Starting phenix.real_space_refine on Thu Mar 6 01:48:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sj0_25149/03_2025/7sj0_25149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj0_25149/03_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_25149/03_2025/7sj0_25149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj0_25149/03_2025/7sj0_25149.map" model { file = "/net/cci-nas-00/data/ceres_data/7sj0_25149/03_2025/7sj0_25149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj0_25149/03_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-5624/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: 4.39, per 1000 atoms: 1.22 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: 0.81 Conformation dependent library (CDL) restraints added in 365.7 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: 0.44 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: 0.85 Time building geometry restraints manager: 1.04 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: 4.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 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: 0.030 Process input model: 14.390 Find NCS groups from input model: 0.030 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.400 ------------------------------------------------------------------------------- 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 : 0.361 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: 0.1630 time to fit residues: 20.7563 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 : 0.359 ------------------------------------------------------------------------------- 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 = 0.102833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.085796 restraints weight = 8831.656| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.20 r_work: 0.3198 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- 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 58.371 587 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 : 0.402 Fit side-chains REVERT: A 128 ILE cc_start: 0.8686 (mp) cc_final: 0.8404 (mp) REVERT: A 172 SER cc_start: 0.7886 (t) cc_final: 0.7141 (m) REVERT: A 202 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8580 (mtpt) REVERT: B 62 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8307 (tm-30) REVERT: B 107 ASN cc_start: 0.8380 (p0) cc_final: 0.8119 (p0) REVERT: L 55 ARG cc_start: 0.7863 (ptm160) cc_final: 0.7562 (ptm160) outliers start: 9 outliers final: 4 residues processed: 101 average time/residue: 0.1847 time to fit residues: 22.2629 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 : 0.406 ------------------------------------------------------------------------------- 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: 0.4980 chunk 21 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN 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 = 0.3624 r_free = 0.3624 target = 0.103123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.086043 restraints weight = 8858.817| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.26 r_work: 0.3190 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3676 Z= 0.246 Angle : 0.665 7.993 4996 Z= 0.348 Chirality : 0.053 0.500 565 Planarity : 0.005 0.037 632 Dihedral : 7.743 58.882 587 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.57 % Allowed : 13.62 % Favored : 83.80 % 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 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.53 (0.41), residues: 152 loop : -2.11 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 104 HIS 0.002 0.000 HIS B 35 PHE 0.013 0.002 PHE A 86 TYR 0.012 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 111 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.362 Fit side-chains REVERT: A 128 ILE cc_start: 0.8667 (mp) cc_final: 0.8426 (mp) REVERT: A 202 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8506 (mtpt) REVERT: B 6 GLN cc_start: 0.7781 (pm20) cc_final: 0.7570 (pm20) REVERT: B 107 ASN cc_start: 0.8532 (p0) cc_final: 0.8253 (p0) outliers start: 10 outliers final: 6 residues processed: 105 average time/residue: 0.1697 time to fit residues: 21.2822 Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR 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: 0.8980 chunk 39 optimal weight: 0.0010 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 25 optimal weight: 0.2980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086611 restraints weight = 8753.274| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.17 r_work: 0.3207 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3676 Z= 0.210 Angle : 0.650 8.151 4996 Z= 0.338 Chirality : 0.051 0.483 565 Planarity : 0.005 0.042 632 Dihedral : 7.432 59.859 587 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.08 % Allowed : 14.65 % Favored : 82.26 % 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: -1.35 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.59 (0.40), residues: 167 loop : -2.02 (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 0.012 0.002 PHE A 86 TYR 0.010 0.001 TYR B 27 ARG 0.009 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 108 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8696 (mp) cc_final: 0.8438 (mp) REVERT: A 195 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8795 (ttpp) REVERT: A 202 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8521 (mtpt) REVERT: B 81 MET cc_start: 0.8885 (tmm) cc_final: 0.8639 (ttm) REVERT: B 107 ASN cc_start: 0.8483 (p0) cc_final: 0.8182 (p0) REVERT: L 54 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8088 (tppt) REVERT: L 93 ASP cc_start: 0.9338 (t0) cc_final: 0.9112 (t0) outliers start: 12 outliers final: 6 residues processed: 101 