Starting phenix.real_space_refine on Wed Jul 1 23:54:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sj0_25149/07_2026/7sj0_25149.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sj0_25149/07_2026/7sj0_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_25149/07_2026/7sj0_25149.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sj0_25149/07_2026/7sj0_25149.map" model { file = "/net/cci-nas-00/data/ceres_data/7sj0_25149/07_2026/7sj0_25149.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sj0_25149/07_2026/7sj0_25149.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sj0_25149/07_2026/7sj0_25149.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sj0_25149/07_2026/7sj0_25149.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 chiralities: 5 Time building chain proxies: 0.86, per 1000 atoms: 0.24 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: 0.16 Conformation dependent library (CDL) restraints added in 80.2 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: 0.11 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: 0.29 Time building geometry restraints manager: 0.24 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: 1942 17.30 - 34.60: 132 34.60 - 51.90: 27 51.90 - 69.20: 4 69.20 - 86.49: 3 Dihedral angle restraints: 2108 sinusoidal: 817 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 2105 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: 7.020 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.960 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 3685 Z= 0.150 Angle : 0.695 11.271 5019 Z= 0.340 Chirality : 0.052 0.410 565 Planarity : 0.004 0.030 632 Dihedral : 12.583 86.494 1272 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.007 0.001 ARG A 190 TYR 0.010 0.001 TYR B 27 PHE 0.012 0.001 PHE A 238 TRP 0.007 0.001 TRP B 108 HIS 0.001 0.000 HIS A 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 3676) covalent geometry : angle 0.65582 / 0.33 ( 4996) SS BOND : bond 0.00359 / 0.18 ( 4) SS BOND : angle 1.09922 / 0.62 ( 8) hydrogen bonds : bond 0.31461 / 20.73 ( 83) hydrogen bonds : angle 10.57815 / 7.18 ( 228) link_NAG-ASN : bond 0.01028 / 0.60 ( 5) link_NAG-ASN : angle 4.20517 / 2.60 ( 15) *********************** 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 : 0.149 Fit side-chains REVERT: A 69 HIS cc_start: 0.7608 (t-90) cc_final: 0.7232 (t-90) 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: 0.0580 time to fit residues: 7.4691 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.2218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.089072 restraints weight = 8895.111| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.25 r_work: 0.3261 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3685 Z= 0.123 Angle : 0.702 13.205 5019 Z= 0.347 Chirality : 0.051 0.447 565 Planarity : 0.004 0.031 632 Dihedral : 5.040 22.750 482 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.29 % Allowed : 11.05 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.50 (0.42), residues: 144 loop : -2.07 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.012 0.001 TYR A 145 PHE 0.010 0.001 PHE A 92 TRP 0.009 0.002 TRP B 108 HIS 0.001 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 3676) covalent geometry : angle 0.65478 / 0.34 ( 4996) SS BOND : bond 0.00597 / 0.30 ( 4) SS BOND : angle 1.14736 / 0.59 ( 8) hydrogen bonds : bond 0.04116 / 2.67 ( 83) hydrogen bonds : angle 6.86519 / 4.69 ( 228) link_NAG-ASN : bond 0.01114 / 0.62 ( 5) link_NAG-ASN : angle 4.61300 / 2.88 ( 15) *********************** 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 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.098 Fit side-chains REVERT: A 177 MET cc_start: 0.7578 (ppp) cc_final: 0.7372 (ppp) REVERT: A 187 LYS cc_start: 0.7455 (mmtt) cc_final: 0.7214 (mmmt) REVERT: A 202 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8551 (mtpt) REVERT: A 218 GLN cc_start: 0.8530 (pp30) cc_final: 0.8286 (tm-30) REVERT: B 107 ASN cc_start: 0.8409 (p0) cc_final: 0.8086 (p0) REVERT: L 32 ASN cc_start: 0.7820 (m-40) cc_final: 0.7581 (m-40) REVERT: L 55 ARG cc_start: 0.7845 (ptm160) cc_final: 0.7572 (ptm160) REVERT: L 76 ILE cc_start: 0.7991 (tp) cc_final: 0.7756 (tt) outliers start: 5 outliers final: 1 residues processed: 102 average time/residue: 0.0665 time to fit residues: 8.1573 Evaluate side-chains 90 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.0980 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.103681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.086530 restraints weight = 8831.162| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.19 r_work: 0.3204 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3685 Z= 0.169 Angle : 0.702 12.917 5019 Z= 0.353 Chirality : 0.052 0.486 565 Planarity : 0.005 0.060 632 Dihedral : 5.224 22.767 482 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.31 % Allowed : 13.