Starting phenix.real_space_refine on Wed Mar 5 21:44:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygu_39264/03_2025/8ygu_39264_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygu_39264/03_2025/8ygu_39264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygu_39264/03_2025/8ygu_39264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygu_39264/03_2025/8ygu_39264.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygu_39264/03_2025/8ygu_39264_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygu_39264/03_2025/8ygu_39264_neut.cif" } resolution = 3.13 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= 0.000 sd= 0.016 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 11 5.16 5 C 2353 2.51 5 N 617 2.21 5 O 712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3693 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 117 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "B" Number of atoms: 1726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1726 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 207} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 152 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain breaks: 2 Chain: "H" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 880 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 101} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N SER H 17 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER H 17 " occ=0.50 residue: pdb=" N SER H 61 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER H 61 " occ=0.50 residue: pdb=" N MET L 11 " occ=0.50 ... (6 atoms not shown) pdb=" CE MET L 11 " occ=0.50 residue: pdb=" N ARG L 18 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG L 18 " occ=0.50 residue: pdb=" N GLN L 27 " occ=0.83 ... (7 atoms not shown) pdb=" NE2 GLN L 27 " occ=0.83 residue: pdb=" N SER L 43 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER L 43 " occ=0.50 residue: pdb=" N SER L 50 " occ=0.90 ... (4 atoms not shown) pdb=" OG SER L 50 " occ=0.90 residue: pdb=" N SER L 67 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER L 67 " occ=0.50 residue: pdb=" N GLU L 105 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU L 105 " occ=0.50 Time building chain proxies: 3.21, per 1000 atoms: 0.87 Number of scatterers: 3693 At special positions: 0 Unit cell: (68.076, 90.036, 96.624, 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 11 16.00 O 712 8.00 N 617 7.00 C 2353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 751.0 milliseconds 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 866 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 10 sheets defined 1.1% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'B' and resid 361 through 365 removed outlier: 4.155A pdb=" N VAL B 365 " --> pdb=" O PHE B 362 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 420 through 423 removed outlier: 4.481A pdb=" N VAL B 409 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARG B 427 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 409 " --> pdb=" O ARG B 425 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG B 425 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LEU B 411 " --> pdb=" O SER B 423 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER B 423 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR B 413 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 421 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 12.048A pdb=" N ASN B 422 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N ASP B 357 " --> pdb=" O ASN B 422 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU B 424 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 351 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP B 356 " --> pdb=" O HIS B 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 423 removed outlier: 4.481A pdb=" N VAL B 409 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL B 378 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 275 removed outlier: 3.596A pdb=" N ILE B 271 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 473 " --> pdb=" O VAL B 368 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL B 368 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 279 through 283 removed outlier: 3.616A pdb=" N GLU B 293 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU B 293 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE B 342 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER B 295 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N VAL B 344 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER B 340 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N PHE B 328 " --> pdb=" O SER B 