Starting phenix.real_space_refine on Tue Mar 11 17:05:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrq_32735/03_2025/7wrq_32735_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrq_32735/03_2025/7wrq_32735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wrq_32735/03_2025/7wrq_32735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrq_32735/03_2025/7wrq_32735.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrq_32735/03_2025/7wrq_32735_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrq_32735/03_2025/7wrq_32735_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 3930 2.51 5 N 1125 2.21 5 O 1151 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "B ARG 36": not complete - not flipped Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6247 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4384 Classifications: {'peptide': 566} Link IDs: {'PTRANS': 32, 'TRANS': 533} Chain: "B" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1269 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 16, 'TRANS': 150} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 499 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.84, per 1000 atoms: 0.61 Number of scatterers: 6247 At special positions: 0 Unit cell: (63.576, 98.896, 123.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1151 8.00 N 1125 7.00 C 3930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 47 " distance=2.03 Simple disulfide: pdb=" SG CYS A 45 " - pdb=" SG CYS A 60 " distance=2.03 Simple disulfide: pdb=" SG CYS A 373 " - pdb=" SG CYS A 397 " distance=1.73 Simple disulfide: pdb=" SG CYS A 540 " - pdb=" SG CYS A 583 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 566 " - pdb=" SG CYS A 571 " distance=2.09 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 42 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 43 " distance=2.01 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS B 46 " distance=2.10 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 67 " distance=2.19 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 213 " distance=2.02 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.04 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 258 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " distance=2.03 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 52 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A 701 " - " ASN A 64 " " NAG A 702 " - " ASN A 96 " " NAG A 703 " - " ASN A 515 " " NAG A 704 " - " ASN A 580 " " NAG D 1 " - " ASN A 368 " Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 840.9 milliseconds 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 8.6% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.754A pdb=" N LEU A 502 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 75 through 82 Processing helix chain 'B' and resid 186 through 195 removed outlier: 3.883A pdb=" N ASP B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 19 Processing helix chain 'C' and resid 42 through 50 Processing helix chain 'C' and resid 53 through 59 removed outlier: 3.567A pdb=" N LEU C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.722A pdb=" N VAL A 58 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 79 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200 removed outlier: 3.523A pdb=" N LEU A 199 " --> pdb=" O GLU A 222 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP A 224 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 223 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 248 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 366 through 367 removed outlier: 3.666A pdb=" N MET A 367 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 463 through 464 removed outlier: 7.082A pdb=" N LEU A 463 " --> pdb=" O ASP A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.300A pdb=" N VAL B 10 " --> pdb=" O LEU B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 222 through 223 50 hydrogen bonds defined for protein. 