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.38), residues: 438 helix: None (None), residues: 0 sheet: 0.57 (0.41), residues: 152 loop : -1.97 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.013 0.001 TYR B 27 PHE 0.015 0.002 PHE A 86 TRP 0.021 0.002 TRP B 108 HIS 0.002 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 3676) covalent geometry : angle 0.65602 / 0.34 ( 4996) SS BOND : bond 0.00598 / 0.30 ( 4) SS BOND : angle 1.51357 / 0.86 ( 8) hydrogen bonds : bond 0.04572 / 2.98 ( 83) hydrogen bonds : angle 6.32607 / 4.26 ( 228) link_NAG-ASN : bond 0.01131 / 0.66 ( 5) link_NAG-ASN : angle 4.52034 / 2.86 ( 15) *********************** 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 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.130 Fit side-chains REVERT: A 153 MET cc_start: 0.8641 (tmm) cc_final: 0.8424 (tmm) REVERT: A 177 MET cc_start: 0.7665 (ppp) cc_final: 0.7412 (ppp) REVERT: A 187 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7450 (mmtt) REVERT: A 202 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8510 (mtpt) REVERT: B 34 MET cc_start: 0.8692 (tpp) cc_final: 0.8305 (mmm) REVERT: B 107 ASN cc_start: 0.8407 (p0) cc_final: 0.8121 (p0) REVERT: L 76 ILE cc_start: 0.8031 (tp) cc_final: 0.7766 (tt) outliers start: 9 outliers final: 7 residues processed: 99 average time/residue: 0.0611 time to fit residues: 7.3894 Evaluate side-chains 98 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 0.0970 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.0670 chunk 10 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.104290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.087209 restraints weight = 8848.660| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 4.20 r_work: 0.3226 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3685 Z= 0.137 Angle : 0.672 11.862 5019 Z= 0.333 Chirality : 0.050 0.457 565 Planarity : 0.005 0.045 632 Dihedral : 5.082 22.567 482 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.83 % Allowed : 13.88 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.74 (0.41), residues: 155 loop : -1.94 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 55 TYR 0.010 0.001 TYR B 95 PHE 0.009 0.001 PHE A 92 TRP 0.009 0.001 TRP B 108 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 3676) covalent geometry : angle 0.63096 / 0.32 ( 4996) SS BOND : bond 0.00536 / 0.27 ( 4) SS BOND : angle 1.36000 / 0.77 ( 8) hydrogen bonds : bond 0.03765 / 2.46 ( 83) hydrogen bonds : angle 5.90897 / 4.01 ( 228) link_NAG-ASN : bond 0.01042 / 0.61 ( 5) link_NAG-ASN : angle 4.18319 / 2.65 ( 15) *********************** 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 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 147 LYS cc_start: 0.8828 (ptmt) cc_final: 0.8555 (tttt) REVERT: A 195 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8802 (ttpp) REVERT: A 202 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8539 (mtpt) REVERT: A 218 GLN cc_start: 0.8362 (pp30) cc_final: 0.7976 (pp30) REVERT: B 81 MET cc_start: 0.8873 (tmm) cc_final: 0.8574 (ttm) REVERT: B 107 ASN cc_start: 0.8404 (p0) cc_final: 0.8078 (p0) REVERT: L 32 ASN cc_start: 0.7613 (m110) cc_final: 0.7363 (m-40) REVERT: L 33 TYR cc_start: 0.8094 (m-80) cc_final: 0.6948 (m-80) REVERT: L 62 ARG cc_start: 0.7383 (mmt180) cc_final: 0.6699 (mmp80) REVERT: L 93 ASP cc_start: 0.9344 (t0) cc_final: 0.9081 (t0) outliers start: 11 outliers final: 6 residues processed: 97 average time/residue: 0.0706 time to fit residues: 8.3027 Evaluate side-chains 97 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 191 GLU Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain B residue 2 VAL 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 24 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.0050 chunk 38 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.086047 restraints weight = 8795.208| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.25 r_work: 0.3192 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3685 