Starting phenix.real_space_refine on Fri Aug 22 14:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sbb_40303/08_2025/8sbb_40303.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sbb_40303/08_2025/8sbb_40303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sbb_40303/08_2025/8sbb_40303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sbb_40303/08_2025/8sbb_40303.map" model { file = "/net/cci-nas-00/data/ceres_data/8sbb_40303/08_2025/8sbb_40303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sbb_40303/08_2025/8sbb_40303.cif" } resolution = 3.59 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= 0.012 sd= 0.152 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: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 10 5.16 5 C 2634 2.51 5 N 705 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4049 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3110 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 26, 'TRANS': 353} Chain: "B" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 925 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Unusual residues: {' FE': 2, 'D12': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.28, per 1000 atoms: 0.32 Number of scatterers: 4049 At special positions: 0 Unit cell: (96.9, 88.35, 69.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 10 16.00 O 698 8.00 N 705 7.00 C 2634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 97 " 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 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 157.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 918 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 52.3% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 removed outlier: 3.650A pdb=" N TRP A 29 " --> pdb=" O ARG A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 30 through 35 Processing helix chain 'A' and resid 37 through 49 Processing helix chain 'A' and resid 52 through 56 removed outlier: 3.748A pdb=" N PHE A 55 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 removed outlier: 3.553A pdb=" N TYR A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.835A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 92 through 100 removed outlier: 4.516A pdb=" N THR A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 119 removed outlier: 4.060A pdb=" N ILE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 147 removed outlier: 3.882A pdb=" N ILE A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 154 through 167 removed outlier: 3.938A pdb=" N ARG A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 199 through 225 Proline residue: A 209 - end of helix removed outlier: 3.895A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 256 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 259 through 282 removed outlier: 3.543A pdb=" N LEU A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 315 removed outlier: 3.636A pdb=" N ASN A 312 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.543A pdb=" N HIS A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 3.671A pdb=" N MET A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.546A pdb=" N TRP A 361 " --> pdb=" O PHE A 357 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 9 removed outlier: 3.623A pdb=" N GLN B 7 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 23 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR B 70 " --> pdb=" O GLN B 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 54 removed outlier: 6.128A pdb=" N TRP B 38 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY B 52 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N MET B 36 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 94 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 95 " --> pdb=" O GLY B 117 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 483 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: 0.56 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 681 1.32 - 1.44: 1229 1.44 - 1.56: 2249 1.56 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 4175 Sorted by residual: bond pdb=" CA TYR A 21 " pdb=" C TYR A 21 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.34e-02 5.57e+03 2.67e+01 bond pdb=" N ARG B 73 " pdb=" CA ARG B 73 " ideal model delta sigma weight residual 1.458 1.488 -0.030 6.30e-03 2.52e+04 2.22e+01 bond pdb=" N ARG B 32 " pdb=" CA ARG B 32 " ideal model delta sigma weight residual 1.459 1.490 -0.031 9.10e-03 1.21e+04 1.16e+01 bond pdb=" CA ALA A 142 " pdb=" CB ALA A 142 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.57e-02 4.06e+03 1.10e+01 bond pdb=" C LEU A 141 " pdb=" O LEU A 141 " ideal model delta sigma weight residual 1.236 1.195 0.042 1.26e-02 6.30e+03 