Starting phenix.real_space_refine on Wed Aug 5 18:29:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z64_73833/08_2026/9z64_73833_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z64_73833/08_2026/9z64_73833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z64_73833/08_2026/9z64_73833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z64_73833/08_2026/9z64_73833.map" model { file = "/net/cci-nas-00/data/ceres_data/9z64_73833/08_2026/9z64_73833_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z64_73833/08_2026/9z64_73833_trim.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 3489 2.51 5 N 858 2.21 5 O 961 1.98 5 H 5412 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10749 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7191 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 19, 'TRANS': 442} Chain breaks: 3 Chain: "B" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1872 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1658 Classifications: {'peptide': 111} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.59, per 1000 atoms: 0.15 Number of scatterers: 10749 At special positions: 0 Unit cell: (74.675, 78.3, 129.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 961 8.00 N 858 7.00 C 3489 6.00 H 5412 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 146.7 milliseconds 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1278 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 58.9% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 68 through 101 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 151 through 164 Proline residue: A 157 - end of helix removed outlier: 3.778A pdb=" N ASN A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 176 through 179 removed outlier: 4.405A pdb=" N GLY A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 179' Processing helix chain 'A' and resid 180 through 213 removed outlier: 4.500A pdb=" N HIS A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 235 through 250 removed outlier: 3.913A pdb=" N ASN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.520A pdb=" N MET A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 361 removed outlier: 3.673A pdb=" N CYS A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.522A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 402 Processing helix chain 'A' and resid 403 through 417 Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 421 through 446 Proline residue: A 427 - end of helix removed outlier: 3.751A pdb=" N ALA A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 4.420A pdb=" N GLY A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ASN A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.776A pdb=" N ARG A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 3.994A pdb=" N ALA A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 removed outlier: 4.004A pdb=" N LEU A 513 " --> pdb=" O PHE A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 550 Proline residue: A 532 - end of helix Processing helix chain 'A' and resid 556 through 560 removed outlier: 3.912A pdb=" N SER A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.526A pdb=" N HIS A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.187A pdb=" N VAL C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.285A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LYS B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TRP B 47 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA B 40 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N LEU B 45 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.285A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR B 111 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.324A pdb=" N HIS C 41 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU C 50 " --> pdb=" O HIS C 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 14 removed outlier: 3.507A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 31 347 hydrogen bonds defined for protein. 