132 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: 1.71 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1181 1.32 - 1.45: 1573 1.45 - 1.58: 3579 1.58 - 1.70: 0 1.70 - 1.83: 44 Bond restraints: 6377 Sorted by residual: bond pdb=" C GLU A 567 " pdb=" N GLY A 568 " ideal model delta sigma weight residual 1.331 1.574 -0.244 1.46e-02 4.69e+03 2.79e+02 bond pdb=" C VAL B 30 " pdb=" N CYS B 31 " ideal model delta sigma weight residual 1.332 1.525 -0.192 1.40e-02 5.10e+03 1.89e+02 bond pdb=" C ILE A 565 " pdb=" N CYS A 566 " ideal model delta sigma weight residual 1.331 1.206 0.125 1.24e-02 6.50e+03 1.01e+02 bond pdb=" C LEU C 64 " pdb=" N LYS C 65 " ideal model delta sigma weight residual 1.329 1.463 -0.134 1.40e-02 5.10e+03 9.10e+01 bond pdb=" C GLU A 394 " pdb=" N GLY A 395 " ideal model delta sigma weight residual 1.333 1.460 -0.127 1.41e-02 5.03e+03 8.09e+01 ... (remaining 6372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.68: 8503 3.68 - 7.35: 113 7.35 - 11.03: 16 11.03 - 14.70: 9 14.70 - 18.38: 4 Bond angle restraints: 8645 Sorted by residual: angle pdb=" O ILE A 565 " pdb=" C ILE A 565 " pdb=" N CYS A 566 " ideal model delta sigma weight residual 122.57 106.94 15.63 1.25e+00 6.40e-01 1.56e+02 angle pdb=" O GLU A 394 " pdb=" C GLU A 394 " pdb=" N GLY A 395 " ideal model delta sigma weight residual 122.85 135.51 -12.66 1.14e+00 7.69e-01 1.23e+02 angle pdb=" C ALA B 32 " pdb=" N GLU B 33 " pdb=" CA GLU B 33 " ideal model delta sigma weight residual 122.68 138.10 -15.42 1.47e+00 4.63e-01 1.10e+02 angle pdb=" C SER A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta sigma weight residual 121.69 140.07 -18.38 1.85e+00 2.92e-01 9.87e+01 angle pdb=" O ALA A 603 " pdb=" C ALA A 603 " pdb=" N PRO A 604 " ideal model delta sigma weight residual 121.32 109.96 11.36 1.15e+00 7.56e-01 9.75e+01 ... (remaining 8640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 3901 35.98 - 71.97: 88 71.97 - 107.95: 13 107.95 - 143.93: 0 143.93 - 179.91: 1 Dihedral angle restraints: 4003 sinusoidal: 1743 harmonic: 2260 Sorted by residual: dihedral pdb=" CD ARG B 36 " pdb=" NE ARG B 36 " pdb=" CZ ARG B 36 " pdb=" NH1 ARG B 36 " ideal model delta sinusoidal sigma weight residual 0.00 -179.91 179.91 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG A 160 " pdb=" NE ARG A 160 " pdb=" CZ ARG A 160 " pdb=" NH1 ARG A 160 " ideal model delta sinusoidal sigma weight residual 0.00 -79.75 79.75 1 1.00e+01 1.00e-02 7.89e+01 dihedral pdb=" CB CYS B 24 " pdb=" SG CYS B 24 " pdb=" SG CYS B 43 " pdb=" CB CYS B 43 " ideal model delta sinusoidal sigma weight residual 93.00 167.98 -74.98 1 1.00e+01 1.00e-02 7.11e+01 ... (remaining 4000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 831 0.096 - 0.193: 116 0.193 - 0.289: 21 0.289 - 0.386: 4 0.386 - 0.482: 3 Chirality restraints: 975 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.30e+02 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 368 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" CA LEU A 398 " pdb=" N LEU A 398 " pdb=" C LEU A 398 " pdb=" CB LEU A 398 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.60e+00 ... (remaining 972 not shown) Planarity restraints: 1142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.345 2.00e-02 2.50e+03 2.93e-01 1.07e+03 pdb=" C7 NAG D 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.514 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 702 " -0.286 2.00e-02 2.50e+03 2.45e-01 7.53e+02 pdb=" C7 NAG A 702 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 702 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A 702 " 0.429 2.00e-02 2.50e+03 pdb=" O7 NAG A 702 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " 0.212 2.00e-02 2.50e+03 1.76e-01 3.89e+02 pdb=" C7 NAG A 704 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " -0.290 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " -0.015 2.00e-02 2.50e+03 ... (remaining 1139 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2230 2.87 - 3.37: 4769 3.37 - 3.88: 8412 3.88 - 4.39: 9122 4.39 - 4.90: 16849 Nonbonded interactions: 41382 Sorted by model distance: nonbonded pdb=" O SER A 195 " pdb=" OG SER A 195 " model vdw 2.357 3.040 nonbonded pdb=" O GLU B 189 " pdb=" OG1 THR B 193 " model vdw 2.361 3.040 nonbonded pdb=" O SER C 34 " pdb=" OG SER C 34 " model vdw 2.386 3.040 nonbonded pdb=" N GLN A 95 " pdb=" O GLN A 95 " model vdw 2.398 2.496 nonbonded