1.09e+01 ... (remaining 4170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 5112 2.11 - 4.22: 497 4.22 - 6.33: 68 6.33 - 8.44: 13 8.44 - 10.55: 3 Bond angle restraints: 5693 Sorted by residual: angle pdb=" N LEU A 318 " pdb=" CA LEU A 318 " pdb=" C LEU A 318 " ideal model delta sigma weight residual 114.31 104.74 9.57 1.29e+00 6.01e-01 5.50e+01 angle pdb=" N GLY A 140 " pdb=" CA GLY A 140 " pdb=" C GLY A 140 " ideal model delta sigma weight residual 112.73 105.63 7.10 1.20e+00 6.94e-01 3.50e+01 angle pdb=" N ILE B 30 " pdb=" CA ILE B 30 " pdb=" C ILE B 30 " ideal model delta sigma weight residual 112.90 107.36 5.54 9.60e-01 1.09e+00 3.32e+01 angle pdb=" N THR A 145 " pdb=" CA THR A 145 " pdb=" C THR A 145 " ideal model delta sigma weight residual 113.50 106.73 6.77 1.23e+00 6.61e-01 3.03e+01 angle pdb=" CA GLY A 256 " pdb=" C GLY A 256 " pdb=" O GLY A 256 " ideal model delta sigma weight residual 122.29 118.00 4.29 8.10e-01 1.52e+00 2.81e+01 ... (remaining 5688 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 2071 15.29 - 30.58: 242 30.58 - 45.86: 69 45.86 - 61.15: 25 61.15 - 76.44: 8 Dihedral angle restraints: 2415 sinusoidal: 971 harmonic: 1444 Sorted by residual: dihedral pdb=" CA PHE A 316 " pdb=" C PHE A 316 " pdb=" N HIS A 317 " pdb=" CA HIS A 317 " ideal model delta harmonic sigma weight residual -180.00 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ARG A 320 " pdb=" C ARG A 320 " pdb=" N HIS A 321 " pdb=" CA HIS A 321 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA GLY A 374 " pdb=" C GLY A 374 " pdb=" N ARG A 375 " pdb=" CA ARG A 375 " ideal model delta harmonic sigma weight residual 180.00 156.08 23.92 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 2412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 325 0.053 - 0.105: 212 0.105 - 0.157: 51 0.157 - 0.210: 15 0.210 - 0.262: 5 Chirality restraints: 608 Sorted by residual: chirality pdb=" CB VAL A 37 " pdb=" CA VAL A 37 " pdb=" CG1 VAL A 37 " pdb=" CG2 VAL A 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA TYR A 21 " pdb=" N TYR A 21 " pdb=" C TYR A 21 " pdb=" CB TYR A 21 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA TYR A 348 " pdb=" N TYR A 348 " pdb=" C TYR A 348 " pdb=" CB TYR A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 ... (remaining 605 not shown) Planarity restraints: 717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 344 " 0.050 5.00e-02 4.00e+02 7.66e-02 9.39e+00 pdb=" N PRO A 345 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 345 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 345 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 80 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.53e+00 pdb=" N PRO A 81 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 180 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.54e+00 pdb=" C GLY A 180 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY A 180 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS A 181 " 0.016 2.00e-02 2.50e+03 ... (remaining 714 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 351 2.70 - 3.25: 4125 3.25 - 3.80: 6375 3.80 - 4.35: 7734 4.35 - 4.90: 12694 Nonbonded interactions: 31279 Sorted by model distance: nonbonded pdb=" NE2 HIS A 325 " pdb="FE FE A 401 " model vdw 2.146 2.340 nonbonded pdb=" O GLY B 44 " pdb=" NZ LYS B 45 " model vdw 2.147 3.120 nonbonded pdb=" NE2 HIS A 282 " pdb="FE FE A 401 " model vdw 2.156 2.340 nonbonded pdb=" OG SER B 19 " pdb=" O MET B 84 " model vdw 2.210 3.040 nonbonded pdb=" NE2 HIS A 324 " pdb="FE FE A 402 " model vdw 2.227 2.340 ... (remaining 31274 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.100 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.016 0.108 4176 Z= 0.797 Angle : 1.327 10.553 5695 Z= 0.830 Chirality : 0.071 0.262 608 Planarity : 0.009 0.077 717 Dihedral : 15.679 76.438 1494 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.95 % Favored : 85.05 % Rotamer: Outliers : 3.99 % Allowed : 12.68 % Favored : 83.33 % 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 aren not related in a simple way. whole: -5.32 (0.28), residues: 495 helix: -2.80 (0.28), residues: 230 sheet: -3.34 (0.71), residues: 34 loop : -4.42 (0.28), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 92 TYR 0.032 0.004 TYR A 93 PHE 0.022 0.004 PHE A 173 TRP 0.042 0.004 TRP A 125 HIS 0.010 0.002 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.01598 ( 4175) covalent geometry : angle 1.32623 ( 5693) SS BOND : bond 0.00403 ( 1) SS BOND : angle 2.33507 ( 2) hydrogen bonds : bond 0.20912 ( 165) hydrogen bonds : angle 8.27586 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 64 LEU cc_start: 0.8790 (tp) cc_final: 0.8464 (mt) REVERT: B 35 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7734 (t) REVERT: B 54 SER cc_start: 0.8234 (t) cc_final: 0.7888 (m) outliers start: 17 outliers final: 3 residues processed: 106 average time/residue: 0.0873 time to fit residues: 11.0263 Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 319 GLN Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 72 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 144 ASN A 385 ASN B 119 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.185824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.143511 restraints weight = 5550.