Starting phenix.real_space_refine on Thu Jul 2 04:29:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7urf_26711/07_2026/7urf_26711.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urf_26711/07_2026/7urf_26711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7urf_26711/07_2026/7urf_26711.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7urf_26711/07_2026/7urf_26711.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7urf_26711/07_2026/7urf_26711.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urf_26711/07_2026/7urf_26711.map" model { file = "/net/cci-nas-00/data/ceres_data/7urf_26711/07_2026/7urf_26711.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urf_26711/07_2026/7urf_26711.cif" } resolution = 2.8 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= 0.003 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: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 S 42 5.16 5 C 4072 2.51 5 N 957 2.21 5 O 1058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6133 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 4031 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 16, 'TRANS': 474} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 47 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "O" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 914 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 282 Unusual residues: {'AJP': 5, 'HEM': 1, 'PKZ': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 126 Planarities with less than four sites: {'PKZ:plan-1': 1, 'PKZ:plan-2': 1, 'PKZ:plan-3': 1, 'PKZ:plan-4': 1, 'PKZ:plan-5': 1} Unresolved non-hydrogen planarities: 26 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2682 SG CYS A 324 44.053 47.482 32.785 1.00 36.62 S Time building chain proxies: 1.42, per 1000 atoms: 0.23 Number of scatterers: 6133 At special positions: 0 Unit cell: (74.938, 85.042, 118.722, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 1 26.01 S 42 16.00 P 3 15.00 O 1058 8.00 N 957 7.00 C 4072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 115 " distance=2.03 Simple disulfide: pdb=" SG CYS P 42 " - pdb=" SG CYS P 112 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 287.4 milliseconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 60.8% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 3 through 32 Processing helix chain 'A' and resid 32 through 40 Processing helix chain 'A' and resid 57 through 68 Processing helix chain 'A' and resid 70 through 89 Processing helix chain 'A' and resid 92 through 129 removed outlier: 7.887A pdb=" N THR A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.837A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 160 Processing helix chain 'A' and resid 164 through 190 removed outlier: 3.856A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 200 through 209 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 236 through 265 removed outlier: 3.738A pdb=" N CYS A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 273 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 281 through 315 removed outlier: 3.756A pdb=" N VAL A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 324 through 328 Processing helix chain 'A' and resid 330 through 338 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.501A pdb=" N VAL A 354 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 380 removed outlier: 3.981A pdb=" N GLY A 363 " --> pdb=" O HIS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 407 Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 420 through 448 removed outlier: 4.029A pdb=" N MET A 438 " --> pdb=" O CYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 462 Processing helix chain 'A' and resid 464 through 488 removed outlier: 3.625A pdb=" N THR A 469 " --> pdb=" O TRP A 465 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 51 removed outlier: 3.709A pdb=" N TYR O 51 " --> pdb=" O PHE O 48 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 