pdb=" NH1 ARG A 269 " pdb=" OH TYR B 183 " model vdw 2.417 3.120 ... (remaining 41377 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: 1.130 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.850 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.011 0.244 6377 Z= 0.735 Angle : 1.291 18.381 8645 Z= 0.818 Chirality : 0.076 0.482 975 Planarity : 0.024 0.484 1137 Dihedral : 15.483 179.913 2499 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.04 Ramachandran Plot: Outliers : 0.51 % Allowed : 19.87 % Favored : 79.62 % Rotamer: Outliers : 1.06 % Allowed : 6.65 % Favored : 92.30 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.87 (0.21), residues: 790 helix: -2.24 (0.61), residues: 60 sheet: -4.22 (0.40), residues: 100 loop : -4.45 (0.17), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 179 HIS 0.014 0.002 HIS A 389 PHE 0.017 0.002 PHE A 262 TYR 0.012 0.002 TYR B 183 ARG 0.007 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 LYS cc_start: 0.9073 (tttp) cc_final: 0.8872 (tptp) REVERT: B 37 GLU cc_start: 0.9295 (pt0) cc_final: 0.8467 (pm20) REVERT: B 49 SER cc_start: 0.9460 (t) cc_final: 0.9195 (p) REVERT: B 68 GLN cc_start: 0.9127 (mt0) cc_final: 0.8816 (mt0) REVERT: B 72 ASP cc_start: 0.8863 (p0) cc_final: 0.8576 (p0) REVERT: B 209 HIS cc_start: 0.8327 (m170) cc_final: 0.8090 (m170) REVERT: B 243 GLN cc_start: 0.8755 (mp10) cc_final: 0.8243 (mp10) REVERT: B 259 TYR cc_start: 0.8094 (m-80) cc_final: 0.7892 (m-10) REVERT: C 5 LEU cc_start: 0.8986 (tp) cc_final: 0.8707 (tt) outliers start: 7 outliers final: 3 residues processed: 89 average time/residue: 0.2327 time to fit residues: 26.2963 Evaluate side-chains 53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 571 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS B 196 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.088562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.062913 restraints weight = 15079.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.064661 restraints weight = 10129.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.065724 restraints weight = 6215.327| |-----------------------------------------------------------------------------| r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6377 Z= 0.227 Angle : 0.695 6.414 8645 Z= 0.348 Chirality : 0.044 0.155 975 Planarity : 0.005 0.050 1137 Dihedral : 10.264 179.935 1019 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.27 % Favored : 88.48 % Rotamer: Outliers : 2.11 % Allowed : 11.03 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.23), residues: 790 helix: -1.63 (0.59), residues: 68 sheet: -4.03 (0.37), residues: 113 loop : -3.90 (0.19), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 173 HIS 0.014 0.001 HIS A 601 PHE 0.012 0.001 PHE A 416 TYR 0.017 0.001 TYR A 208 ARG 0.011 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 LYS cc_start: 0.9126 (tttp) cc_final: 0.8809 (tptp) REVERT: B 37 GLU cc_start: 0.9265 (pt0) cc_final: 0.8442 (pm20) REVERT: B 49 SER cc_start: 0.9451 (t) cc_final: 0.9166 (p) REVERT: B 73 GLU cc_start: 0.8644 (tp30) cc_final: 0.8365 (tm-30) REVERT: B 209 HIS cc_start: 0.8372 (m170) cc_final: 0.8128 (m170) REVERT: B 243 GLN cc_start: 0.8812 (mp10) cc_final: 0.8518 (mp10) REVERT: B 259 TYR cc_start: 0.8353 (m-80) cc_final: 0.8060 (m-10) outliers start: 14 outliers final: 7 residues processed: 64 average time/residue: 0.2201 time to fit residues: 18.3761 Evaluate side-chains 54 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 33 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 10 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.058879 restraints weight = 15395.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.061275 restraints weight = 8667.