Z= 0.162 Angle : 0.693 11.866 5019 Z= 0.346 Chirality : 0.051 0.487 565 Planarity : 0.005 0.035 632 Dihedral : 5.163 23.103 482 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.83 % Allowed : 15.17 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.85 (0.41), residues: 155 loop : -1.97 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 62 TYR 0.011 0.001 TYR B 27 PHE 0.012 0.002 PHE A 86 TRP 0.009 0.002 TRP B 112 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 3676) covalent geometry : angle 0.65206 / 0.34 ( 4996) SS BOND : bond 0.00558 / 0.28 ( 4) SS BOND : angle 1.45261 / 0.84 ( 8) hydrogen bonds : bond 0.04140 / 2.73 ( 83) hydrogen bonds : angle 5.87672 / 4.00 ( 228) link_NAG-ASN : bond 0.01048 / 0.62 ( 5) link_NAG-ASN : angle 4.25191 / 2.71 ( 15) *********************** 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: 11 poor density : 99 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.7807 (ppp) cc_final: 0.7604 (ppp) REVERT: A 195 LYS cc_start: 0.9049 (ttpt) cc_final: 0.8833 (ttpp) REVERT: A 202 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8531 (mtpt) REVERT: B 81 MET cc_start: 0.8882 (tmm) cc_final: 0.8581 (ttm) REVERT: L 32 ASN cc_start: 0.7651 (m110) cc_final: 0.7285 (m110) REVERT: L 62 ARG cc_start: 0.7515 (mmt180) cc_final: 0.6887 (mmp80) REVERT: L 93 ASP cc_start: 0.9364 (t0) cc_final: 0.9103 (t0) outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.0730 time to fit residues: 8.8418 Evaluate side-chains 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.097 ------------------------------------------------------------------------------- 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 239 GLN 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 30 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 39 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3634 r_free = 0.3634 target = 0.103527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086293 restraints weight = 8977.876| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.25 r_work: 0.3206 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3685 Z= 0.151 Angle : 0.695 11.407 5019 Z= 0.346 Chirality : 0.050 0.472 565 Planarity : 0.005 0.032 632 Dihedral : 5.082 23.255 482 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.34 % Allowed : 16.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.39), residues: 438 helix: None (None), residues: 0 sheet: 0.80 (0.40), residues: 155 loop : -1.90 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 62 TYR 0.010 0.001 TYR B 27 PHE 0.010 0.001 PHE A 92 TRP 0.008 0.001 TRP A 104 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 3676) covalent geometry : angle 0.65724 / 0.34 ( 4996) SS BOND : bond 0.00520 / 0.26 ( 4) SS BOND : angle 1.40901 / 0.82 ( 8) hydrogen bonds : bond 0.03919 / 2.59 ( 83) hydrogen bonds : angle 5.76612 / 3.93 ( 228) link_NAG-ASN : bond 0.01021 / 0.60 ( 5) link_NAG-ASN : angle 4.06554 / 2.59 ( 15) *********************** 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 110 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8567 (mtpt) REVERT: B 81 MET cc_start: 0.8869 (tmm) cc_final: 0.8581 (ttm) REVERT: L 32 ASN cc_start: 0.7647 (m110) cc_final: 0.7299 (m110) REVERT: L 54 LYS cc_start: 0.8476 (ttmm) cc_final: 0.8113 (tppt) REVERT: L 62 ARG cc_start: 0.7454 (mmt180) cc_final: 0.6819 (mmp80) REVERT: L 93 ASP cc_start: 0.9365 (t0) cc_final: 0.9114 (t0) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.0751 time to fit residues: 9.0630 Evaluate side-chains 103 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 B residue 2 VAL Chi-restraints excluded: chain B residue 107 ASN 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 28 optimal weight: 0.0050 chunk 23 optimal weight: 0.0050 chunk 32 optimal weight: 0.0570 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.0170 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3687 r_free = 0.3687 target = 0.107099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089748 restraints weight = 8957.042| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 4.29 r_work: 0.3265 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3685 Z= 0.111 Angle : 0.671 9.770 5019 Z= 0.333 Chirality : 0.048 0.379 565 Planarity : 0.004 0.032 632 Dihedral : 4.676 20.833 482 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.06 % Allowed : 17.