22 through 25 Processing sheet with id=AA2, first strand: chain 'O' and resid 29 through 30 removed outlier: 6.462A pdb=" N GLU O 29 " --> pdb=" O THR O 135 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N MET O 53 " --> pdb=" O TRP O 69 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP O 69 " --> pdb=" O MET O 53 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP O 55 " --> pdb=" O MET O 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 29 through 30 removed outlier: 6.462A pdb=" N GLU O 29 " --> pdb=" O THR O 135 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR O 127 " --> pdb=" O ARG O 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 24 through 26 Processing sheet with id=AA5, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.570A pdb=" N TRP P 59 " --> pdb=" O LEU P 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 29 through 32 removed outlier: 3.756A pdb=" N THR P 121 " --> pdb=" O GLN P 114 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1080 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: 1.07 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 2479 1.38 - 1.55: 3734 1.55 - 1.71: 67 1.71 - 1.88: 68 1.88 - 2.04: 6 Bond restraints: 6354 Sorted by residual: bond pdb=" C2B PKZ A 602 " pdb=" C3B PKZ A 602 " ideal model delta sigma weight residual 1.529 1.294 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C3B PKZ A 602 " pdb=" C4B PKZ A 602 " ideal model delta sigma weight residual 1.529 1.749 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C1B PKZ A 602 " pdb=" O4B PKZ A 602 " ideal model delta sigma weight residual 1.390 1.591 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C2B PKZ A 602 " pdb=" O2B PKZ A 602 " ideal model delta sigma weight residual 1.390 1.589 -0.199 2.00e-02 2.50e+03 9.85e+01 bond pdb=" C9P PKZ A 602 " pdb=" N8P PKZ A 602 " ideal model delta sigma weight residual 1.336 1.531 -0.195 2.00e-02 2.50e+03 9.50e+01 ... (remaining 6349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 8556 2.94 - 5.87: 136 5.87 - 8.81: 18 8.81 - 11.74: 3 11.74 - 14.68: 2 Bond angle restraints: 8715 Sorted by residual: angle pdb=" O3A PKZ A 602 " pdb=" P1A PKZ A 602 " pdb=" O5B PKZ A 602 " ideal model delta sigma weight residual 94.17 108.85 -14.68 3.00e+00 1.11e-01 2.39e+01 angle pdb=" O1A PKZ A 602 " pdb=" P1A PKZ A 602 " pdb=" O2A PKZ A 602 " ideal model delta sigma weight residual 122.06 109.36 12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" N ILE P 48 " pdb=" CA ILE P 48 " pdb=" C ILE P 48 " ideal model delta sigma weight residual 112.29 108.53 3.76 9.40e-01 1.13e+00 1.60e+01 angle pdb=" O3A PKZ A 602 " pdb=" P2A PKZ A 602 " pdb=" O6A PKZ A 602 " ideal model delta sigma weight residual 97.18 108.03 -10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C LYS O 106 " pdb=" N ASP O 107 " pdb=" CA ASP O 107 " ideal model delta sigma weight residual 122.08 128.40 -6.32 1.84e+00 2.95e-01 1.18e+01 ... (remaining 8710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 3378 32.59 - 65.17: 78 65.17 - 97.76: 10 97.76 - 130.35: 16 130.35 - 162.94: 2 Dihedral angle restraints: 3484 sinusoidal: 1396 harmonic: 2088 Sorted by residual: dihedral pdb=" C12 PKZ A 602 " pdb=" C10 PKZ A 602 " pdb=" C11 PKZ A 602 " pdb=" C9 PKZ A 602 " ideal model delta sinusoidal sigma weight residual 179.58 -17.48 -162.94 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C3 PKZ A 602 " pdb=" C1 PKZ A 602 " pdb=" C2 PKZ A 602 " pdb=" O1 PKZ A 602 " ideal model delta sinusoidal sigma weight residual -33.60 104.49 -138.09 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" CA LEU O 105 " pdb=" C LEU O 105 " pdb=" N LYS O 106 " pdb=" CA LYS O 106 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 3481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.215: 899 1.215 - 2.430: 0 2.430 - 3.644: 0 3.644 - 4.859: 16 4.859 - 6.074: 38 Chirality restraints: 953 Sorted by residual: chirality pdb=" C12 AJP A 604 " pdb=" C07 AJP A 604 " pdb=" C11 AJP A 604 " pdb=" C13 AJP A 604 " both_signs ideal model delta sigma weight residual False 3.01 -3.07 6.07 2.00e-01 2.50e+01 9.22e+02 chirality pdb=" C12 AJP A 606 " pdb=" C07 AJP A 606 " pdb=" C11 AJP A 606 " pdb=" C13 AJP A 606 " both_signs ideal model delta sigma weight residual False 3.01 -3.06 6.07 2.00e-01 2.50e+01 9.20e+02 chirality pdb=" C12 AJP A 607 " pdb=" C07 AJP A 607 " pdb=" C11 AJP A 607 " pdb=" C13 AJP A 607 " both_signs ideal model delta sigma weight residual False 3.01 -3.04 6.05 2.00e-01 2.50e+01 9.14e+02 ... (remaining 950 not shown) Planarity restraints: 1014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P 82 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO P 83 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO P 83 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO P 83 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 201 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A 202 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 2 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 3 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 3 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 3 " 0.019 5.00e-02 4.00e+02 ... (remaining 1011 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 114 2.70 - 3.25: 5721 3.25 - 3.80: 9782 3.80 - 4.35: 12675 4.35 - 4.90: 21512 Nonbonded interactions: 49804 Sorted by model distance: nonbonded pdb=" O MET A 328 " pdb=" OH TYR A 479 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR A 207 " pdb=" O LEU A 220 " model vdw 2.196 3.040 nonbonded pdb=" O GLY O 129 " pdb=" OG SER P 67 " model vdw 2.243 3.040 nonbonded pdb=" NH1 ARG P 85 " pdb=" OD2 ASP P 106 " model vdw 2.285 3.120 nonbonded pdb=" NH2 ARG A 176 " pdb=" O VAL A 213 " model vdw 2.310 3.120 ... (remaining 49799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 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 : 0.014 0.637 6357 Z= 0.592 Angle : 0.852 14.676 8719 Z= 0.389 Chirality : 1.243 6.074 953 Planarity : 0.004 0.042 1014 Dihedral : 17.436 162.935 2150 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.29), residues: 712 helix: 0.22 (0.24), residues: 406 sheet: -0.52 (0.48), residues: 120 loop : -2.47 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 250 TYR 0.019 0.002 TYR P 73 PHE 0.018 0.001 PHE A 17 TRP 0.008 0.001 TRP O 66 HIS 0.008 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.01153 / 0.57 ( 6354) covalent geometry : angle 0.85208 / 0.39 ( 8715) SS BOND : bond 0.00422 / 0.20 ( 2) SS BOND : angle 0.93584 / 0.49 ( 4) hydrogen bonds : bond 0.07462 / 5.24 ( 371) hydrogen bonds : angle 4.69125 / 3.54 ( 1080) Misc. bond : bond 0.63671 / 33.51 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.209 Fit side-chains REVERT: A 68 LYS cc_start: 0.8360 (ptmm) cc_final: 0.7750 (mttt) REVERT: A 238 LYS cc_start: 0.7237 (tptt) cc_final: 0.6791 (tppt) REVERT: A 403 ARG cc_start: 0.7739 (ttp80) cc_final: 0.6869 (tpp-160) REVERT: O 110 MET cc_start: 0.7853 (mtp) cc_final: 0.7623 (mtm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.6253 time to fit residues: 67.5788 Evaluate side-chains 74 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 232 GLN A 234 HIS A 428 HIS A 443 ASN O 25 GLN O 103 ASN P 25 GLN P 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.089662 restraints weight = 8406.852| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.74 r_work: 0.2870 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6357 Z= 0.132 Angle : 1.892 34.858 8719 Z= 0.661 Chirality : 0.193 1.895 953 Planarity : 0.004 0.044 1014 Dihedral : 13.064 171.983 855 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.09 % Allowed : 9.00 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.70 (0.32), residues: 712 helix: 1.66 (0.25), residues: 410 sheet: -0.04 (0.50), residues: 121 loop : -2.00 (0.40), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.026 0.002 TYR A 180 PHE 