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.062883 restraints weight = 6102.693| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6377 Z= 0.300 Angle : 0.700 9.311 8645 Z= 0.351 Chirality : 0.044 0.182 975 Planarity : 0.005 0.051 1137 Dihedral : 8.721 179.426 1018 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.43 % Favored : 85.44 % Rotamer: Outliers : 1.96 % Allowed : 12.99 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.24), residues: 790 helix: -1.30 (0.57), residues: 75 sheet: -3.33 (0.54), residues: 62 loop : -3.75 (0.19), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 173 HIS 0.002 0.001 HIS A 323 PHE 0.010 0.001 PHE A 416 TYR 0.010 0.001 TYR C 24 ARG 0.010 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7941 (t80) cc_final: 0.7618 (t80) REVERT: A 545 LYS cc_start: 0.9157 (tttp) cc_final: 0.8855 (tptp) REVERT: B 37 GLU cc_start: 0.9197 (pt0) cc_final: 0.8368 (pm20) REVERT: B 49 SER cc_start: 0.9487 (t) cc_final: 0.9202 (p) REVERT: B 259 TYR cc_start: 0.8283 (m-80) cc_final: 0.8067 (m-10) outliers start: 13 outliers final: 7 residues processed: 61 average time/residue: 0.2362 time to fit residues: 19.4082 Evaluate side-chains 51 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 571 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS B 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.057184 restraints weight = 15832.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.059468 restraints weight = 8945.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.060972 restraints weight = 6354.960| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 6377 Z= 0.446 Angle : 0.768 9.099 8645 Z= 0.387 Chirality : 0.047 0.154 975 Planarity : 0.005 0.052 1137 Dihedral : 8.654 179.009 1018 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.82 % Favored : 84.05 % Rotamer: Outliers : 1.51 % Allowed : 15.26 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.24), residues: 790 helix: -1.21 (0.58), residues: 75 sheet: -3.63 (0.58), residues: 52 loop : -3.65 (0.20), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 173 HIS 0.005 0.001 HIS B 209 PHE 0.012 0.002 PHE A 602 TYR 0.012 0.001 TYR C 24 ARG 0.015 0.001 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7976 (t80) cc_final: 0.7662 (t80) REVERT: B 37 GLU cc_start: 0.9146 (pt0) cc_final: 0.8568 (pt0) REVERT: B 49 SER cc_start: 0.9495 (t) cc_final: 0.9214 (p) REVERT: B 259 TYR cc_start: 0.8235 (m-80) cc_final: 0.7956 (m-10) REVERT: C 46 GLU cc_start: 0.9048 (tt0) cc_final: 0.8411 (tt0) REVERT: C 56 ARG cc_start: 0.8746 (mtt90) cc_final: 0.8333 (mtp85) outliers start: 10 outliers final: 8 residues processed: 53 average time/residue: 0.2522 time to fit residues: 17.3756 Evaluate side-chains 49 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 347 HIS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS B 196 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.058333 restraints weight = 15602.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.060676 restraints weight = 8795.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.062221 restraints weight = 6215.727| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6377 Z= 0.224 Angle : 0.650 8.696 8645 Z= 0.331 Chirality : 0.043 0.173 975 Planarity : 0.004 0.049 1137 Dihedral : 8.253 179.405 1017 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.41 % Favored : 87.47 % Rotamer: Outliers : 2.27 % Allowed : 15.56 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.25), residues: 790 helix: -0.97 (0.57), residues: 75 sheet: -3.54 (0.51), residues: 70 loop : -3.39 (0.21), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 173 HIS 0.012 0.001 HIS A 601 PHE 0.010 0.001 PHE A 416 TYR 0.007 0.001 TYR B 183 ARG 0.005 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7955 (t80) cc_final: 0.7704 (t80) REVERT: B 37 GLU cc_start: 0.9103 (pt0) cc_final: 0.8517 (pt0) REVERT: B 49 SER cc_start: 0.9496 (t) cc_final: 0.9200 (p) REVERT: B 259 TYR cc_start: 0.8223 (m-80) cc_final: 0.7969 (m-10) REVERT: C 65 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7787 (ptmt) outliers start: 15 outliers final: 5 residues processed: 56 average time/residue: 0.2116 time to fit residues: 15.7264 Evaluate side-chains 46 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 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 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.085812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.059408 restraints weight = 15338.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.061764 restraints weight = 8632.