Starting phenix.real_space_refine on Fri Dec 27 18:31:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wrq_32735/12_2024/7wrq_32735_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrq_32735/12_2024/7wrq_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_32735/12_2024/7wrq_32735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrq_32735/12_2024/7wrq_32735.map" model { file = "/net/cci-nas-00/data/ceres_data/7wrq_32735/12_2024/7wrq_32735_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrq_32735/12_2024/7wrq_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-5532/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: 4.21, per 1000 atoms: 0.67 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: 1.55 Conformation dependent library (CDL) restraints added in 885.3 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: 0.49 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: 1.32 Time building geometry restraints manager: 1.79 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 16.950 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.390 ------------------------------------------------------------------------------- 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 : 0.705 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: 0.2339 time to fit residues: 26.4346 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 : 0.953 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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= 0.228 Angle : 0.694 6.416 8645 Z= 0.348 Chirality : 0.044 0.155 975 Planarity : 0.005 0.050 1137 Dihedral : 10.259 179.933 1019 Min Nonbonded Distance : 2.459 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 0.016 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 : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 GLU cc_start: 0.9238 (pt0) cc_final: 0.8456 (pm20) REVERT: B 49 SER cc_start: 0.9467 (t) cc_final: 0.9199 (p) REVERT: B 209 HIS cc_start: 0.8365 (m170) cc_final: 0.8122 (m170) REVERT: B 243 GLN cc_start: 0.8819 (mp10) cc_final: 0.8517 (mp10) REVERT: B 259 TYR cc_start: 0.8146 (m-80) cc_final: 0.7927 (m-10) outliers start: 14 outliers final: 7 residues processed: 64 average time/residue: 0.2218 time to fit residues: 18.5940 Evaluate side-chains 53 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 39 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6377 Z= 0.326 Angle : 0.713 9.068 8645 Z= 0.357 Chirality : 0.045 0.174 975 Planarity : 0.005 0.051 1137 Dihedral : 8.880 179.534 1018 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.81 % Favored : 85.06 % Rotamer: Outliers : 1.81 % Allowed : 13.14 % 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: -4.80 (0.24), residues: 790 helix: -1.27 (0.57), residues: 75 sheet: -3.39 (0.53), residues: 62 loop : -3.79 (0.19), 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 0.010 0.001 PHE A 416 TYR 0.010 0.001 TYR C 24 ARG 0.011 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 60 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.748 Fit side-chains REVERT: A 49 TYR cc_start: 0.7704 (t80) cc_final: 0.7345 (t80) REVERT: B 37 GLU cc_start: 0.9180 (pt0) cc_final: 0.8390 (pm20) REVERT: B 49 SER cc_start: 0.9498 (t) cc_final: 0.9231 (p) outliers start: 12 outliers final: 8 residues processed: 58 average time/residue: 0.2089 time to fit residues: 16.3729 Evaluate side-chains 51 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 33 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 75 optimal weight: 0.0970 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 HIS B 209 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6377 Z= 0.237 Angle : 0.641 9.306 8645 Z= 0.324 Chirality : 0.042 0.148 975 Planarity : 0.005 0.048 1137 Dihedral : 8.362 179.534 1018 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.77 % Favored : 88.10 % Rotamer: Outliers : 1.66 % Allowed : 14.80 % Favored : 83.53 % 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: -4.48 (0.25), residues: 790 helix: -1.15 (0.58), residues: 75 sheet: -3.15 (0.61), residues: 52 loop : -3.56 (0.20), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 173 HIS 0.005 0.001 HIS B 209 PHE 0.010 0.001 PHE A 416 TYR 0.009 0.001 TYR B 259 ARG 0.013 0.000 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 60 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 208 TYR cc_start: 0.8372 (t80) cc_final: 0.8127 (t80) REVERT: B 37 GLU cc_start: 0.9129 (pt0) cc_final: 0.8356 (pm20) REVERT: B 49 SER cc_start: 0.9515 (t) cc_final: 0.9237 (p) outliers start: 11 outliers final: 7 residues processed: 57 average time/residue: 0.2307 time to fit residues: 17.1041 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 : 0.718 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 B 196 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6377 Z= 0.262 Angle : 0.646 8.452 8645 Z= 0.328 Chirality : 0.043 0.178 975 Planarity : 0.005 0.049 1137 Dihedral : 8.152 179.448 1017 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.16 % Favored : 86.71 % Rotamer: Outliers : 2.57 % Allowed : 14.35 % Favored : 83.08 % 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: -4.34 (0.25), residues: 790 helix: -0.92 (0.58), residues: 75 sheet: -3.52 (0.51), residues: 70 loop : -3.38 (0.21), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 173 HIS 0.011 0.001 HIS A 601 PHE 0.010 0.001 PHE A 416 TYR 0.034 0.001 TYR A 49 ARG 0.004 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 62 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.676 Fit side-chains REVERT: B 37 GLU cc_start: 0.9108 (pt0) cc_final: 0.8320 (pm20) REVERT: B 49 SER cc_start: 0.9520 (t) cc_final: 0.9237 (p) outliers start: 17 outliers final: 9 residues processed: 58 average time/residue: 0.1785 time to fit residues: 14.4889 Evaluate side-chains 52 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 33 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6377 Z= 0.364 Angle : 0.708 9.351 8645 Z= 0.357 Chirality : 0.045 0.167 975 Planarity : 0.005 0.049 1137 Dihedral : 8.293 178.699 1017 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.06 % Favored : 84.81 % Rotamer: Outliers : 2.11 % Allowed : 15.86 % Favored : 82.02 % 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: -4.30 (0.25), residues: 790 helix: -0.75 (0.60), residues: 75 sheet: -3.72 (0.53), residues: 60 loop : -3.37 (0.20), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 236 HIS 0.006 0.001 HIS A 601 PHE 0.011 0.001 PHE A 416 TYR 0.036 0.002 TYR A 49 ARG 0.007 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 59 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: B 37 GLU cc_start: 0.9063 (pt0) cc_final: 0.8513 (pt0) REVERT: B 49 SER cc_start: 0.9522 (t) cc_final: 0.9238 (p) REVERT: B 86 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7204 (mt) outliers start: 14 outliers final: 8 residues processed: 56 average time/residue: 0.1909 time to fit residues: 14.6338 Evaluate side-chains 49 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 B residue 86 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 33 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0370 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 0.0000 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.5866 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3155 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 : 0.621 9.440 8645 Z= 0.313 Chirality : 0.041 0.154 975 Planarity : 0.004 0.047 1137 Dihedral : 7.966 179.561 1017 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.01 % Favored : 88.86 % Rotamer: Outliers : 1.66 % Allowed : 16.62 % Favored : 81.72 % 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: -4.05 (0.26), residues: 790 helix: -0.60 (0.61), residues: 75 sheet: -3.12 (0.60), residues: 52 loop : -3.24 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 236 HIS 0.006 0.001 HIS B 196 PHE 0.007 0.001 PHE A 416 TYR 0.011 0.001 TYR A 208 ARG 0.005 0.000 ARG C 37 *********************** 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 55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7636 (t80) cc_final: 0.7392 (t80) REVERT: B 37 GLU cc_start: 0.9032 (pt0) cc_final: 0.8482 (pt0) REVERT: B 49 SER cc_start: 0.9535 (t) cc_final: 0.9227 (p) outliers start: 11 outliers final: 7 residues processed: 51 average time/residue: 0.2188 time to fit residues: 14.8040 Evaluate side-chains 48 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6377 Z= 0.186 Angle : 0.615 9.439 8645 Z= 0.309 Chirality : 0.041 0.149 975 Planarity : 0.004 0.048 1137 Dihedral : 7.817 179.726 1017 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.39 % Favored : 88.48 % Rotamer: Outliers : 1.36 % Allowed : 17.22 % Favored : 81.42 % 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: -3.85 (0.26), residues: 790 helix: -0.43 (0.61), residues: 75 sheet: -3.33 (0.77), residues: 32 loop : -3.11 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 