0.027 0.001 PHE A 17 TRP 0.014 0.001 TRP A 465 HIS 0.005 0.001 HIS A 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 6354) covalent geometry : angle 1.89202 / 0.66 ( 8715) SS BOND : bond 0.00456 / 0.22 ( 2) SS BOND : angle 0.75191 / 0.38 ( 4) hydrogen bonds : bond 0.04656 / 3.17 ( 371) hydrogen bonds : angle 4.13603 / 3.07 ( 1080) Misc. bond : bond 0.03105 / 1.63 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.207 Fit side-chains REVERT: A 31 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7171 (tm-30) REVERT: A 238 LYS cc_start: 0.6941 (tptt) cc_final: 0.6404 (tppt) REVERT: A 403 ARG cc_start: 0.7971 (ttp80) cc_final: 0.6811 (tpp-160) REVERT: O 110 MET cc_start: 0.8002 (mtp) cc_final: 0.7756 (mtm) REVERT: O 122 ASP cc_start: 0.8363 (m-30) cc_final: 0.8071 (m-30) REVERT: P 22 LEU cc_start: 0.8464 (mm) cc_final: 0.8224 (tp) REVERT: P 58 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8864 (mt-10) outliers start: 13 outliers final: 5 residues processed: 88 average time/residue: 0.4867 time to fit residues: 44.8756 Evaluate side-chains 85 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 14 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS P 37 GLN P 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.091239 restraints weight = 8225.357| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.77 r_work: 0.2882 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6357 Z= 0.126 Angle : 1.862 33.843 8719 Z= 0.649 Chirality : 0.198 1.952 953 Planarity : 0.004 0.050 1014 Dihedral : 11.708 133.268 855 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.25 % Allowed : 10.77 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.38 (0.32), residues: 712 helix: 2.22 (0.26), residues: 410 sheet: 0.21 (0.51), residues: 121 loop : -1.72 (0.41), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.022 0.002 TYR A 180 PHE 0.024 0.001 PHE A 17 TRP 0.010 0.001 TRP A 465 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 6354) covalent geometry : angle 1.86259 / 0.65 ( 8715) SS BOND : bond 0.00511 / 0.25 ( 2) SS BOND : angle 0.64231 / 0.30 ( 4) hydrogen bonds : bond 0.04495 / 3.06 ( 371) hydrogen bonds : angle 3.98912 / 2.95 ( 1080) Misc. bond : bond 0.03060 / 1.61 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.215 Fit side-chains REVERT: A 31 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 57 ASP cc_start: 0.8689 (t0) cc_final: 0.8473 (t70) REVERT: A 238 LYS cc_start: 0.6985 (tptt) cc_final: 0.6476 (tppt) REVERT: A 403 ARG cc_start: 0.7974 (ttp80) cc_final: 0.6817 (tpp-160) REVERT: O 110 MET cc_start: 0.8017 (mtp) cc_final: 0.7809 (mtm) REVERT: O 122 ASP cc_start: 0.8381 (m-30) cc_final: 0.8112 (m-30) REVERT: P 22 LEU cc_start: 0.8494 (mm) cc_final: 0.8252 (tp) outliers start: 14 outliers final: 7 residues processed: 94 average time/residue: 0.5122 time to fit residues: 50.6055 Evaluate side-chains 89 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS P 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.089977 restraints weight = 8219.312| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.76 r_work: 0.2869 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6357 Z= 0.138 Angle : 1.869 33.803 8719 Z= 0.652 Chirality : 0.197 1.932 953 Planarity : 0.004 0.053 1014 Dihedral : 11.552 137.820 855 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.25 % Allowed : 12.70 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.56 (0.32), residues: 712 helix: 2.40 (0.26), residues: 405 sheet: 0.30 (0.51), residues: 121 loop : -1.64 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 43 TYR 0.020 0.002 TYR A 180 PHE 0.026 0.001 PHE A 17 TRP 0.009 0.001 TRP A 465 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6354) covalent geometry : angle 1.86926 / 0.65 ( 8715) SS BOND : bond 0.00441 / 0.22 ( 2) SS BOND : angle 0.65793 / 0.30 ( 4) hydrogen bonds : bond 0.04853 / 3.31 ( 371) hydrogen bonds : angle 4.04386 / 3.00 ( 1080) Misc. bond : bond 