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 0.98 (0.41), residues: 159 loop : -1.87 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 62 TYR 0.009 0.001 TYR A 145 PHE 0.009 0.001 PHE B 109 TRP 0.009 0.001 TRP A 104 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 3676) covalent geometry : angle 0.64303 / 0.33 ( 4996) SS BOND : bond 0.00403 / 0.20 ( 4) SS BOND : angle 1.16427 / 0.69 ( 8) hydrogen bonds : bond 0.02559 / 1.70 ( 83) hydrogen bonds : angle 5.34251 / 3.70 ( 228) link_NAG-ASN : bond 0.00897 / 0.54 ( 5) link_NAG-ASN : angle 3.49278 / 2.21 ( 15) *********************** 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 106 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: A 187 LYS cc_start: 0.6908 (mmmt) cc_final: 0.6685 (mmmt) REVERT: A 202 LYS cc_start: 0.8826 (mtpt) cc_final: 0.8499 (mtpt) REVERT: B 81 MET cc_start: 0.8908 (tmm) cc_final: 0.8666 (ttm) REVERT: L 32 ASN cc_start: 0.7449 (m110) cc_final: 0.7015 (m110) REVERT: L 33 TYR cc_start: 0.8018 (m-80) cc_final: 0.6844 (m-80) REVERT: L 62 ARG cc_start: 0.7411 (mmt180) cc_final: 0.6760 (mmp80) REVERT: L 76 ILE cc_start: 0.7787 (tp) cc_final: 0.7532 (tt) REVERT: L 93 ASP cc_start: 0.9332 (t0) cc_final: 0.9071 (t0) outliers start: 8 outliers final: 6 residues processed: 100 average time/residue: 0.0695 time to fit residues: 8.2818 Evaluate side-chains 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 196 ASN Chi-restraints excluded: chain A residue 216 LEU 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 39 optimal weight: 0.2980 chunk 15 optimal weight: 0.2980 chunk 33 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.0040 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.087555 restraints weight = 8891.850| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.30 r_work: 0.3233 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3685 Z= 0.138 Angle : 0.693 10.627 5019 Z= 0.349 Chirality : 0.049 0.450 565 Planarity : 0.004 0.030 632 Dihedral : 4.736 20.886 482 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.06 % Allowed : 20.31 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.40), residues: 438 helix: None (None), residues: 0 sheet: 1.03 (0.41), residues: 154 loop : -1.75 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.010 0.001 TYR B 27 PHE 0.009 0.001 PHE A 86 TRP 0.007 0.001 TRP B 112 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3676) covalent geometry : angle 0.66197 / 0.34 ( 4996) SS BOND : bond 0.00430 / 0.21 ( 4) SS BOND : angle 1.25789 / 0.73 ( 8) hydrogen bonds : bond 0.03479 / 2.32 ( 83) hydrogen bonds : angle 5.44298 / 3.74 ( 228) link_NAG-ASN : bond 0.00944 / 0.55 ( 5) link_NAG-ASN : angle 3.75134 / 2.39 ( 15) *********************** 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 102 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 202 LYS cc_start: 0.8886 (mtpt) cc_final: 0.8537 (mtpt) REVERT: B 72 GLU cc_start: 0.8427 (mp0) cc_final: 0.7986 (mp0) REVERT: B 81 MET cc_start: 0.8938 (tmm) cc_final: 0.8705 (ttm) REVERT: L 32 ASN cc_start: 0.7452 (m110) cc_final: 0.6994 (m110) REVERT: L 33 TYR cc_start: 0.8044 (m-80) cc_final: 0.6906 (m-80) REVERT: L 62 ARG cc_start: 0.7494 (mmt180) cc_final: 0.6894 (mmp80) outliers start: 8 outliers final: 7 residues processed: 97 average time/residue: 0.0788 time to fit residues: 9.1358 Evaluate side-chains 100 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 216 LEU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.105521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.088311 restraints weight = 8815.548| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.22 r_work: 0.3230 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3685 Z= 0.137 Angle : 0.719 10.317 5019 Z= 0.358 Chirality : 0.049 0.437 565 Planarity : 0.004 0.030 632 Dihedral : 4.767 21.317 482 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.31 % Allowed : 20.82 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.41), residues: 438 helix: None (None), residues: 0 sheet: 1.24 (0.43), residues: 153 loop : -1.90 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.010 0.001 TYR B 27 PHE 0.009 0.001 PHE A 92 TRP 0.008 0.001 TRP B 36 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 3676) covalent geometry : angle 0.69022 / 0.35 ( 4996) SS BOND : bond 0.00431 / 0.22 ( 4) SS BOND : angle 1.27491 / 0.76 ( 8) hydrogen bonds : bond 0.03297 / 2.18 ( 83) hydrogen bonds : angle 5.46217 / 3.75 ( 228) link_NAG-ASN : bond 