236 HIS 0.002 0.000 HIS A 601 PHE 0.008 0.001 PHE A 416 TYR 0.021 0.001 TYR B 259 ARG 0.009 0.000 ARG C 55 *********************** 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 55 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: B 37 GLU cc_start: 0.9002 (pt0) cc_final: 0.8245 (pm20) REVERT: B 49 SER cc_start: 0.9529 (t) cc_final: 0.9211 (p) REVERT: C 36 ARG cc_start: 0.8254 (tpp-160) cc_final: 0.7693 (tpp80) outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.2212 time to fit residues: 14.9027 Evaluate side-chains 52 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 0.0570 chunk 74 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 196 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3366 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= 0.192 Angle : 0.625 9.408 8645 Z= 0.313 Chirality : 0.041 0.149 975 Planarity : 0.005 0.053 1137 Dihedral : 7.769 179.806 1017 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.89 % Favored : 88.99 % Rotamer: Outliers : 1.21 % Allowed : 17.52 % 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: -3.76 (0.27), residues: 790 helix: -0.19 (0.60), residues: 75 sheet: -3.17 (0.79), residues: 32 loop : -3.06 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 173 HIS 0.007 0.001 HIS B 196 PHE 0.007 0.001 PHE A 416 TYR 0.010 0.001 TYR A 208 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 52 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7612 (t80) cc_final: 0.7296 (t80) REVERT: A 578 TYR cc_start: 0.8961 (m-80) cc_final: 0.8397 (m-10) REVERT: B 37 GLU cc_start: 0.8987 (pt0) cc_final: 0.8259 (pm20) REVERT: B 49 SER cc_start: 0.9532 (t) cc_final: 0.9217 (p) REVERT: C 36 ARG cc_start: 0.8281 (tpp-160) cc_final: 0.7735 (tpp80) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.2075 time to fit residues: 13.7373 Evaluate side-chains 49 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 33 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 61 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3379 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= 0.307 Angle : 0.683 9.301 8645 Z= 0.344 Chirality : 0.043 0.146 975 Planarity : 0.005 0.049 1137 Dihedral : 7.936 179.386 1017 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.43 % Favored : 85.44 % Rotamer: Outliers : 1.36 % Allowed : 17.22 % Favored : 81.42 % 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 (0.27), residues: 790 helix: -0.11 (0.62), residues: 75 sheet: -3.37 (0.53), residues: 68 loop : -3.10 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 173 HIS 0.005 0.001 HIS A 601 PHE 0.011 0.001 PHE A 416 TYR 0.009 0.001 TYR C 24 ARG 0.010 0.000 ARG C 37 ********************** 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 51 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 49 TYR cc_start: 0.7653 (t80) cc_final: 0.7321 (t80) REVERT: A 173 TRP cc_start: 0.7299 (m-10) cc_final: 0.7034 (m-10) REVERT: A 578 TYR cc_start: 0.8991 (m-80) cc_final: 0.8341 (m-10) REVERT: B 37 GLU cc_start: 0.8975 (pt0) cc_final: 0.8450 (pt0) REVERT: B 49 SER cc_start: 0.9535 (t) cc_final: 0.9217 (p) REVERT: B 189 GLU cc_start: 0.8893 (tp30) cc_final: 0.8686 (tp30) REVERT: C 65 LYS cc_start: 0.8317 (mmtm) cc_final: 0.8099 (mtmm) outliers start: 9 outliers final: 6 residues processed: 48 average time/residue: 0.1925 time to fit residues: 12.9287 Evaluate side-chains 47 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 3 optimal weight: 0.0970 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.087266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.060846 restraints weight = 15278.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.063205 restraints weight = 8497.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.064810 restraints weight = 5954.060| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3528 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= 0.184 Angle : 0.629 9.472 8645 Z= 0.314 Chirality : 0.041 0.165 975 Planarity : 0.004 0.047 1137 Dihedral : 7.726 179.809 1017 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.00 % Favored : 89.87 % Rotamer: Outliers : 1.21 % Allowed : 17.52 % 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: -3.62 (0.27), residues: 790 helix: -0.01 (0.63), residues: 75 sheet: -2.83 (0.84), residues: 31 loop : -2.99 (0.21), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1467.90 seconds wall clock time: 27 minutes 21.62 seconds (1641.62 seconds total)