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.147324 restraints weight = 2739.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.149656 restraints weight = 1802.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.150892 restraints weight = 1420.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.151707 restraints weight = 1251.570| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4176 Z= 0.167 Angle : 0.766 6.694 5695 Z= 0.400 Chirality : 0.045 0.156 608 Planarity : 0.007 0.057 717 Dihedral : 5.886 37.708 574 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.26 % Favored : 93.54 % Rotamer: Outliers : 3.05 % Allowed : 17.84 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -3.55 (0.33), residues: 495 helix: -1.08 (0.34), residues: 236 sheet: -2.61 (0.65), residues: 39 loop : -3.83 (0.30), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 362 TYR 0.019 0.002 TYR A 126 PHE 0.018 0.002 PHE A 262 TRP 0.022 0.002 TRP A 125 HIS 0.006 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4175) covalent geometry : angle 0.76605 ( 5693) SS BOND : bond 0.00194 ( 1) SS BOND : angle 1.35144 ( 2) hydrogen bonds : bond 0.06653 ( 165) hydrogen bonds : angle 5.86570 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.148 Fit side-chains REVERT: A 64 LEU cc_start: 0.8665 (tp) cc_final: 0.8412 (mp) REVERT: A 176 GLU cc_start: 0.7990 (tp30) cc_final: 0.7682 (tm-30) REVERT: A 288 GLN cc_start: 0.7355 (mm-40) cc_final: 0.7016 (mm-40) REVERT: B 23 SER cc_start: 0.7900 (p) cc_final: 0.7488 (m) REVERT: B 54 SER cc_start: 0.7854 (t) cc_final: 0.7445 (m) outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 0.0595 time to fit residues: 5.7529 Evaluate side-chains 62 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.177413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133448 restraints weight = 5686.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136917 restraints weight = 2966.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.138981 restraints weight = 2030.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.140013 restraints weight = 1644.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.140916 restraints weight = 1468.780| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4176 Z= 0.211 Angle : 0.750 6.479 5695 Z= 0.392 Chirality : 0.046 0.159 608 Planarity : 0.006 0.047 717 Dihedral : 5.421 27.180 568 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 4.93 % Allowed : 16.90 % Favored : 78.17 % 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 aren not related in a simple way. whole: -2.74 (0.35), residues: 495 helix: -0.32 (0.36), residues: 230 sheet: -2.31 (0.64), residues: 39 loop : -3.44 (0.32), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.016 0.002 TYR B 61 PHE 0.013 0.002 PHE A 262 TRP 0.014 0.001 TRP A 125 HIS 0.004 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 4175) covalent geometry : angle 0.75043 ( 5693) SS BOND : bond 0.00325 ( 1) SS BOND : angle 0.90480 ( 2) hydrogen bonds : bond 0.06744 ( 165) hydrogen bonds : angle 5.44862 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.7944 (mmm) cc_final: 0.7599 (mmm) outliers start: 21 outliers final: 13 residues processed: 61 average time/residue: 0.0558 time to fit residues: 4.4463 Evaluate side-chains 56 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 266 GLN A 302 HIS A 385 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.168349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130500 restraints weight = 5309.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133233 restraints weight = 3084.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.134670 restraints weight = 2213.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135983 restraints weight = 1840.