Starting phenix.real_space_refine on Tue Feb 3 13:59:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s35_54523/02_2026/9s35_54523.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s35_54523/02_2026/9s35_54523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s35_54523/02_2026/9s35_54523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s35_54523/02_2026/9s35_54523.map" model { file = "/net/cci-nas-00/data/ceres_data/9s35_54523/02_2026/9s35_54523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s35_54523/02_2026/9s35_54523.cif" } resolution = 3.0 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2190 2.51 5 N 541 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3361 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 952 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 930 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Conformer: "B" Number of residues, atoms: 122, 930 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} bond proxies already assigned to first conformer: 921 Chain: "A" Number of atoms: 2402 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 2385 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 306, 2385 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain breaks: 1 bond proxies already assigned to first conformer: 2419 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP B 104 " occ=0.53 ... (26 atoms not shown) pdb=" CH2BTRP B 104 " occ=0.47 Time building chain proxies: 1.41, per 1000 atoms: 0.42 Number of scatterers: 3361 At special positions: 0 Unit cell: (88.572, 54.9, 78.324, 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 21 16.00 O 609 8.00 N 541 7.00 C 2190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 230.5 milliseconds 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 62.6% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 60 through 63 Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'A' and resid 55 through 76 removed outlier: 3.504A pdb=" N SER A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 107 Processing helix chain 'A' and resid 116 through 141 removed outlier: 3.975A pdb=" N LYS A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.629A pdb=" N TYR A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 166 " --> pdb=" O TYR A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 192 Processing helix chain 'A' and resid 204 through 232 removed outlier: 3.679A pdb=" N TYR A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 217 " --> pdb=" O TRP A 213 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 249 Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.932A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 262 " --> pdb=" O SER A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 removed outlier: 3.527A pdb=" N SER A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 removed outlier: 3.954A pdb=" N GLY A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 removed outlier: 3.803A pdb=" N ALA A 300 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 318 Processing helix chain 'A' and resid 319 through 330 Processing helix chain 'A' and resid 335 through 361 removed outlier: 4.559A pdb=" N SER A 341 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 1 through 6 removed outlier: 5.969A pdb=" N GLY B 15 " --> pdb=" O SER B 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.575A pdb=" N VAL B 91 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL B 32 " --> pdb=" O HIS B 97 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B 99 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE B 30 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU B 46 " --> pdb=" O ARG B 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 11 231 hydrogen bonds defined for protein. 661 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: 0.50 Time building geometry restraints manager: 0.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1011 1.34 - 1.46: 723 1.46 - 1.57: 1666 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 3434 Sorted by residual: bond pdb=" C GLY A 169 " pdb=" N GLY A 170 " ideal model delta sigma weight residual 1.331 1.317 0.013 1.46e-02 4.69e+03 8.32e-01 bond pdb=" CG LEU A 141 " pdb=" CD1 LEU A 141 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.81e-01 bond pdb=" CB TRP B 112 " pdb=" CG TRP B 112 " ideal model delta sigma weight residual 1.498 1.473 0.025 3.10e-02 1.04e+03 6.33e-01 bond pdb=" CG GLU B 5 " pdb=" CD GLU B 5 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.30e-01 bond pdb=" CA GLY B 25 " pdb=" C GLY B 25 " ideal model delta sigma weight residual 1.523 1.514 0.009 1.19e-02 7.06e+03 6.00e-01 ... (remaining 3429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 4522 1.25 - 2.50: 128 2.50 - 3.76: 9 3.76 - 5.01: 7 5.01 - 6.26: 2 Bond angle restraints: 4668 Sorted by