981 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: 2.08 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5404 1.03 - 1.23: 8 1.23 - 1.42: 2229 1.42 - 1.61: 3187 1.61 - 1.81: 44 Bond restraints: 10872 Sorted by residual: bond pdb=" N VAL A 240 " pdb=" CA VAL A 240 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.25e+00 bond pdb=" C20 CLR A 801 " pdb=" C22 CLR A 801 " ideal model delta sigma weight residual 1.535 1.589 -0.054 2.00e-02 2.50e+03 7.42e+00 bond pdb=" N ASN A 239 " pdb=" CA ASN A 239 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.40e+00 bond pdb=" CA TYR C 40 " pdb=" C TYR C 40 " ideal model delta sigma weight residual 1.522 1.492 0.031 1.23e-02 6.61e+03 6.21e+00 bond pdb=" C6 CLR A 801 " pdb=" C7 CLR A 801 " ideal model delta sigma weight residual 1.492 1.536 -0.044 2.00e-02 2.50e+03 4.89e+00 ... (remaining 10867 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 18992 1.22 - 2.44: 625 2.44 - 3.66: 47 3.66 - 4.88: 18 4.88 - 6.10: 3 Bond angle restraints: 19685 Sorted by residual: angle pdb=" CA THR A 246 " pdb=" C THR A 246 " pdb=" O THR A 246 " ideal model delta sigma weight residual 120.42 116.34 4.08 1.06e+00 8.90e-01 1.48e+01 angle pdb=" CA ASN A 239 " pdb=" C ASN A 239 " pdb=" O ASN A 239 " ideal model delta sigma weight residual 120.55 116.84 3.71 1.06e+00 8.90e-01 1.22e+01 angle pdb=" CA VAL A 240 " pdb=" C VAL A 240 " pdb=" O VAL A 240 " ideal model delta sigma weight residual 121.17 117.67 3.50 1.06e+00 8.90e-01 1.09e+01 angle pdb=" CA GLN A 132 " pdb=" C GLN A 132 " pdb=" O GLN A 132 " ideal model delta sigma weight residual 120.55 116.88 3.67 1.28e+00 6.10e-01 8.23e+00 angle pdb=" CA LEU A 238 " pdb=" C LEU A 238 " pdb=" O LEU A 238 " ideal model delta sigma weight residual 120.51 116.43 4.08 1.43e+00 4.89e-01 8.15e+00 ... (remaining 19680 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4531 15.94 - 31.88: 411 31.88 - 47.82: 153 47.82 - 63.76: 77 63.76 - 79.69: 8 Dihedral angle restraints: 5180 sinusoidal: 2810 harmonic: 2370 Sorted by residual: dihedral pdb=" CA ASN A 170 " pdb=" CB ASN A 170 " pdb=" CG ASN A 170 " pdb=" OD1 ASN A 170 " ideal model delta sinusoidal sigma weight residual -90.00 -157.41 67.41 2 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" N LYS B 65 " pdb=" CA LYS B 65 " pdb=" CB LYS B 65 " pdb=" CG LYS B 65 " ideal model delta sinusoidal sigma weight residual -180.00 -123.98 -56.02 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CG LYS A 74 " pdb=" CD LYS A 74 " pdb=" CE LYS A 74 " pdb=" NZ LYS A 74 " ideal model delta sinusoidal sigma weight residual 60.00 115.12 -55.12 3 1.50e+01 4.44e-03 9.33e+00 ... (remaining 5177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 833 0.076 - 0.153: 56 0.153 - 0.229: 1 0.229 - 0.305: 1 0.305 - 0.381: 3 Chirality restraints: 894 Sorted by residual: chirality pdb=" C17 CLR A 801 " pdb=" C13 CLR A 801 " pdb=" C16 CLR A 801 " pdb=" C20 CLR A 801 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" C20 CLR A 801 " pdb=" C17 CLR A 801 " pdb=" C21 CLR A 801 " pdb=" C22 CLR A 801 " both_signs ideal model delta sigma weight residual False 2.59 2.95 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C13 CLR A 801 " pdb=" C12 CLR A 801 " pdb=" C14 CLR A 801 " pdb=" C17 CLR A 801 " both_signs ideal model delta sigma weight residual False -2.93 -3.26 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 891 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 40 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C TYR C 40 " -0.059 2.00e-02 2.50e+03 pdb=" O TYR C 40 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS C 41 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 237 " -0.011 2.00e-02 2.50e+03 2.34e-02 5.46e+00 pdb=" C LEU A 237 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A 237 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU A 238 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 40 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" N HIS C 41 " -0.037 2.00e-02 2.50e+03 pdb=" CA HIS C 41 " 0.010 2.00e-02 2.50e+03 pdb=" H HIS C 41 " 0.016 2.00e-02 2.50e+03 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 946 2.22 - 2.82: 23647 2.82 - 3.41: 29515 3.41 - 4.01: 39268 4.01 - 4.60: 59953 Nonbonded interactions: 153329 Sorted by model distance: nonbonded pdb="HE21 GLN A 547 " pdb=" O LEU A 558 " model vdw 1.631 2.450 nonbonded pdb=" HE2 LYS A 274 " pdb=" HB3 CYS A 277 " model vdw 1.653 2.440 nonbonded pdb=" OD1 ASN B 35 " pdb=" HE1 TRP B 47 " model vdw 1.689 2.450 nonbonded pdb=" O ALA A 557 " pdb=" HH TYR B 106 " model vdw 1.716 2.450 nonbonded pdb=" O HIS A 323 " pdb=" H PHE A 325 " model vdw 1.717 2.450 ... (remaining 