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.136144 restraints weight = 1648.478| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4176 Z= 0.136 Angle : 0.662 6.285 5695 Z= 0.342 Chirality : 0.042 0.128 608 Planarity : 0.006 0.043 717 Dihedral : 5.202 26.589 568 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.58 % Allowed : 19.25 % Favored : 78.17 % 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 aren not related in a simple way. whole: -2.13 (0.37), residues: 495 helix: 0.10 (0.37), residues: 229 sheet: -1.63 (0.69), residues: 39 loop : -3.10 (0.34), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.015 0.001 TYR B 61 PHE 0.014 0.001 PHE A 262 TRP 0.013 0.001 TRP A 125 HIS 0.003 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4175) covalent geometry : angle 0.66105 ( 5693) SS BOND : bond 0.00457 ( 1) SS BOND : angle 1.74958 ( 2) hydrogen bonds : bond 0.05363 ( 165) hydrogen bonds : angle 5.22317 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.103 Fit side-chains REVERT: A 288 GLN cc_start: 0.7343 (mm-40) cc_final: 0.7118 (mm-40) REVERT: A 365 MET cc_start: 0.8006 (mmm) cc_final: 0.7676 (mmm) REVERT: A 379 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7579 (mtpt) outliers start: 11 outliers final: 9 residues processed: 54 average time/residue: 0.0675 time to fit residues: 4.6247 Evaluate side-chains 55 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN ** B 75 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 = 0.4009 r_free = 0.4009 target = 0.167814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129159 restraints weight = 5411.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131890 restraints weight = 3222.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.133352 restraints weight = 2320.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.134491 restraints weight = 1927.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.135316 restraints weight = 1712.942| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4176 Z= 0.131 Angle : 0.652 9.612 5695 Z= 0.332 Chirality : 0.042 0.125 608 Planarity : 0.005 0.040 717 Dihedral : 4.958 25.178 567 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.05 % Allowed : 19.48 % Favored : 77.46 % 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 aren not related in a simple way. whole: -1.90 (0.37), residues: 495 helix: 0.26 (0.37), residues: 229 sheet: -1.41 (0.68), residues: 39 loop : -2.95 (0.34), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 47 TYR 0.011 0.001 TYR B 96 PHE 0.015 0.001 PHE A 262 TRP 0.012 0.001 TRP A 125 HIS 0.002 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4175) covalent geometry : angle 0.65185 ( 5693) SS BOND : bond 0.00547 ( 1) SS BOND : angle 1.36349 ( 2) hydrogen bonds : bond 0.05199 ( 165) hydrogen bonds : angle 5.09111 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.150 Fit side-chains REVERT: A 288 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7127 (mm-40) REVERT: A 379 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7545 (mtpt) outliers start: 13 outliers final: 10 residues processed: 57 average time/residue: 0.0690 time to fit residues: 5.0629 Evaluate side-chains 57 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN B 75 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.168556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132976 restraints weight = 5503.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133511 restraints weight = 3685.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.134594 restraints weight = 2692.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.134991 restraints weight = 2186.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135271 restraints weight = 1960.679| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4176 Z= 0.129 Angle : 0.654 9.061 5695 Z= 0.331 Chirality : 0.042 0.194 608 Planarity : 0.005 0.040 717 Dihedral : 4.816 24.591 567 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.99 % Allowed : 19.25 % Favored : 76.76 % 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 aren not related in a simple way. whole: -1.50 (0.38), residues: 495 helix: 0.56 (0.38), residues: 225 sheet: -0.80 (0.72), residues: 50 loop : -2.81 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 47 TYR 0.011 0.001 TYR B 96 PHE 0.013 0.001 PHE A 262 TRP 0.012 0.001 TRP B 34 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4175) covalent geometry : angle 0.65356 ( 5693) SS BOND : bond 0.00567 ( 1) SS BOND : angle 1.09514 ( 2) hydrogen bonds : bond 0.04964 ( 165) hydrogen bonds : angle 4.91344 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.154 Fit side-chains REVERT: A 176 GLU cc_start: 0.7973 (tp30) cc_final: 0.7691 (tm-30) REVERT: A 379 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7140 (tptp) outliers start: 17 outliers final: 12 residues processed: 59 average time/residue: 0.0708 time to fit residues: 5.3505 Evaluate side-chains 57 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.0050 chunk 45 optimal weight: 0.0020 chunk 38 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 15 optimal weight: 0.0050 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.2216 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.173630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137160 restraints weight = 5377.