0.03033 / 1.60 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.221 Fit side-chains REVERT: A 31 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 57 ASP cc_start: 0.8737 (t0) cc_final: 0.8533 (t70) REVERT: A 238 LYS cc_start: 0.6994 (tptt) cc_final: 0.6532 (tppt) REVERT: A 403 ARG cc_start: 0.8009 (ttp80) cc_final: 0.6845 (tpp-160) REVERT: O 110 MET cc_start: 0.8099 (mtp) cc_final: 0.7873 (mtm) REVERT: O 122 ASP cc_start: 0.8424 (m-30) cc_final: 0.8220 (m-30) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.5273 time to fit residues: 47.6388 Evaluate side-chains 86 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 66 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS P 37 GLN P 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.088592 restraints weight = 8383.085| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.78 r_work: 0.2857 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6357 Z= 0.145 Angle : 1.872 33.837 8719 Z= 0.655 Chirality : 0.197 1.935 953 Planarity : 0.004 0.054 1014 Dihedral : 11.604 140.195 855 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.57 % Allowed : 13.34 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.66 (0.32), residues: 712 helix: 2.45 (0.25), residues: 405 sheet: 0.44 (0.51), residues: 121 loop : -1.60 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 336 TYR 0.020 0.002 TYR P 73 PHE 0.027 0.002 PHE A 17 TRP 0.008 0.001 TRP A 465 HIS 0.005 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 6354) covalent geometry : angle 1.87277 / 0.65 ( 8715) SS BOND : bond 0.00458 / 0.22 ( 2) SS BOND : angle 0.70752 / 0.32 ( 4) hydrogen bonds : bond 0.05054 / 3.45 ( 371) hydrogen bonds : angle 4.07751 / 3.02 ( 1080) Misc. bond : bond 0.03040 / 1.60 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.222 Fit side-chains REVERT: A 238 LYS cc_start: 0.6992 (tptt) cc_final: 0.6521 (tppt) REVERT: A 403 ARG cc_start: 0.8010 (ttp80) cc_final: 0.6860 (tpp-160) REVERT: O 110 MET cc_start: 0.8093 (mtp) cc_final: 0.7841 (mtm) outliers start: 16 outliers final: 11 residues processed: 88 average time/residue: 0.4868 time to fit residues: 45.0223 Evaluate side-chains 86 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 130 GLN Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 32 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 1 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS A 443 ASN P 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.090297 restraints weight = 8239.429| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.75 r_work: 0.2884 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6357 Z= 0.130 Angle : 1.863 33.637 8719 Z= 0.650 Chirality : 0.198 1.932 953 Planarity : 0.004 0.056 1014 Dihedral : 11.487 140.274 855 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.57 % Allowed : 13.83 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.79 (0.33), residues: 712 helix: 2.66 (0.26), residues: 398 sheet: 0.58 (0.52), residues: 121 loop : -1.72 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 43 TYR 0.019 0.002 TYR A 180 PHE 0.024 0.001 PHE A 17 TRP 0.007 0.001 TRP A 465 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 6354) covalent geometry : angle 1.86365 / 0.65 ( 8715) SS BOND : bond 0.00403 / 0.20 ( 2) SS BOND : angle 0.62839 / 0.29 ( 4) hydrogen bonds : bond 0.04665 / 3.18 ( 371) hydrogen bonds : angle 3.99687 / 2.96 ( 1080) Misc. bond : bond 0.02844 / 1.50 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.167 Fit side-chains REVERT: A 238 LYS cc_start: 0.6932 (tptt) cc_final: 0.6468 (tppt) REVERT: A 403 ARG cc_start: 0.7986 (ttp80) cc_final: 0.6850 (tpp-160) REVERT: O 110 MET cc_start: 0.8073 (mtp) cc_final: 0.7836 (mtm) REVERT: P 22 LEU cc_start: 0.8523 (mm) cc_final: 0.8265 (tp) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.4889 time to fit residues: 44.1204 Evaluate side-chains 87 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 32 