153324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.610 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: 0.070 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.640 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.003 0.054 5463 Z= 0.148 Angle : 0.482 6.099 7449 Z= 0.259 Chirality : 0.044 0.381 894 Planarity : 0.003 0.034 909 Dihedral : 15.334 79.694 1959 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.51 % Allowed : 20.17 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.28 (0.34), residues: 682 helix: 3.52 (0.27), residues: 354 sheet: 1.57 (0.53), residues: 110 loop : 0.15 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 65 TYR 0.009 0.001 TYR C 40 PHE 0.006 0.001 PHE B 95 TRP 0.004 0.000 TRP A 199 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 ( 5460) covalent geometry : angle 0.48237 / 0.26 ( 7443) SS BOND : bond 0.00118 / 0.06 ( 3) SS BOND : angle 0.13911 / 0.07 ( 6) hydrogen bonds : bond 0.14561 / 9.28 ( 339) hydrogen bonds : angle 5.66605 / 4.31 ( 981) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 130 LEU cc_start: 0.8256 (mm) cc_final: 0.7933 (mt) REVERT: A 203 LEU cc_start: 0.8361 (tp) cc_final: 0.7872 (mp) REVERT: A 253 ASP cc_start: 0.7970 (p0) cc_final: 0.7510 (p0) REVERT: B 13 LYS cc_start: 0.6587 (ptpt) cc_final: 0.6364 (ptpp) REVERT: B 82 GLN cc_start: 0.7689 (tt0) cc_final: 0.7439 (tt0) outliers start: 3 outliers final: 1 residues processed: 123 average time/residue: 0.1309 time to fit residues: 21.2599 Evaluate side-chains 96 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.183627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148163 restraints weight = 16175.481| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.40 r_work: 0.3624 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5463 Z= 0.152 Angle : 0.521 5.691 7449 Z= 0.275 Chirality : 0.040 0.136 894 Planarity : 0.004 0.027 909 Dihedral : 4.181 44.216 797 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.54 % Allowed : 21.20 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.33), residues: 682 helix: 3.02 (0.27), residues: 357 sheet: 0.93 (0.52), residues: 115 loop : 0.06 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 65 TYR 0.017 0.002 TYR C 53 PHE 0.013 0.001 PHE A 85 TRP 0.009 0.001 TRP B 112 HIS 0.005 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 5460) covalent geometry : angle 0.51922 / 0.27 ( 7443) SS BOND : bond 0.00425 / 0.17 ( 3) SS BOND : angle 1.53282 / 0.81 ( 6) hydrogen bonds : bond 0.04153 / 2.71 ( 339) hydrogen bonds : angle 4.85547 / 3.72 ( 981) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.8029 (tp) cc_final: 0.7479 (mp) REVERT: A 257 MET cc_start: 0.6590 (mmt) cc_final: 0.6160 (mmp) REVERT: A 349 THR cc_start: 0.8689 (t) cc_final: 0.8485 (p) REVERT: B 13 LYS cc_start: 0.6698 (ptpt) cc_final: 0.6433 (ptpp) REVERT: C 83 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7073 (mt-10) outliers start: 9 outliers final: 8 residues processed: 90 average time/residue: 0.1047 time to fit residues: 13.1286 Evaluate side-chains 88 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 40 optimal weight: 0.0470 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 62 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.179087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.142806 restraints weight = 16318.244| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.47 r_work: 0.3563 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5463 Z= 0.139 Angle : 0.478 4.393 7449 Z= 0.253 Chirality : 0.039 0.140 894 Planarity : 0.004 0.032 909 Dihedral : 3.711 35.016 793 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.39 % Allowed : 20.34 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.33), residues: 682 helix: 2.91 (0.28), residues: 356 sheet: 0.70 (0.49), residues: 121 loop : 0.00 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 54 TYR 0.009 0.001 TYR C 53 PHE 0.007 0.001 PHE A 509 TRP 0.006 0.001 TRP B 50 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 5460) covalent geometry : angle 0.47730 / 0.25 ( 7443) SS BOND : bond 0.00303 / 0.13 ( 3) SS BOND : angle 0.70018 / 0.36 ( 6) hydrogen bonds : bond 0.04335 / 2.81 ( 339) hydrogen bonds : angle 4.66712 / 3.59 ( 981) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.8045 (tp) cc_final: 0.7478 (mp) REVERT: A 349 THR cc_start: 