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.139306 restraints weight = 2990.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.141436 restraints weight = 1949.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141711 restraints weight = 1536.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142133 restraints weight = 1421.463| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4176 Z= 0.116 Angle : 0.617 7.306 5695 Z= 0.316 Chirality : 0.041 0.128 608 Planarity : 0.005 0.038 717 Dihedral : 4.629 23.859 567 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.11 % Allowed : 20.66 % Favored : 77.23 % 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 aren not related in a simple way. whole: -1.13 (0.38), residues: 495 helix: 0.78 (0.38), residues: 226 sheet: -0.44 (0.75), residues: 50 loop : -2.59 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.011 0.001 TYR B 96 PHE 0.013 0.001 PHE A 262 TRP 0.016 0.001 TRP B 34 HIS 0.004 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 4175) covalent geometry : angle 0.61720 ( 5693) SS BOND : bond 0.00832 ( 1) SS BOND : angle 0.79646 ( 2) hydrogen bonds : bond 0.04065 ( 165) hydrogen bonds : angle 4.77149 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.9045 (tp) cc_final: 0.8408 (tt) REVERT: A 176 GLU cc_start: 0.7805 (tp30) cc_final: 0.7563 (tm-30) REVERT: A 388 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 96 TYR cc_start: 0.6106 (OUTLIER) cc_final: 0.5338 (m-80) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.0774 time to fit residues: 5.5397 Evaluate side-chains 55 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 378 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 0.0270 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.170565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135293 restraints weight = 5356.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134542 restraints weight = 3625.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136077 restraints weight = 2926.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136127 restraints weight = 2218.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138036 restraints weight = 2118.365| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4176 Z= 0.123 Angle : 0.634 10.718 5695 Z= 0.320 Chirality : 0.041 0.135 608 Planarity : 0.005 0.038 717 Dihedral : 4.569 23.005 567 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.11 % Allowed : 21.13 % Favored : 76.76 % 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 aren not related in a simple way. whole: -1.08 (0.38), residues: 495 helix: 0.81 (0.38), residues: 226 sheet: -0.44 (0.73), residues: 50 loop : -2.54 (0.36), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 73 TYR 0.010 0.001 TYR B 61 PHE 0.010 0.001 PHE A 262 TRP 0.015 0.001 TRP B 114 HIS 0.003 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4175) covalent geometry : angle 0.63386 ( 5693) SS BOND : bond 0.00310 ( 1) SS BOND : angle 1.07739 ( 2) hydrogen bonds : bond 0.04550 ( 165) hydrogen bonds : angle 4.73030 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.149 Fit side-chains REVERT: A 97 LEU cc_start: 0.9063 (tp) cc_final: 0.8488 (tt) REVERT: A 388 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7446 (mm-30) REVERT: B 96 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5265 (m-80) REVERT: B 114 TRP cc_start: 0.8706 (p90) cc_final: 0.8400 (p90) outliers start: 9 outliers final: 8 residues processed: 53 average time/residue: 0.0704 time to fit residues: 4.8069 Evaluate side-chains 51 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.168691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130319 restraints weight = 5380.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.133144 restraints weight = 3008.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134879 restraints weight = 2109.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.136085 restraints weight = 1708.