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.063377 restraints weight = 6090.938| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6377 Z= 0.187 Angle : 0.614 9.498 8645 Z= 0.310 Chirality : 0.041 0.152 975 Planarity : 0.004 0.047 1137 Dihedral : 7.991 179.117 1017 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.01 % Favored : 88.86 % Rotamer: Outliers : 1.96 % Allowed : 15.86 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.26), residues: 790 helix: -0.82 (0.59), residues: 75 sheet: -3.34 (0.66), residues: 42 loop : -3.26 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 179 HIS 0.013 0.001 HIS A 601 PHE 0.008 0.001 PHE A 416 TYR 0.009 0.001 TYR A 208 ARG 0.005 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7914 (t80) cc_final: 0.7698 (t80) REVERT: B 37 GLU cc_start: 0.9075 (pt0) cc_final: 0.8260 (pm20) REVERT: B 49 SER cc_start: 0.9520 (t) cc_final: 0.9205 (p) REVERT: B 259 TYR cc_start: 0.8228 (m-80) cc_final: 0.7984 (m-10) REVERT: C 65 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7911 (ptmt) outliers start: 13 outliers final: 6 residues processed: 55 average time/residue: 0.2033 time to fit residues: 15.0173 Evaluate side-chains 48 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 75 optimal weight: 0.0670 chunk 51 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.0370 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.060117 restraints weight = 15401.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.062509 restraints weight = 8634.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.064103 restraints weight = 6086.512| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6377 Z= 0.183 Angle : 0.608 9.382 8645 Z= 0.304 Chirality : 0.041 0.151 975 Planarity : 0.004 0.047 1137 Dihedral : 7.852 179.756 1017 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.89 % Favored : 88.99 % Rotamer: Outliers : 1.66 % Allowed : 17.07 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.26), residues: 790 helix: -0.52 (0.63), residues: 69 sheet: -3.37 (0.77), residues: 32 loop : -3.14 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 173 HIS 0.001 0.000 HIS B 196 PHE 0.007 0.001 PHE A 416 TYR 0.006 0.001 TYR B 183 ARG 0.003 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: B 37 GLU cc_start: 0.9037 (pt0) cc_final: 0.8462 (pt0) REVERT: B 49 SER cc_start: 0.9525 (t) cc_final: 0.9200 (p) REVERT: B 259 TYR cc_start: 0.8223 (m-80) cc_final: 0.7990 (m-10) outliers start: 11 outliers final: 8 residues processed: 49 average time/residue: 0.2199 time to fit residues: 14.5226 Evaluate side-chains 48 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 41 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A 601 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.059490 restraints weight = 15438.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.061889 restraints weight = 9962.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.063233 restraints weight = 5962.916| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6377 Z= 0.288 Angle : 0.664 9.402 8645 Z= 0.335 Chirality : 0.043 0.145 975 Planarity : 0.004 0.047 1137 Dihedral : 7.956 179.259 1017 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.29 % Favored : 86.58 % Rotamer: Outliers : 2.11 % Allowed : 17.07 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.26), residues: 790 helix: -0.23 (0.64), residues: 69 sheet: -3.52 (0.53), residues: 68 loop : -3.14 (0.21), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 173 HIS 0.002 0.001 HIS A 323 PHE 0.011 0.001 PHE A 416 TYR 0.050 0.002 TYR A 49 ARG 0.009 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 173 TRP cc_start: 0.7261 (m-10) cc_final: 0.7014 (m-10) REVERT: B 37 GLU cc_start: 0.8994 (pt0) cc_final: 0.8430 (pt0) REVERT: B 49 SER cc_start: 0.9515 (t) cc_final: 0.9188 (p) REVERT: B 259 TYR cc_start: 0.8327 (m-80) cc_final: 0.8045 (m-10) outliers start: 14 outliers final: 10 residues processed: 54 average time/residue: 0.1877 time to fit residues: 14.2103 Evaluate side-chains 53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain A residue 601 HIS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 41 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.0030 chunk 62 optimal weight: 4.