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 279 through 283 removed outlier: 3.616A pdb=" N GLU B 293 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLU B 293 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE B 342 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER B 295 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N VAL B 344 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 384 through 386 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.788A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N MET H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL H 34 " --> pdb=" O MET H 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 6 removed outlier: 6.152A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.403A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.81 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1163 1.34 - 1.46: 975 1.46 - 1.58: 1627 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3781 Sorted by residual: bond pdb=" C GLN L 42 " pdb=" N SER L 43 " ideal model delta sigma weight residual 1.331 1.359 -0.028 1.59e-02 3.96e+03 3.11e+00 bond pdb=" CG ARG B 269 " pdb=" CD ARG B 269 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CA GLU B 347 " pdb=" C GLU B 347 " ideal model delta sigma weight residual 1.523 1.540 -0.017 1.34e-02 5.57e+03 1.67e+00 bond pdb=" CB PRO B 435 " pdb=" CG PRO B 435 " ideal model delta sigma weight residual 1.506 1.456 0.050 3.90e-02 6.57e+02 1.66e+00 bond pdb=" CG LEU B 375 " pdb=" CD1 LEU B 375 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 3776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 4983 2.38 - 4.77: 127 4.77 - 7.15: 17 7.15 - 9.54: 1 9.54 - 11.92: 1 Bond angle restraints: 5129 Sorted by residual: angle pdb=" C GLN L 42 " pdb=" N SER L 43 " pdb=" CA SER L 43 " ideal model delta sigma weight residual 122.38 134.30 -11.92 2.90e+00 1.19e-01 1.69e+01 angle pdb=" N GLY H 54 " pdb=" CA GLY H 54 " pdb=" C GLY H 54 " ideal model delta sigma weight residual 112.82 107.98 4.84 1.38e+00 5.25e-01 1.23e+01 angle pdb=" N LYS B 346 " pdb=" CA LYS B 346 " pdb=" C LYS B 346 " ideal model delta sigma weight residual 107.61 113.44 -5.83 1.74e+00 3.30e-01 1.12e+01 angle pdb=" C LYS B 346 " pdb=" N GLU B 347 " pdb=" CA GLU B 347 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" N TYR L 55 " pdb=" CA TYR L 55 " pdb=" C TYR L 55 " ideal model delta sigma weight residual 110.46 105.79 4.67 1.48e+00 4.57e-01 9.95e+00 ... (remaining 5124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.97: 2086 13.97 - 27.93: 96 27.93 - 41.90: 16 41.90 - 55.87: 3 55.87 - 69.83: 1 Dihedral angle restraints: 2202 sinusoidal: 845 harmonic: 1357 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 145.02 -52.02 1 1.00e+01 1.00e-02 3.69e+01 dihedral pdb=" CA ASN B 456 " pdb=" C ASN B 456 " pdb=" N ASN B 457 " pdb=" CA ASN B 457 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LYS B 346 " pdb=" C LYS B 346 " pdb=" N GLU B 347 " pdb=" CA GLU B 347 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 2199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 343 0.041 - 0.082: 147 0.082 - 0.123: 45 0.123 - 0.164: 25 0.164 - 0.205: 5 Chirality restraints: 565 Sorted by residual: chirality pdb=" CB VAL B 320 " pdb=" CA VAL B 320 " pdb=" CG1 VAL B 320 " pdb=" CG2 VAL B 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE B 294 " pdb=" N ILE B 294 " pdb=" C ILE B 294 " pdb=" CB ILE B 294 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CB ILE B 271 " pdb=" CA ILE B 271 " pdb=" CG1 ILE B 271 " pdb=" CG2 ILE B 271 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 562 not shown) Planarity restraints: 653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 333 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO C 334 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 334 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 334 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 43 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO L 44 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO L 44 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 44 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 39 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO L 40 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO L 40 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 40 " -0.026 5.00e-02 4.00e+02 ... (remaining 650 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 195 2.72 - 3.27: 2952 3.27 - 3.81: 5378 3.81 - 4.36: 6219 4.36 - 4.90: 11619 Nonbonded interactions: 26363 Sorted by model distance: nonbonded pdb=" NH1 ARG L 54 " pdb=" OD1 ASP L 60 " model vdw 2.179 3.120 nonbonded pdb=" OD2 ASP B 270 " pdb=" OG1 THR L 94 " model vdw 2.182 3.040 nonbonded pdb=" O ASN H 53 " pdb=" NZ LYS H 71 " model vdw 2.324 3.120 nonbonded pdb=" NZ LYS H 5 " pdb=" OE1 GLN H 109 " model vdw 2.378 3.120 nonbonded pdb=" O SER B 476 " pdb=" OG SER B 476 " model vdw 2.458 3.040 ... (remaining 26358 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=0.50 max=1.00 mean=0.99 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: 1.820 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 0.006 0.055 3781 Z= 0.372 Angle : 0.923 11.923 5129 Z= 0.513 Chirality : 0.057 0.205 565 Planarity : 0.007 0.054 653 Dihedral : 8.810 69.834 1330 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -3.27 (0.34), residues: 460 helix: -5.53 (0.22), residues: 9 sheet: -0.96 (0.35), residues: 221 loop : -3.38 (0.28), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP H 52 HIS 0.007 0.002 HIS L 91 PHE 0.031 0.003 PHE B 362 TYR 0.020 0.002 TYR H 93 ARG 0.005 0.001 ARG B 274 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: B 280 THR cc_start: 0.8341 (m) cc_final: 0.7951 (p) REVERT: H 50 MET cc_start: 0.8136 (ttt) cc_final: 0.7816 (ttp) REVERT: H 112 THR cc_start: 0.8145 (t) cc_final: 0.7721 (m) REVERT: L 45 LYS cc_start: 0.7018 (mmtp) cc_final: 0.6760 (mmtp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1733 time to fit residues: 19.1698 Evaluate side-chains 67 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 35 optimal weight: 0.0010 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN B 266 GLN B 302 GLN B 324 ASN B 374 ASN B 414 GLN C 329 ASN H 73 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.094094 restraints weight = 5738.484| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.84 r_work: 0.3008 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3781 Z= 0.264 Angle : 0.624 6.070 5129 Z= 0.335 Chirality : 0.047 0.187 565 Planarity : 0.005 0.039 653 Dihedral : 5.777 30.886 511 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.96 % Allowed : 7.09 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.10 (0.37), residues: 460 helix: None (None), residues: 0 sheet: -0.10 (0.35), residues: 234 loop : -2.96 (0.33), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 107 HIS 0.005 0.002 HIS L 8 PHE 0.019 0.002 PHE C 337 TYR 0.015 0.002 TYR B 305 ARG 0.004 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8119 (t0) cc_final: 0.7807 (t0) REVERT: H 4 LEU cc_start: 0.7928 (mp) cc_final: 0.7671 (mt) REVERT: H 20 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7245 (mt) REVERT: H 50 MET cc_start: 0.8415 (ttt) cc_final: 0.8195 (ttp) REVERT: H 105 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: H 112 THR cc_start: 0.8411 (t) cc_final: 0.8019 (m) outliers start: 8 outliers final: 4 residues processed: 73 average time/residue: 0.1536 time to fit residues: 14.1325 Evaluate side-chains 67 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 105 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN B 414 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.109404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090135 restraints weight = 5714.075| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.93 r_work: 0.2938 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3781 Z= 0.306 Angle : 0.632 5.073 5129 Z= 0.340 Chirality : 0.047 0.146 565 Planarity : 0.005 0.037 653 Dihedral : 5.703 31.743 511 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.42 % Allowed : 8.07 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.68 (0.38), residues: 460 helix: None (None), residues: 0 sheet: 0.19 (0.33), residues: 239 loop : -2.74 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 356 HIS 0.005 0.002 HIS L 91 PHE 0.020 0.002 PHE C 337 TYR 0.016 0.002 TYR L 86 ARG 0.003 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8114 (t0) cc_final: 0.7646 (t0) REVERT: B 388 SER cc_start: 0.8788 (t) cc_final: 0.8516 (p) REVERT: B 414 GLN cc_start: 0.8413 (tt0) cc_final: 0.8201 (tt0) REVERT: H 4 LEU cc_start: 0.7955 (mp) cc_final: 0.7667 (mt) REVERT: H 50 MET cc_start: 0.8430 (ttt) cc_final: 0.8155 (ttp) REVERT: H 105 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: H 112 THR cc_start: 0.8313 (t) cc_final: 0.7943 (m) REVERT: L 45 LYS cc_start: 0.7459 (mmtp) cc_final: 0.7148 (mmtp) outliers start: 14 outliers final: 11 residues processed: 73 average time/residue: 0.1588 time to fit residues: 14.5173 Evaluate side-chains 78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 105 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 36 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.091871 restraints weight = 5721.697| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.92 r_work: 0.2964 