0.8747 (t) cc_final: 0.8545 (p) REVERT: A 464 PHE cc_start: 0.7841 (m-80) cc_final: 0.7583 (m-10) REVERT: B 13 LYS cc_start: 0.6790 (ptpt) cc_final: 0.6516 (ptpp) REVERT: B 87 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.6515 (mttm) REVERT: C 74 ASP cc_start: 0.6967 (t70) cc_final: 0.6652 (t0) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.1349 time to fit residues: 16.6760 Evaluate side-chains 92 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139275 restraints weight = 16281.678| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.47 r_work: 0.3536 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5463 Z= 0.150 Angle : 0.484 4.443 7449 Z= 0.257 Chirality : 0.039 0.141 894 Planarity : 0.004 0.037 909 Dihedral : 3.782 34.116 793 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.91 % Allowed : 20.34 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.33), residues: 682 helix: 2.84 (0.28), residues: 356 sheet: 0.60 (0.49), residues: 120 loop : -0.10 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 54 TYR 0.011 0.001 TYR C 53 PHE 0.010 0.001 PHE A 85 TRP 0.007 0.001 TRP B 36 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 5460) covalent geometry : angle 0.48441 / 0.26 ( 7443) SS BOND : bond 0.00291 / 0.11 ( 3) SS BOND : angle 0.49647 / 0.24 ( 6) hydrogen bonds : bond 0.04087 / 2.67 ( 339) hydrogen bonds : angle 4.63069 / 3.57 ( 981) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.8075 (tp) cc_final: 0.7457 (mp) REVERT: A 349 THR cc_start: 0.8752 (t) cc_final: 0.8534 (p) REVERT: A 464 PHE cc_start: 0.7858 (m-80) cc_final: 0.7603 (m-10) REVERT: B 13 LYS cc_start: 0.6891 (ptpt) cc_final: 0.6598 (ptpp) REVERT: B 87 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6513 (mttm) REVERT: C 74 ASP cc_start: 0.7093 (t70) cc_final: 0.6748 (t0) outliers start: 17 outliers final: 14 residues processed: 95 average time/residue: 0.1418 time to fit residues: 17.9198 Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.172473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.136055 restraints weight = 16340.728| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.46 r_work: 0.3498 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5463 Z= 0.160 Angle : 0.500 4.745 7449 Z= 0.266 Chirality : 0.040 0.163 894 Planarity : 0.004 0.040 909 Dihedral : 3.919 34.266 793 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.42 % Allowed : 19.66 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.33), residues: 682 helix: 2.66 (0.28), residues: 356 sheet: 0.33 (0.49), residues: 114 loop : -0.34 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 54 TYR 0.009 0.001 TYR C 53 PHE 0.011 0.001 PHE A 85 TRP 0.008 0.001 TRP B 36 HIS 0.004 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 5460) covalent geometry : angle 0.50028 / 0.27 ( 7443) SS BOND : bond 0.00246 / 0.10 ( 3) SS BOND : angle 0.42540 / 0.20 ( 6) hydrogen bonds : bond 0.04246 / 2.77 ( 339) hydrogen bonds : angle 4.65239 / 3.60 ( 981) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.8097 (tp) cc_final: 0.7449 (mp) REVERT: A 349 THR cc_start: 0.8743 (t) cc_final: 0.8507 (p) REVERT: A 424 ARG cc_start: 0.8015 (tpp-160) cc_final: 0.7538 (tpp-160) REVERT: A 464 PHE cc_start: 0.7890 (m-80) cc_final: 0.7635 (m-10) REVERT: B 13 LYS cc_start: 0.7001 (ptpt) cc_final: 0.6701 (ptpp) outliers start: 20 outliers final: 16 residues processed: 99 average time/residue: 0.1652 time to fit residues: 21.1615 Evaluate side-chains 95 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.172701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.136328 restraints weight = 16378.787| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.45 r_work: 0.3505 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5463 Z= 0.131 Angle : 0.472 4.496 7449 Z= 0.251 Chirality : 0.039 0.146 894 Planarity : 0.004 0.041 909 Dihedral : 3.871 33.924 793 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.25 % Allowed : 18.97 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.33), residues: 682 helix: 2.72 (0.28), residues: 356 sheet: 0.29 (0.49), residues: 114 loop : -0.36 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 54 TYR 0.010 0.001 TYR C 53 PHE 0.010 0.001 PHE A 85 TRP 0.007 0.001 TRP B 50 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 5460) covalent geometry : angle 0.47196 / 