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 65 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS P 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.090029 restraints weight = 8185.401| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.75 r_work: 0.2875 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6357 Z= 0.135 Angle : 1.865 33.648 8719 Z= 0.651 Chirality : 0.197 1.935 953 Planarity : 0.004 0.057 1014 Dihedral : 11.512 141.356 855 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.57 % Allowed : 14.31 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.85 (0.33), residues: 712 helix: 2.65 (0.26), residues: 399 sheet: 0.73 (0.53), residues: 120 loop : -1.65 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 43 TYR 0.019 0.002 TYR A 180 PHE 0.025 0.001 PHE A 17 TRP 0.007 0.001 TRP O 66 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 6354) covalent geometry : angle 1.86587 / 0.65 ( 8715) SS BOND : bond 0.00422 / 0.21 ( 2) SS BOND : angle 0.67102 / 0.32 ( 4) hydrogen bonds : bond 0.04790 / 3.27 ( 371) hydrogen bonds : angle 4.00660 / 2.97 ( 1080) Misc. bond : bond 0.02827 / 1.49 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.224 Fit side-chains REVERT: A 238 LYS cc_start: 0.6976 (tptt) cc_final: 0.6493 (tppt) REVERT: A 403 ARG cc_start: 0.7988 (ttp80) cc_final: 0.6864 (tpp-160) REVERT: O 31 LYS cc_start: 0.6314 (mttm) cc_final: 0.5983 (mtmm) REVERT: O 110 MET cc_start: 0.8117 (mtp) cc_final: 0.7906 (mtm) outliers start: 16 outliers final: 15 residues processed: 87 average time/residue: 0.4729 time to fit residues: 43.4076 Evaluate side-chains 91 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 130 GLN Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.088603 restraints weight = 8300.062| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.77 r_work: 0.2852 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6357 Z= 0.149 Angle : 1.876 33.790 8719 Z= 0.657 Chirality : 0.197 1.938 953 Planarity : 0.004 0.058 1014 Dihedral : 11.627 142.410 855 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.73 % Allowed : 13.83 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.81 (0.33), residues: 712 helix: 2.59 (0.25), residues: 399 sheet: 0.76 (0.52), residues: 120 loop : -1.64 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 43 TYR 0.020 0.002 TYR A 300 PHE 0.027 0.002 PHE A 17 TRP 0.007 0.001 TRP O 66 HIS 0.005 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 6354) covalent geometry : angle 1.87665 / 0.66 ( 8715) SS BOND : bond 0.00451 / 0.22 ( 2) SS BOND : angle 0.72633 / 0.35 ( 4) hydrogen bonds : bond 0.05134 / 3.51 ( 371) hydrogen bonds : angle 4.07676 / 3.02 ( 1080) Misc. bond : bond 0.02861 / 1.51 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.154 Fit side-chains REVERT: A 238 LYS cc_start: 0.7024 (tptt) cc_final: 0.6550 (tppt) REVERT: A 403 ARG cc_start: 0.8027 (ttp80) cc_final: 0.6914 (tpp-160) REVERT: O 31 LYS cc_start: 0.6389 (mttm) cc_final: 0.6130 (mtmm) REVERT: O 35 GLU cc_start: 0.6377 (mt-10) cc_final: 0.6169 (mt-10) REVERT: O 110 MET cc_start: 0.8116 (mtp) cc_final: 0.7858 (mtm) outliers start: 17 outliers final: 16 residues processed: 88 average time/residue: 0.4735 time to fit residues: 43.7373 Evaluate side-chains 93 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 130 GLN Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.084942 restraints weight = 8376.695| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.80 r_work: 0.2755 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 6357 Z= 0.234 Angle : 1.925 34.357 8719 Z= 0.685 Chirality : 0.196 1.950 953 Planarity : 0.005 0.057 1014 Dihedral : 12.124 145.123 855 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.73 % Allowed : 13.67 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.47 (0.32), residues: 712 helix: 2.17 (0.25), residues: 405 sheet: 0.61 (0.51), residues: 120 loop : -1.54 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 