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.136085 restraints weight = 1512.816| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4176 Z= 0.128 Angle : 0.637 10.320 5695 Z= 0.323 Chirality : 0.042 0.126 608 Planarity : 0.005 0.038 717 Dihedral : 4.575 25.682 567 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.82 % Allowed : 20.89 % Favored : 76.29 % 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 aren not related in a simple way. whole: -1.01 (0.38), residues: 495 helix: 0.83 (0.38), residues: 225 sheet: -0.18 (0.74), residues: 50 loop : -2.51 (0.35), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.010 0.001 TYR B 61 PHE 0.010 0.001 PHE A 262 TRP 0.017 0.001 TRP B 34 HIS 0.003 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4175) covalent geometry : angle 0.63739 ( 5693) SS BOND : bond 0.00436 ( 1) SS BOND : angle 0.83645 ( 2) hydrogen bonds : bond 0.04881 ( 165) hydrogen bonds : angle 4.72560 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.168 Fit side-chains REVERT: A 97 LEU cc_start: 0.9122 (tp) cc_final: 0.8528 (tt) REVERT: A 314 ILE cc_start: 0.8621 (mm) cc_final: 0.8363 (mt) REVERT: A 388 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7359 (mm-30) REVERT: B 96 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5221 (m-80) REVERT: B 114 TRP cc_start: 0.8711 (p90) cc_final: 0.8425 (p90) outliers start: 12 outliers final: 9 residues processed: 54 average time/residue: 0.0656 time to fit residues: 4.6031 Evaluate side-chains 55 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.166024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.127561 restraints weight = 5344.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.130339 restraints weight = 3014.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.132132 restraints weight = 2115.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133021 restraints weight = 1721.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.133672 restraints weight = 1536.776| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4176 Z= 0.157 Angle : 0.681 10.305 5695 Z= 0.345 Chirality : 0.043 0.149 608 Planarity : 0.005 0.039 717 Dihedral : 4.696 27.646 567 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.11 % Allowed : 21.83 % Favored : 76.06 % 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 aren not related in a simple way. whole: -1.04 (0.38), residues: 495 helix: 0.76 (0.38), residues: 225 sheet: -0.02 (0.75), residues: 50 loop : -2.52 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 73 TYR 0.011 0.001 TYR A 93 PHE 0.012 0.001 PHE A 262 TRP 0.016 0.001 TRP B 34 HIS 0.003 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4175) covalent geometry : angle 0.68099 ( 5693) SS BOND : bond 0.00432 ( 1) SS BOND : angle 1.05444 ( 2) hydrogen bonds : bond 0.05395 ( 165) hydrogen bonds : angle 4.78470 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.137 Fit side-chains REVERT: A 314 ILE cc_start: 0.8650 (mm) cc_final: 0.8419 (mt) REVERT: B 96 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.5179 (m-80) outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.0687 time to fit residues: 4.5601 Evaluate side-chains 56 residues out of total 427 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 231 TRP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 96 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 41 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 0.0000 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 0.0470 overall best weight: 0.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 302 HIS ** 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 = 0.4019 r_free = 0.4019 target = 0.171503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137851 restraints weight = 5243.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137174 restraints weight = 3128.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137720 restraints weight = 2635.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139618 restraints weight = 2233.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.139712 restraints weight = 2034.532| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4176 Z= 0.117 Angle : 0.633 10.202 5695 Z= 0.318 Chirality : 0.041 0.123 608 Planarity : 0.005 0.039 717 Dihedral : 4.565 26.369 567 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.64 % Allowed : 22.77 % Favored : 75.59 % 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 aren not related in a simple way. whole: -0.87 (0.38), residues: 495 helix: 0.86 (0.38), residues: 225 sheet: 0.14 (0.76), residues: 50 loop : -2.38 (0.36), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 387 TYR 0.009 0.001 TYR A 279 PHE 0.012 0.001 PHE A 262 TRP 0.017 0.001 TRP B 34 HIS 0.003 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4175) covalent geometry : angle 0.63307 ( 5693) SS BOND : bond 0.00433 ( 1) SS BOND : angle 0.86814 ( 2) hydrogen bonds : bond 0.04292 ( 165) hydrogen bonds : angle 4.66518 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 854.35 seconds wall clock time: 15 minutes 17.98 seconds (917.98 seconds total)