0.25 ( 7443) SS BOND : bond 0.00166 / 0.07 ( 3) SS BOND : angle 0.34943 / 0.17 ( 6) hydrogen bonds : bond 0.04024 / 2.62 ( 339) hydrogen bonds : angle 4.60075 / 3.56 ( 981) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.8111 (tp) cc_final: 0.7457 (mp) REVERT: A 349 THR cc_start: 0.8742 (t) cc_final: 0.8512 (p) REVERT: A 424 ARG cc_start: 0.7983 (tpp-160) cc_final: 0.7498 (tpp-160) REVERT: A 464 PHE cc_start: 0.7876 (m-80) cc_final: 0.7619 (m-10) REVERT: B 13 LYS cc_start: 0.7073 (ptpt) cc_final: 0.6785 (ptpp) outliers start: 19 outliers final: 18 residues processed: 89 average time/residue: 0.1451 time to fit residues: 16.8310 Evaluate side-chains 96 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.170807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.133578 restraints weight = 16233.401| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.49 r_work: 0.3444 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5463 Z= 0.130 Angle : 0.466 4.545 7449 Z= 0.248 Chirality : 0.039 0.140 894 Planarity : 0.004 0.039 909 Dihedral : 3.867 33.847 793 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.91 % Allowed : 18.80 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.33), residues: 682 helix: 2.75 (0.28), residues: 356 sheet: 0.38 (0.48), residues: 112 loop : -0.38 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 54 TYR 0.009 0.001 TYR C 53 PHE 0.009 0.001 PHE A 85 TRP 0.006 0.001 TRP B 36 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5460) covalent geometry : angle 0.46563 / 0.25 ( 7443) SS BOND : bond 0.00163 / 0.07 ( 3) SS BOND : angle 0.34967 / 0.17 ( 6) hydrogen bonds : bond 0.03944 / 2.58 ( 339) hydrogen bonds : angle 4.55365 / 3.51 ( 981) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.8034 (tp) cc_final: 0.7342 (mp) REVERT: A 349 THR cc_start: 0.8713 (t) cc_final: 0.8409 (p) REVERT: A 424 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7435 (tpp-160) REVERT: A 464 PHE cc_start: 0.7743 (m-80) cc_final: 0.7479 (m-10) REVERT: B 13 LYS cc_start: 0.7117 (ptpt) cc_final: 0.6789 (ptpp) outliers start: 17 outliers final: 17 residues processed: 93 average time/residue: 0.1494 time to fit residues: 18.4015 Evaluate side-chains 95 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.168912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131623 restraints weight = 16330.639| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.49 r_work: 0.3423 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5463 Z= 0.158 Angle : 0.486 4.668 7449 Z= 0.260 Chirality : 0.039 0.142 894 Planarity : 0.004 0.039 909 Dihedral : 3.956 33.719 793 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.08 % Allowed : 19.15 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.33), residues: 682 helix: 2.66 (0.28), residues: 356 sheet: 0.26 (0.48), residues: 112 loop : -0.49 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 54 TYR 0.009 0.001 TYR C 53 PHE 0.011 0.001 PHE A 85 TRP 0.008 0.001 TRP B 36 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 5460) covalent geometry : angle 0.48654 / 0.26 ( 7443) SS BOND : bond 0.00180 / 0.08 ( 3) SS BOND : angle 0.34924 / 0.17 ( 6) hydrogen bonds : bond 0.04147 / 2.71 ( 339) hydrogen bonds : angle 4.60674 / 3.57 ( 981) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 LEU cc_start: 0.8042 (tp) cc_final: 0.7330 (mp) REVERT: A 349 THR cc_start: 0.8689 (t) cc_final: 0.8370 (p) REVERT: A 424 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.7539 (tpp-160) REVERT: A 464 PHE cc_start: 0.7755 (m-80) cc_final: 0.7499 (m-10) REVERT: B 13 LYS cc_start: 0.7203 (ptpt) cc_final: 0.6817 (ptpp) outliers start: 18 outliers final: 17 residues processed: 92 average time/residue: 0.1353 time to fit residues: 16.3789 Evaluate side-chains 97 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 ASN A 466 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130326 restraints weight = 16202.233| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.48 r_work: 0.3406 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5463 Z= 0.160 Angle : 0.486 4.780 7449 Z= 0.260 Chirality : 0.039 0.161 894 Planarity : 0.004 0.039 909 Dihedral : 4.005 33.408 793 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.08 % Allowed : 20.00 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.33), residues: 682 helix: 2.62 (0.28), residues: 356 sheet: 0.37 (0.49), residues: 107 loop : -0.54 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 54 TYR 0.015 0.002 TYR B 101 PHE 0.011 0.001 PHE A 85 TRP 0.008 0.001 TRP B 36 HIS 0.003 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 5460) covalent geometry : angle 0.48589 / 0.26 ( 7443) SS BOND : bond 0.00184 / 0.08 ( 3) SS BOND : angle 0.35992 / 0.17 ( 6) hydrogen bonds : bond 0.04180 / 2.72 ( 339) hydrogen bonds : angle 4.63634 / 3.59 ( 981) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6180 (ppp) REVERT: A 130 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8437 (mt) REVERT: A 203 LEU cc_start: 0.8046 (tp) cc_final: 0.7324 (mp) REVERT: A 349 THR cc_start: 0.8642 (t) cc_final: 0.8322 (p) REVERT: A 424 ARG cc_start: 0.8115 (tpp-160) cc_final: 0.7505 (ttm170) REVERT: B 13 LYS cc_start: 0.7270 (ptpt) cc_final: 0.6883 (ptpp) outliers start: 18 outliers final: 15 residues processed: 93 average time/residue: 0.1464 time to fit residues: 17.6343 Evaluate side-chains 95 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.0000 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 63 optimal weight: 0.0970 chunk 53 optimal weight: 0.6980 overall best weight: 0.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.170228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133100 restraints weight = 16303.610| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.49 r_work: 0.3440 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5463 Z= 0.106 Angle : 0.461 4.476 7449 Z= 0.244 Chirality : 0.038 0.156 894 Planarity : 0.004 0.039 909 Dihedral : 3.897 33.086 793 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.39 % Allowed : 20.51 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.33), residues: 682 helix: 2.75 (0.28), residues: 357 sheet: 0.44 (0.49), residues: 107 loop : -0.44 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 480 TYR 0.011 0.001 TYR C 53 PHE 0.007 0.001 PHE A 85 TRP 0.006 0.001 TRP B 50 HIS 0.007 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 5460) covalent geometry : angle 0.46092 / 0.24 ( 7443) SS BOND : bond 0.00114 / 0.05 ( 3) SS BOND : angle 0.45167 / 0.22 ( 6) hydrogen bonds : bond 0.03797 / 2.48 ( 339) hydrogen bonds : angle 4.53358 / 3.51 ( 981) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1364 Ramachandran restraints generated. 682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.6169 (ppp) REVERT: A 203 LEU cc_start: 0.8039 (tp) cc_final: 0.7350 (mp) REVERT: A 349 THR cc_start: 0.8648 (t) cc_final: 0.8341 (p) REVERT: A 374 VAL cc_start: 0.6976 (t) cc_final: 0.6764 (p) REVERT: A 424 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7328 (ttm170) REVERT: B 13 LYS cc_start: 0.7249 (ptpt) cc_final: 0.6870 (ptpp) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.1467 time to fit residues: 15.8961 Evaluate side-chains 89 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 570 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain C residue 41 HIS Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 40 optimal weight: 0.0000 chunk 62 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 overall best weight: 0.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.171924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134938 restraints weight = 16236.262| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.48 r_work: 0.3461 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5463 Z= 0.098 Angle : 0.445 4.378 7449 Z= 0.236 Chirality : 0.038 0.141 894 Planarity : 0.004 0.039 909 Dihedral : 3.879 32.397 793 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.88 % Allowed : 21.03 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.33), residues: 682 helix: 2.88 (0.28), residues: 357 sheet: 0.46 (0.49), residues: 107 loop : -0.38 (0.42), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 480 TYR 0.011 0.001 TYR C 53 PHE 0.006 0.001 PHE A 85 TRP 0.005 0.001 TRP B 112 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 5460) covalent geometry : angle 0.44496 / 0.24 ( 7443) SS BOND : bond 0.00110 / 0.05 ( 3) SS BOND : angle 0.38877 / 0.20 ( 6) hydrogen bonds : bond 0.03615 / 2.37 ( 339) hydrogen bonds : angle 4.43092 / 3.41 ( 981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.80 seconds wall clock time: 47 minutes 39.15 seconds (2859.15 seconds total)