average time/residue: 0.1886 time to fit residues: 22.6305 Evaluate side-chains 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.0000 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.4980 chunk 35 optimal weight: 0.0010 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.103557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.086437 restraints weight = 8981.589| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.24 r_work: 0.3198 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3676 Z= 0.208 Angle : 0.656 7.677 4996 Z= 0.340 Chirality : 0.051 0.483 565 Planarity : 0.005 0.043 632 Dihedral : 7.127 59.433 587 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.60 % Allowed : 15.68 % Favored : 80.72 % 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: -1.39 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.75 (0.41), residues: 155 loop : -2.06 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.002 0.001 HIS B 35 PHE 0.012 0.002 PHE A 86 TYR 0.010 0.001 TYR B 95 ARG 0.010 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 110 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.361 Fit side-chains REVERT: A 100 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8694 (pt) REVERT: A 128 ILE cc_start: 0.8672 (mp) cc_final: 0.8410 (mp) REVERT: A 202 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8515 (mtpt) REVERT: B 81 MET cc_start: 0.8934 (tmm) cc_final: 0.8692 (ttm) REVERT: B 107 ASN cc_start: 0.8615 (p0) cc_final: 0.8323 (p0) REVERT: L 54 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8057 (tppt) REVERT: L 88 TYR cc_start: 0.9242 (m-80) cc_final: 0.8932 (m-80) REVERT: L 93 ASP cc_start: 0.9332 (t0) cc_final: 0.9053 (t0) outliers start: 14 outliers final: 9 residues processed: 101 average time/residue: 0.1770 time to fit residues: 21.2646 Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 43 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.103885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.086578 restraints weight = 8919.891| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 4.25 r_work: 0.3201 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3676 Z= 0.202 Angle : 0.655 8.008 4996 Z= 0.339 Chirality : 0.051 0.476 565 Planarity : 0.005 0.047 632 Dihedral : 6.954 59.159 587 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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: -1.31 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.65 (0.39), residues: 166 loop : -2.01 (0.36), residues: 272 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 0.010 0.001 PHE A 86 TYR 0.009 0.001 TYR A 91 ARG 0.010 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 113 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8662 (mp) cc_final: 0.8409 (mp) REVERT: A 202 LYS cc_start: 0.8879 (mtpt) cc_final: 0.8512 (mtpt) REVERT: B 81 MET cc_start: 0.8945 (tmm) cc_final: 0.8715 (ttm) REVERT: L 54 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8076 (tppt) REVERT: L 88 TYR cc_start: 0.9240 (m-80) cc_final: 0.8943 (m-80) REVERT: L 93 ASP cc_start: 0.9329 (t0) cc_final: 0.9063 (t0) outliers start: 14 outliers final: 10 residues processed: 104 average time/residue: 0.1722 time to fit residues: 21.4293 Evaluate side-chains 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 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: 0.0270 chunk 15 optimal weight: 0.3980 chunk 16 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.103327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.086127 restraints weight = 8843.966| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.25 r_work: 0.3191 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3676 Z= 0.230 Angle : 0.677 8.135 4996 Z= 0.351 Chirality : 0.051 0.491 565 Planarity : 0.004 0.030 632 Dihedral : 6.936 59.645 587 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.11 % Allowed : 15.94 % 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: -1.26 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.59 (0.39), residues: 173 loop : -1.96 (0.38), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 112 HIS 0.002 0.001 HIS B 35 PHE 0.012 0.002 PHE A 86 TYR 0.009 0.001 TYR B 95 ARG 0.004 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 113 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8667 (mp) cc_final: 0.8397 (mp) REVERT: A 202 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8523 (mtpt) REVERT: B 34 MET cc_start: 0.8609 (tpp) cc_final: 0.8093 (mmm) REVERT: B 81 MET cc_start: 0.8917 (tmm) cc_final: 0.8510 (ttm) REVERT: L 54 LYS cc_start: 0.8474 (ttmm) cc_final: 0.8080 (tppt) REVERT: L 88 TYR cc_start: 0.9247 (m-80) cc_final: 0.8966 (m-80) REVERT: L 93 ASP cc_start: 0.9360 (t0) cc_final: 0.9119 (t0) outliers start: 16 outliers final: 13 residues processed: 103 average time/residue: 0.1853 time to fit residues: 22.6611 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 : 0.378 ------------------------------------------------------------------------------- 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 107 ASN Chi-restraints excluded: chain L residue 23 SER Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 47 LEU 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: 0.8980 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.100789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.083615 restraints weight = 8964.151| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 4.21 r_work: 0.3150 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3676 Z= 0.359 Angle : 0.753 7.894 4996 Z= 0.395 Chirality : 0.055 0.557 565 Planarity : 0.005 0.035 632 Dihedral : 7.316 59.638 587 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.34 % Allowed : 16.97 % Favored : 