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.085171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.059234 restraints weight = 15556.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.061855 restraints weight = 9845.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063245 restraints weight = 5825.929| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6377 Z= 0.268 Angle : 0.664 9.251 8645 Z= 0.333 Chirality : 0.042 0.146 975 Planarity : 0.004 0.046 1137 Dihedral : 7.989 179.546 1017 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.91 % Favored : 86.96 % Rotamer: Outliers : 1.51 % Allowed : 17.52 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.26), residues: 790 helix: -0.20 (0.64), residues: 69 sheet: -3.51 (0.55), residues: 60 loop : -3.10 (0.21), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 173 HIS 0.007 0.001 HIS A 601 PHE 0.010 0.001 PHE A 416 TYR 0.042 0.001 TYR A 49 ARG 0.004 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 578 TYR cc_start: 0.8979 (m-80) cc_final: 0.8407 (m-10) REVERT: B 37 GLU cc_start: 0.8986 (pt0) cc_final: 0.8411 (pt0) REVERT: B 49 SER cc_start: 0.9518 (t) cc_final: 0.9189 (p) REVERT: B 259 TYR cc_start: 0.8318 (m-80) cc_final: 0.8041 (m-10) outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.1763 time to fit residues: 12.2141 Evaluate side-chains 49 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN A 601 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.059460 restraints weight = 15756.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.062019 restraints weight = 9931.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.063504 restraints weight = 5926.283| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6377 Z= 0.268 Angle : 0.664 9.440 8645 Z= 0.334 Chirality : 0.042 0.145 975 Planarity : 0.004 0.047 1137 Dihedral : 7.956 179.497 1017 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.04 % Favored : 86.84 % Rotamer: Outliers : 1.81 % Allowed : 17.07 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.26), residues: 790 helix: -0.14 (0.66), residues: 69 sheet: -3.39 (0.55), residues: 59 loop : -3.09 (0.21), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 173 HIS 0.003 0.001 HIS A 601 PHE 0.010 0.001 PHE A 416 TYR 0.007 0.001 TYR C 24 ARG 0.004 0.000 ARG C 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TYR cc_start: 0.8053 (t80) cc_final: 0.7451 (t80) REVERT: A 578 TYR cc_start: 0.8979 (m-80) cc_final: 0.8389 (m-10) REVERT: B 37 GLU cc_start: 0.8954 (pt0) cc_final: 0.8337 (pt0) REVERT: B 49 SER cc_start: 0.9516 (t) cc_final: 0.9184 (p) REVERT: B 259 TYR cc_start: 0.8315 (m-80) cc_final: 0.8043 (m-10) REVERT: C 65 LYS cc_start: 0.8423 (mmtm) cc_final: 0.8198 (mtmm) outliers start: 12 outliers final: 9 residues processed: 51 average time/residue: 0.1960 time to fit residues: 13.7551 Evaluate side-chains 50 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 566 CYS Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 45 optimal weight: 0.0060 chunk 57 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.0170 chunk 62 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.4834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.060461 restraints weight = 15685.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.062956 restraints weight = 9841.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.064496 restraints weight = 5886.373| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6377 Z= 0.174 Angle : 0.625 9.483 8645 Z= 0.311 Chirality : 0.041 0.151 975 Planarity : 0.004 0.046 1137 Dihedral : 7.819 179.951 1017 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.51 % Favored : 89.37 % Rotamer: Outliers : 1.06 % Allowed : 17.37 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.27), residues: 790 helix: -0.15 (0.66), residues: 69 sheet: -2.89 (0.67), residues: 41 loop : -3.00 (0.21), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 173 HIS 0.002 0.000 HIS A 275 PHE 0.007 0.001 PHE A 485 TYR 0.006 0.001 TYR B 183 ARG 0.007 0.000 ARG C 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2100.31 seconds wall clock time: 36 minutes 54.33 seconds (2214.33 seconds total)