residual: angle pdb=" C VAL A 305 " pdb=" N THR A 306 " pdb=" CA THR A 306 " ideal model delta sigma weight residual 121.71 118.11 3.60 1.39e+00 5.18e-01 6.69e+00 angle pdb=" CB MET B 102 " pdb=" CG MET B 102 " pdb=" SD MET B 102 " ideal model delta sigma weight residual 112.70 106.44 6.26 3.00e+00 1.11e-01 4.35e+00 angle pdb=" CG BARG B 44 " pdb=" CD BARG B 44 " pdb=" NE BARG B 44 " ideal model delta sigma weight residual 112.00 116.28 -4.28 2.20e+00 2.07e-01 3.79e+00 angle pdb=" N MET A 214 " pdb=" CA MET A 214 " pdb=" C MET A 214 " ideal model delta sigma weight residual 113.41 111.49 1.92 1.22e+00 6.72e-01 2.47e+00 angle pdb=" N ILE A 295 " pdb=" CA ILE A 295 " pdb=" C ILE A 295 " ideal model delta sigma weight residual 112.50 110.42 2.08 1.39e+00 5.18e-01 2.24e+00 ... (remaining 4663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 1672 16.11 - 32.22: 240 32.22 - 48.33: 69 48.33 - 64.44: 25 64.44 - 80.55: 2 Dihedral angle restraints: 2008 sinusoidal: 748 harmonic: 1260 Sorted by residual: dihedral pdb=" CA GLN B 0 " pdb=" CB GLN B 0 " pdb=" CG GLN B 0 " pdb=" CD GLN B 0 " ideal model delta sinusoidal sigma weight residual 60.00 119.80 -59.80 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 214 " pdb=" CG MET A 214 " pdb=" SD MET A 214 " pdb=" CE MET A 214 " ideal model delta sinusoidal sigma weight residual -180.00 -122.31 -57.69 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA LYS A 139 " pdb=" CB LYS A 139 " pdb=" CG LYS A 139 " pdb=" CD LYS A 139 " ideal model delta sinusoidal sigma weight residual -60.00 -117.51 57.51 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 2005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 253 0.023 - 0.046: 165 0.046 - 0.068: 82 0.068 - 0.091: 25 0.091 - 0.114: 16 Chirality restraints: 541 Sorted by residual: chirality pdb=" CA VAL B 91 " pdb=" N VAL B 91 " pdb=" C VAL B 91 " pdb=" CB VAL B 91 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 chirality pdb=" CA VAL B 118 " pdb=" N VAL B 118 " pdb=" C VAL B 118 " pdb=" CB VAL B 118 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA VAL B 1 " pdb=" N VAL B 1 " pdb=" C VAL B 1 " pdb=" CB VAL B 1 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.90e-01 ... (remaining 538 not shown) Planarity restraints: 570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD BARG B 44 " -0.171 9.50e-02 1.11e+02 7.67e-02 3.70e+00 pdb=" NE BARG B 44 " 0.009 2.00e-02 2.50e+03 pdb=" CZ BARG B 44 " 0.007 2.00e-02 2.50e+03 pdb=" NH1BARG B 44 " -0.000 2.00e-02 2.50e+03 pdb=" NH2BARG B 44 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 321 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 85 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 86 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 86 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 86 " -0.022 5.00e-02 4.00e+02 ... (remaining 567 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 1823 3.03 - 3.50: 3286 3.50 - 3.96: 5403 3.96 - 4.43: 6660 4.43 - 4.90: 10669 Nonbonded interactions: 27841 Sorted by model distance: nonbonded pdb=" O SER B 26 " pdb=" OG SER B 26 " model vdw 2.558 3.040 nonbonded pdb=" O ALA A 132 " pdb=" OG1 THR A 136 " model vdw 2.605 3.040 nonbonded pdb=" N ILE A 232 " pdb=" N LYS A 233 " model vdw 2.607 2.560 nonbonded pdb=" C SER A 106 " pdb=" OG SER A 106 " model vdw 2.610 2.616 nonbonded pdb=" C SER A 338 " pdb=" OG SER A 338 " model vdw 2.616 2.616 ... (remaining 27836 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=0.38 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.870 Find NCS groups from input model: 0.020 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 : 0.004 0.031 3435 Z= 0.172 Angle : 0.535 6.259 4670 Z= 0.298 Chirality : 0.039 0.114 541 Planarity : 0.006 0.077 570 Dihedral : 17.246 80.551 1201 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.46 % Allowed : 28.42 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.33 (0.38), residues: 428 helix: -1.75 (0.27), residues: 266 sheet: -0.56 (0.66), residues: 68 loop : -0.83 (0.69), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 65 TYR 0.016 0.002 TYR A 211 PHE 0.010 0.001 PHE A 152 TRP 0.012 0.001 TRP B 112 HIS 0.001 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 3434) covalent geometry : angle 0.53385 ( 4668) SS BOND : bond 0.00343 ( 1) SS BOND : angle 1.66534 ( 2) hydrogen bonds : bond 0.22726 ( 226) hydrogen bonds : angle 9.68191 ( 661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.075 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 57 average time/residue: 0.3863 time to fit residues: 22.6570 Evaluate side-chains 39 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 268 ASN A 360 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.087533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.073234 restraints weight = 