908 time to fit residues: 22.6609 Evaluate side-chains 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.0020 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083796 restraints weight = 8771.665| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 4.26 r_work: 0.3155 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3676 Z= 0.302 Angle : 0.758 7.831 4996 Z= 0.396 Chirality : 0.054 0.523 565 Planarity : 0.006 0.067 632 Dihedral : 7.313 59.350 587 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.34 % Allowed : 18.51 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.58 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.53 (0.40), residues: 173 loop : -2.32 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 108 HIS 0.004 0.001 HIS B 35 PHE 0.015 0.002 PHE A 86 TYR 0.013 0.001 TYR B 95 ARG 0.016 0.002 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8706 (mp) cc_final: 0.8440 (mp) REVERT: A 187 LYS cc_start: 0.7093 (mmmt) cc_final: 0.6830 (mmmt) REVERT: A 202 LYS cc_start: 0.8946 (mtpt) cc_final: 0.8549 (mtpt) REVERT: B 81 MET cc_start: 0.8876 (tmm) cc_final: 0.8607 (ttm) REVERT: L 33 TYR cc_start: 0.7987 (m-80) cc_final: 0.6881 (m-80) REVERT: L 62 ARG cc_start: 0.7846 (mmt180) cc_final: 0.7285 (mmp80) REVERT: L 88 TYR cc_start: 0.9244 (m-80) cc_final: 0.8930 (m-80) outliers start: 13 outliers final: 12 residues processed: 99 average time/residue: 0.1877 time to fit residues: 22.0445 Evaluate side-chains 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 0.0470 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.101496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084204 restraints weight = 8861.687| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 4.29 r_work: 0.3163 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3676 Z= 0.271 Angle : 0.755 8.624 4996 Z= 0.391 Chirality : 0.053 0.507 565 Planarity : 0.006 0.067 632 Dihedral : 7.253 59.302 587 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.08 % Allowed : 18.25 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.53 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.59 (0.40), residues: 173 loop : -2.30 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS B 35 PHE 0.012 0.002 PHE A 86 TYR 0.011 0.001 TYR B 95 ARG 0.016 0.001 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2428.43 seconds wall clock time: 43 minutes 46.08 seconds (2626.08 seconds total)