0.00940 / 0.56 ( 5) link_NAG-ASN : angle 3.66516 / 2.34 ( 15) *********************** 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 101 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 187 LYS cc_start: 0.6954 (mmmt) cc_final: 0.6746 (mmmt) REVERT: A 202 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8526 (mtpt) REVERT: B 34 MET cc_start: 0.8460 (tpp) cc_final: 0.8079 (mmm) REVERT: L 32 ASN cc_start: 0.7419 (m110) cc_final: 0.6947 (m110) REVERT: L 33 TYR cc_start: 0.7925 (m-80) cc_final: 0.6872 (m-80) REVERT: L 62 ARG cc_start: 0.7517 (mmt180) cc_final: 0.6838 (mmp80) outliers start: 9 outliers final: 8 residues processed: 95 average time/residue: 0.0648 time to fit residues: 7.3601 Evaluate side-chains 99 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.082 ------------------------------------------------------------------------------- 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 B residue 107 ASN Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 0.0020 chunk 42 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 32 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.104700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087223 restraints weight = 8898.336| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.26 r_work: 0.3212 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3685 Z= 0.157 Angle : 0.753 13.584 5019 Z= 0.374 Chirality : 0.050 0.465 565 Planarity : 0.004 0.033 632 Dihedral : 4.843 21.305 482 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.57 % Allowed : 21.08 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.41), residues: 438 helix: None (None), residues: 0 sheet: 1.19 (0.43), residues: 154 loop : -1.89 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 102 TYR 0.012 0.001 TYR B 27 PHE 0.010 0.001 PHE A 86 TRP 0.007 0.001 TRP B 112 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 3676) covalent geometry : angle 0.72403 / 0.37 ( 4996) SS BOND : bond 0.00448 / 0.22 ( 4) SS BOND : angle 1.38649 / 0.82 ( 8) hydrogen bonds : bond 0.03702 / 2.46 ( 83) hydrogen bonds : angle 5.58858 / 3.80 ( 228) link_NAG-ASN : bond 0.00955 / 0.56 ( 5) link_NAG-ASN : angle 3.78412 / 2.43 ( 15) ********************** 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 105 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8834 (m-30) cc_final: 0.8611 (m-30) REVERT: A 187 LYS cc_start: 0.7023 (mmmt) cc_final: 0.6800 (mmmt) REVERT: A 202 LYS cc_start: 0.8906 (mtpt) cc_final: 0.8536 (mtpt) REVERT: B 34 MET cc_start: 0.8450 (tpp) cc_final: 0.8189 (mmm) REVERT: L 32 ASN cc_start: 0.7478 (m110) cc_final: 0.6980 (m110) REVERT: L 33 TYR cc_start: 0.7854 (m-80) cc_final: 0.6801 (m-80) REVERT: L 62 ARG cc_start: 0.7492 (mmt180) cc_final: 0.6755 (mmp80) REVERT: L 76 ILE cc_start: 0.7893 (tp) cc_final: 0.7599 (tt) outliers start: 10 outliers final: 9 residues processed: 99 average time/residue: 0.0798 time to fit residues: 9.4176 Evaluate side-chains 104 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 B residue 2 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 20 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.3980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3620 r_free = 0.3620 target = 0.102948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085736 restraints weight = 8754.884| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 4.19 r_work: 0.3197 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3685 Z= 0.196 Angle : 0.799 13.190 5019 Z= 0.399 Chirality : 0.052 0.506 565 Planarity : 0.005 0.032 632 Dihedral : 5.183 24.048 482 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.57 % Allowed : 21.08 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.41), residues: 438 helix: None (None), residues: 0 sheet: 1.13 (0.42), residues: 159 loop : -1.86 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 55 TYR 0.013 0.002 TYR B 27 PHE 0.013 0.002 PHE A 86 TRP 0.012 0.002 TRP B 108 HIS 0.004 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 ( 3676) covalent geometry : angle 0.76526 / 0.39 ( 4996) SS BOND : bond 0.00504 / 0.25 ( 4) SS BOND : angle 1.50962 / 0.88 ( 8) hydrogen bonds : bond 0.04300 / 2.85 ( 83) hydrogen bonds : angle 5.83992 / 3.96 ( 228) link_NAG-ASN : bond 0.01033 / 0.61 ( 5) link_NAG-ASN : angle 4.13640 / 2.65 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.10 seconds wall clock time: 20 minutes 32.26 seconds (1232.26 seconds total)