16579.705| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.02 r_work: 0.2796 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3435 Z= 0.182 Angle : 0.589 8.212 4670 Z= 0.311 Chirality : 0.041 0.149 541 Planarity : 0.006 0.086 570 Dihedral : 4.295 28.971 473 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.46 % Allowed : 28.96 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.40), residues: 428 helix: -0.12 (0.30), residues: 267 sheet: -0.01 (0.65), residues: 68 loop : -1.00 (0.69), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 65 TYR 0.017 0.002 TYR A 211 PHE 0.010 0.001 PHE A 336 TRP 0.006 0.001 TRP A 167 HIS 0.001 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 3434) covalent geometry : angle 0.58847 ( 4668) SS BOND : bond 0.00238 ( 1) SS BOND : angle 1.32463 ( 2) hydrogen bonds : bond 0.04749 ( 226) hydrogen bonds : angle 5.47117 ( 661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.080 Fit side-chains REVERT: A 164 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7778 (mt-10) outliers start: 18 outliers final: 6 residues processed: 52 average time/residue: 0.4042 time to fit residues: 21.7060 Evaluate side-chains 48 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 239 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.087359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.072203 restraints weight = 26029.545| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.86 r_work: 0.2753 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3435 Z= 0.150 Angle : 0.551 7.644 4670 Z= 0.283 Chirality : 0.040 0.149 541 Planarity : 0.005 0.062 570 Dihedral : 4.130 28.240 473 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.37 % Allowed : 28.69 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.41), residues: 428 helix: 0.65 (0.32), residues: 268 sheet: 0.05 (0.63), residues: 69 loop : -1.10 (0.69), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 70 TYR 0.013 0.001 TYR A 211 PHE 0.008 0.001 PHE A 273 TRP 0.005 0.001 TRP A 167 HIS 0.001 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 3434) covalent geometry : angle 0.55015 ( 4668) SS BOND : bond 0.00095 ( 1) SS BOND : angle 1.21812 ( 2) hydrogen bonds : bond 0.04127 ( 226) hydrogen bonds : angle 4.89964 ( 661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.078 Fit side-chains REVERT: B 57 ASN cc_start: 0.8314 (t0) cc_final: 0.8100 (t0) REVERT: A 164 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7797 (mt-10) outliers start: 14 outliers final: 7 residues processed: 48 average time/residue: 0.3853 time to fit residues: 19.0672 Evaluate side-chains 46 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.087471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.073509 restraints weight = 15348.931| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.84 r_work: 0.2804 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3435 Z= 0.156 Angle : 0.532 7.021 4670 Z= 0.275 Chirality : 0.041 0.131 541 Planarity : 0.005 0.056 570 Dihedral : 4.096 28.194 473 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.37 % Allowed : 28.69 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.42), residues: 428 helix: 0.99 (0.32), residues: 268 sheet: 0.16 (0.62), residues: 69 loop : -1.12 (0.69), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 70 TYR 0.012 0.001 TYR A 211 PHE 0.009 0.001 PHE A 273 TRP 0.005 0.001 TRP A 167 HIS 0.000 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3434) covalent geometry : angle 0.53220 ( 4668) SS BOND : bond 0.00057 ( 1) SS BOND : angle 1.00583 ( 2) hydrogen bonds : bond 0.03920 ( 226) hydrogen bonds : angle 4.67337 ( 661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.084 Fit side-chains REVERT: B 57 ASN cc_start: 0.8228 (t0) cc_final: 0.7993 (t0) REVERT: B 71 ASP cc_start: 0.8131 (t0) cc_final: 0.7886 (t0) REVERT: A 164 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7818 (mt-10) outliers start: 14 outliers final: 7 residues processed: 48 average time/residue: 0.4382 time to fit residues: 21.7777 Evaluate side-chains 47 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 chunk 6 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.072814 restraints weight = 19947.299| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.31 r_work: 0.2779 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3435 Z= 0.158 Angle : 0.535 6.608 4670 Z= 0.275 Chirality : 0.041 0.130 541 Planarity : 0.005 0.052 570 Dihedral : 3.847 15.357 471 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.64 % Allowed : 28.69 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.42), residues: 428 helix: 1.19 (0.32), residues: 267 sheet: 0.30 (0.62), residues: 69 loop : -1.25 (0.68), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 70 TYR 0.011 0.001 TYR A 211 PHE 0.009 0.001 PHE A 273 TRP 0.005 0.001 TRP