79.69 % 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 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.50 (0.39), residues: 166 loop : -2.17 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 258 HIS 0.004 0.001 HIS B 35 PHE 0.019 0.002 PHE A 86 TYR 0.014 0.002 TYR B 27 ARG 0.003 0.001 ARG B 38 *********************** 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 108 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8688 (mp) cc_final: 0.8423 (mp) REVERT: A 138 ASP cc_start: 0.8906 (m-30) cc_final: 0.8703 (m-30) REVERT: A 202 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8559 (mtpt) REVERT: B 34 MET cc_start: 0.8704 (tpp) cc_final: 0.8206 (mmm) REVERT: B 81 MET cc_start: 0.8855 (tmm) cc_final: 0.8478 (ttm) REVERT: L 88 TYR cc_start: 0.9269 (m-80) cc_final: 0.8855 (m-80) outliers start: 13 outliers final: 11 residues processed: 102 average time/residue: 0.1819 time to fit residues: 22.3610 Evaluate side-chains 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 L residue 23 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ASN 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: 0.4980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.0060 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.102370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.084895 restraints weight = 8698.313| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.26 r_work: 0.3171 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3676 Z= 0.259 Angle : 0.718 8.426 4996 Z= 0.373 Chirality : 0.052 0.500 565 Planarity : 0.005 0.031 632 Dihedral : 7.130 59.527 587 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.08 % Allowed : 18.51 % Favored : 78.41 % 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 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.52 (0.39), residues: 173 loop : -2.22 (0.37), 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 0.013 0.002 PHE B 102 TYR 0.011 0.001 TYR B 95 ARG 0.003 0.001 ARG A 102 *********************** 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 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.440 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8688 (mp) cc_final: 0.8420 (mp) REVERT: A 138 ASP cc_start: 0.8903 (m-30) cc_final: 0.8686 (m-30) REVERT: A 187 LYS cc_start: 0.7027 (mmmt) cc_final: 0.6787 (mmmt) REVERT: A 202 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8546 (mtpt) REVERT: B 34 MET cc_start: 0.8628 (tpp) cc_final: 0.8160 (mmm) REVERT: B 81 MET cc_start: 0.8874 (tmm) cc_final: 0.8621 (ttm) REVERT: L 88 TYR cc_start: 0.9258 (m-80) cc_final: 0.8965 (m-80) outliers start: 12 outliers final: 11 residues processed: 100 average time/residue: 0.2372 time to fit residues: 28.7039 Evaluate side-chains 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 L residue 23 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 15 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.102017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084681 restraints weight = 8773.926| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.20 r_work: 0.3170 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3043 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= 0.279 Angle : 0.733 8.377 4996 Z= 0.381 Chirality : 0.053 0.511 565 Planarity : 0.005 0.032 632 Dihedral : 7.125 59.562 587 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.83 % Allowed : 18.25 % 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: -1.50 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.54 (0.40), residues: 173 loop : -2.22 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 104 HIS 0.004 0.001 HIS B 35 PHE 0.013 0.002 PHE A 86 TYR 0.012 0.001 TYR B 27 ARG 0.005 0.001 ARG L 62 ********************** 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 107 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 128 ILE cc_start: 0.8678 (mp) cc_final: 0.8413 (mp) REVERT: A 134 GLN cc_start: 0.8991 (tp40) cc_final: 0.8787 (tp40) REVERT: A 138 ASP cc_start: 0.8904 (m-30) cc_final: 0.8701 (m-30) REVERT: A 150 LYS cc_start: 0.9156 (mttm) cc_final: 0.8932 (mtpp) REVERT: A 187 LYS cc_start: 0.7123 (mmmt) cc_final: 0.6872 (mmmt) REVERT: A 202 LYS cc_start: 0.8937 (mtpt) cc_final: 0.8541 (mtpt) REVERT: B 34 MET cc_start: 0.8662 (tpp) cc_final: 0.8145 (mmm) REVERT: B 81 MET cc_start: 0.8863 (tmm) cc_final: 0.8601 (ttm) REVERT: L 62 ARG cc_start: 0.7523 (mmt-90) cc_final: 0.6934 (mmp80) REVERT: L 88 TYR cc_start: 0.9259 (m-80) cc_final: 0.8785 (m-80) outliers start: 11 outliers final: 11 residues processed: 101 average time/residue: 0.3198 time to fit residues: 38.6747 Evaluate side-chains 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 L residue 23 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 28 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 32 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.085158 restraints weight = 8833.323| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.23 r_work: 0.3188 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3085 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= 0.252 Angle : 0.755 10.710 4996 Z= 0.383 Chirality : 0.052 0.495 565 Planarity : 0.005 0.031 632 Dihedral : 7.048 59.862 587 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.83 % Allowed : 18.51 % 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: -1.46 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.57 (0.40), residues: 173 loop : -2.20 (0.37), 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 0.015 0.002 PHE B 64 TYR 0.011 0.001 TYR B 95 ARG 0.004 0.001 ARG L 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2808.14 seconds wall clock time: 51 minutes 14.80 seconds (3074.80 seconds total)