43 TYR 0.029 0.002 TYR A 300 PHE 0.038 0.002 PHE A 17 TRP 0.010 0.001 TRP O 128 HIS 0.009 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.23 ( 6354) covalent geometry : angle 1.92509 / 0.68 ( 8715) SS BOND : bond 0.00591 / 0.29 ( 2) SS BOND : angle 0.99571 / 0.46 ( 4) hydrogen bonds : bond 0.06492 / 4.43 ( 371) hydrogen bonds : angle 4.37685 / 3.23 ( 1080) Misc. bond : bond 0.02737 / 1.44 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.198 Fit side-chains REVERT: A 238 LYS cc_start: 0.7198 (tptt) cc_final: 0.6733 (tppt) REVERT: A 403 ARG cc_start: 0.8071 (ttp80) cc_final: 0.6913 (tpp-160) REVERT: O 31 LYS cc_start: 0.6600 (mttm) cc_final: 0.6170 (mtmm) REVERT: O 110 MET cc_start: 0.8097 (mtp) cc_final: 0.7860 (mtm) outliers start: 17 outliers final: 13 residues processed: 90 average time/residue: 0.4993 time to fit residues: 47.3179 Evaluate side-chains 89 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 130 GLN Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.114798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.087835 restraints weight = 8337.889| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.82 r_work: 0.2874 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6357 Z= 0.127 Angle : 1.865 33.758 8719 Z= 0.651 Chirality : 0.197 1.932 953 Planarity : 0.004 0.055 1014 Dihedral : 11.606 140.491 855 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.93 % Allowed : 14.79 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.84 (0.33), residues: 712 helix: 2.65 (0.26), residues: 398 sheet: 0.72 (0.52), residues: 120 loop : -1.65 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 43 TYR 0.020 0.002 TYR A 180 PHE 0.023 0.001 PHE A 17 TRP 0.007 0.001 TRP A 465 HIS 0.003 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 6354) covalent geometry : angle 1.86543 / 0.65 ( 8715) SS BOND : bond 0.00404 / 0.20 ( 2) SS BOND : angle 0.68610 / 0.32 ( 4) hydrogen bonds : bond 0.04556 / 3.11 ( 371) hydrogen bonds : angle 4.01290 / 2.97 ( 1080) Misc. bond : bond 0.02678 / 1.41 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.237 Fit side-chains REVERT: A 238 LYS cc_start: 0.6960 (tptt) cc_final: 0.6517 (tppt) REVERT: A 403 ARG cc_start: 0.7971 (ttp80) cc_final: 0.6841 (tpp-160) REVERT: O 31 LYS cc_start: 0.6350 (mttm) cc_final: 0.6149 (mtmm) REVERT: O 110 MET cc_start: 0.8079 (mtp) cc_final: 0.7841 (mtm) REVERT: P 37 GLN cc_start: 0.7301 (mm110) cc_final: 0.7076 (mm110) outliers start: 12 outliers final: 12 residues processed: 82 average time/residue: 0.5436 time to fit residues: 46.9202 Evaluate side-chains 87 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 115 CYS Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 130 GLN Chi-restraints excluded: chain P residue 28 LEU Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.089147 restraints weight = 8250.497| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.76 r_work: 0.2855 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6357 Z= 0.142 Angle : 1.872 33.753 8719 Z= 0.655 Chirality : 0.197 1.938 953 Planarity : 0.004 0.053 1014 Dihedral : 11.622 141.220 855 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.09 % Allowed : 14.47 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.86 (0.33), residues: 712 helix: 2.61 (0.26), residues: 399 sheet: 0.80 (0.52), residues: 120 loop : -1.60 (0.42), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 43 TYR 0.019 0.002 TYR A 300 PHE 0.026 0.001 PHE A 17 TRP 0.007 0.001 TRP O 66 HIS 0.005 0.001 HIS A 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 6354) covalent geometry : angle 1.87274 / 0.65 ( 8715) SS BOND : bond 0.00437 / 0.21 ( 2) SS BOND : angle 0.67516 / 0.31 ( 4) hydrogen bonds : bond 0.04987 / 3.41 ( 371) hydrogen bonds : angle 4.05768 / 3.01 ( 1080) Misc. bond : bond 0.02789 / 1.47 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2028.43 seconds wall clock time: 35 minutes 27.06 seconds (2127.06 seconds total)