A 167 HIS 0.000 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 3434) covalent geometry : angle 0.53487 ( 4668) SS BOND : bond 0.00178 ( 1) SS BOND : angle 1.24711 ( 2) hydrogen bonds : bond 0.03866 ( 226) hydrogen bonds : angle 4.62177 ( 661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.146 Fit side-chains REVERT: B 57 ASN cc_start: 0.8279 (t0) cc_final: 0.8057 (t0) REVERT: B 71 ASP cc_start: 0.8124 (t0) cc_final: 0.7843 (t0) outliers start: 15 outliers final: 8 residues processed: 50 average time/residue: 0.4167 time to fit residues: 21.5065 Evaluate side-chains 49 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.088238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.073236 restraints weight = 21588.674| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.53 r_work: 0.2787 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3435 Z= 0.131 Angle : 0.518 9.310 4670 Z= 0.263 Chirality : 0.040 0.131 541 Planarity : 0.004 0.046 570 Dihedral : 3.792 17.097 471 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.10 % Allowed : 29.78 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.42), residues: 428 helix: 1.38 (0.32), residues: 265 sheet: 0.39 (0.62), residues: 69 loop : -1.25 (0.67), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 70 TYR 0.011 0.001 TYR A 211 PHE 0.008 0.001 PHE A 273 TRP 0.005 0.001 TRP A 167 HIS 0.000 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 3434) covalent geometry : angle 0.51772 ( 4668) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.86559 ( 2) hydrogen bonds : bond 0.03641 ( 226) hydrogen bonds : angle 4.46280 ( 661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.077 Fit side-chains REVERT: B 57 ASN cc_start: 0.8263 (t0) cc_final: 0.8010 (t0) REVERT: B 71 ASP cc_start: 0.8098 (t0) cc_final: 0.7797 (t0) REVERT: B 93 MET cc_start: 0.8927 (mtp) cc_final: 0.8722 (mtp) REVERT: A 164 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7903 (mt-10) outliers start: 13 outliers final: 8 residues processed: 49 average time/residue: 0.3273 time to fit residues: 16.5772 Evaluate side-chains 49 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 38 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.088716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.073440 restraints weight = 28846.444| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 5.04 r_work: 0.2773 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3435 Z= 0.122 Angle : 0.517 9.118 4670 Z= 0.260 Chirality : 0.040 0.132 541 Planarity : 0.004 0.043 570 Dihedral : 3.740 14.786 471 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.64 % Allowed : 28.69 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.42), residues: 428 helix: 1.56 (0.32), residues: 266 sheet: 0.42 (0.63), residues: 69 loop : -1.26 (0.68), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 70 TYR 0.010 0.001 TYR A 211 PHE 0.007 0.001 PHE A 273 TRP 0.004 0.001 TRP A 337 HIS 0.000 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 3434) covalent geometry : angle 0.51679 ( 4668) SS BOND : bond 0.00118 ( 1) SS BOND : angle 1.04022 ( 2) hydrogen bonds : bond 0.03538 ( 226) hydrogen bonds : angle 4.38132 ( 661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.126 Fit side-chains REVERT: B 57 ASN cc_start: 0.8290 (t0) cc_final: 0.8023 (t0) REVERT: B 70 ARG cc_start: 0.9045 (ttm-80) cc_final: 0.8703 (ttt-90) REVERT: B 71 ASP cc_start: 0.8062 (t0) cc_final: 0.7568 (t0) REVERT: B 93 MET cc_start: 0.8923 (mtp) cc_final: 0.8712 (mtp) REVERT: A 164 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7963 (mt-10) outliers start: 15 outliers final: 13 residues processed: 51 average time/residue: 0.5282 time to fit residues: 27.8216 Evaluate side-chains 52 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.087415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.072547 restraints weight = 24213.780| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.67 r_work: 0.2763 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3435 Z= 0.170 Angle : 0.536 8.694 4670 Z= 0.271 Chirality : 0.041 0.135 541 Planarity : 0.004 0.045 570 Dihedral : 3.784 14.673 471 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.92 % Allowed : 28.14 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.42), residues: 428 helix: 1.54 (0.32), residues: 267 sheet: 0.50 (0.63), residues: 69 loop : -1.22 (0.68), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 70 TYR 0.011 0.001 TYR A 211 PHE 0.009 0.001 PHE A 273 TRP 0.005 0.001 TRP B 112 HIS 0.000 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 3434) covalent geometry : angle 0.53525 ( 4668) SS BOND : bond 0.00063 ( 1) SS BOND : angle 1.11671 ( 2) hydrogen bonds : bond 0.03769 ( 226) hydrogen bonds : angle 4.43187 ( 661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.127 Fit side-chains REVERT: B 57 ASN cc_start: 0.8292 (t0) cc_final: 0.8054 (t0) REVERT: B 70 ARG cc_start: 0.9046 (ttm-80) cc_final: 0.8621 (ttt180) REVERT: B 71 ASP cc_start: 0.8096 (t0) cc_final: 0.7651 (t0) REVERT: B 93 MET cc_start: 0.8938 (mtp) cc_final: 0.8712 (mtp) REVERT: A 164 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8039 (mt-10) outliers start: 16 outliers final: 10 residues processed: 50 average time/residue: 0.4758 time to fit residues: 24.6160 Evaluate side-chains 49 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.087613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.072573 restraints weight = 23929.980| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 4.71 r_work: 0.2768 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3435 Z= 0.153 Angle : 0.525 8.767 4670 Z= 0.266 Chirality : 0.041 0.134 541 Planarity : 0.004 0.045 570 Dihedral : 3.784 14.257 471 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.10 % Allowed : 29.23 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.42), residues: 428 helix: 1.67 (0.32), residues: 265 sheet: 0.58 (0.63), residues: 69 loop : -1.22 (0.67), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 70 TYR 0.011 0.001 TYR A 211 PHE 0.009 0.001 PHE A 273 TRP 0.004 0.001 TRP A 337 HIS 0.000 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 3434) covalent geometry : angle 0.52444 ( 4668) SS BOND : bond 0.00007 ( 1) SS BOND : angle 0.98409 ( 2) hydrogen bonds : bond 0.03701 ( 226) hydrogen bonds : angle 4.39070 ( 661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.129 Fit side-chains REVERT: B 57 ASN cc_start: 0.8282 (t0) cc_final: 0.8051 (t0) REVERT: B 70 ARG cc_start: 0.9026 (ttm-80) cc_final: 0.8697 (ttt180) REVERT: B 71 ASP cc_start: 0.8084 (t0) cc_final: 0.7650 (t0) REVERT: B 93 MET cc_start: 0.8921 (mtp) cc_final: 0.8693 (mtp) REVERT: A 164 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8014 (mt-10) outliers start: 13 outliers final: 10 residues processed: 50 average time/residue: 0.4395 time to fit residues: 22.8034 Evaluate side-chains 49 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.086589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.071870 restraints weight = 19568.695| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.34 r_work: 0.2765 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3435 Z= 0.184 Angle : 0.547 8.453 4670 Z= 0.277 Chirality : 0.041 0.138 541 Planarity : 0.004 0.046 570 Dihedral : 3.856 14.908 471 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.28 % Allowed : 30.05 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.42), residues: 428 helix: 1.59 (0.32), residues: 266 sheet: 0.46 (0.63), residues: 69 loop : -1.12 (0.68), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 70 TYR 0.011 0.001 TYR A 162 PHE 0.010 0.001 PHE A 273 TRP 0.005 0.001 TRP B 112 HIS 0.000 0.000 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 3434) covalent geometry : angle 0.54607 ( 4668) SS BOND : bond 0.00233 ( 1) SS BOND : angle 1.45828 ( 2) hydrogen bonds : bond 0.03869 ( 226) hydrogen bonds : angle 4.47600 ( 661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.136 Fit side-chains REVERT: B 57 ASN cc_start: 0.8293 (t0) cc_final: 0.8054 (t0) REVERT: B 71 ASP cc_start: 0.8144 (t0) cc_final: 0.7691 (t0) REVERT: A 164 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8018 (mt-10) outliers start: 10 outliers final: 9 residues processed: 48 average time/residue: 0.4511 time to fit residues: 22.4222 Evaluate side-chains 47 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 0.0070 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 0.0270 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN B 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.088427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.073841 restraints weight = 17324.072| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.20 r_work: 0.2796 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3435 Z= 0.114 Angle : 0.507 9.013 4670 Z= 0.257 Chirality : 0.040 0.140 541 Planarity : 0.004 0.043 570 Dihedral : 3.748 15.169 471 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.01 % Allowed : 30.33 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.42), residues: 428 helix: 1.78 (0.32), residues: 265 sheet: 0.60 (0.63), residues: 69 loop : -1.17 (0.68), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 70 TYR 0.011 0.001 TYR A 211 PHE 0.007 0.001 PHE A 273 TRP 0.004 0.001 TRP A 337 HIS 0.001 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3434) covalent geometry : angle 0.50688 ( 4668) SS BOND : bond 0.00089 ( 1) SS BOND : angle 0.78355 ( 2) hydrogen bonds : bond 0.03483 ( 226) hydrogen bonds : angle 4.30185 ( 661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1163.78 seconds wall clock time: 20 minutes 36.77 seconds (1236.77 seconds total)