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3781 Z= 0.213 Angle : 0.563 4.852 5129 Z= 0.302 Chirality : 0.045 0.144 565 Planarity : 0.004 0.033 653 Dihedral : 5.312 29.378 511 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.91 % Allowed : 8.07 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.44 (0.37), residues: 460 helix: None (None), residues: 0 sheet: 0.25 (0.33), residues: 231 loop : -2.36 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 356 HIS 0.005 0.002 HIS L 91 PHE 0.013 0.002 PHE B 437 TYR 0.013 0.001 TYR B 305 ARG 0.003 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8014 (t0) cc_final: 0.7653 (t0) REVERT: B 388 SER cc_start: 0.8796 (t) cc_final: 0.8524 (p) REVERT: H 50 MET cc_start: 0.8400 (ttt) cc_final: 0.8137 (ttp) REVERT: H 112 THR cc_start: 0.8283 (t) cc_final: 0.7914 (m) outliers start: 16 outliers final: 12 residues processed: 71 average time/residue: 0.1615 time to fit residues: 14.2764 Evaluate side-chains 74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 36 optimal weight: 0.0050 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN B 324 ASN L 90 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.090555 restraints weight = 5872.931| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.95 r_work: 0.2943 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3781 Z= 0.311 Angle : 0.630 7.233 5129 Z= 0.334 Chirality : 0.047 0.149 565 Planarity : 0.004 0.035 653 Dihedral : 5.500 31.207 511 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.42 % Allowed : 9.78 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.21 (0.38), residues: 460 helix: None (None), residues: 0 sheet: 0.45 (0.32), residues: 245 loop : -2.43 (0.38), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 356 HIS 0.004 0.002 HIS L 8 PHE 0.016 0.002 PHE C 337 TYR 0.016 0.002 TYR L 86 ARG 0.003 0.001 ARG B 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8029 (t0) cc_final: 0.7663 (t0) REVERT: B 388 SER cc_start: 0.8783 (t) cc_final: 0.8529 (p) REVERT: B 427 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8139 (ttp-170) REVERT: H 50 MET cc_start: 0.8457 (ttt) cc_final: 0.8199 (ttp) REVERT: H 112 THR cc_start: 0.8285 (t) cc_final: 0.7956 (m) REVERT: L 45 LYS cc_start: 0.7473 (mmtp) cc_final: 0.7194 (mmtp) outliers start: 14 outliers final: 12 residues processed: 71 average time/residue: 0.1541 time to fit residues: 13.6947 Evaluate side-chains 74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN L 90 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.090662 restraints weight = 5840.061| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.93 r_work: 0.2947 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3781 Z= 0.291 Angle : 0.624 7.447 5129 Z= 0.330 Chirality : 0.046 0.148 565 Planarity : 0.004 0.036 653 Dihedral : 5.495 31.808 511 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.67 % Allowed : 9.29 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.10 (0.38), residues: 460 helix: None (None), residues: 0 sheet: 0.59 (0.33), residues: 239 loop : -2.37 (0.37), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 356 HIS 0.005 0.002 HIS L 91 PHE 0.015 0.002 PHE B 437 TYR 0.014 0.002 TYR B 305 ARG 0.003 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8015 (t0) cc_final: 0.7760 (t0) REVERT: B 388 SER cc_start: 0.8796 (t) cc_final: 0.8539 (p) REVERT: B 427 ARG cc_start: 0.8387 (ttp80) cc_final: 0.8147 (ttp-170) REVERT: H 50 MET cc_start: 0.8460 (ttt) cc_final: 0.8199 (ttp) REVERT: H 112 THR cc_start: 0.8283 (t) cc_final: 0.7957 (m) outliers start: 15 outliers final: 14 residues processed: 70 average time/residue: 0.1549 time to fit residues: 13.5792 Evaluate side-chains 76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 16 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN B 302 GLN L 90 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.091605 restraints weight = 5734.652| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.98 r_work: 0.2960 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3781 Z= 0.189 Angle : 0.565 7.506 5129 Z= 0.298 Chirality : 0.044 0.146 565 Planarity : 0.004 0.033 653 Dihedral : 5.161 29.620 511 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.42 % Allowed : 10.27 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.06 (0.38), residues: 460 helix: None (None), residues: 0 sheet: 0.67 (0.34), residues: 225 loop : -2.23 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 356 HIS 0.004 0.001 HIS H 35 PHE 0.015 0.002 PHE B 437 TYR 0.012 0.001 TYR B 305 ARG 0.003 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 420 SER cc_start: 0.8685 (m) cc_final: 0.8480 (p) REVERT: B 358 ASP cc_start: 0.8036 (t0) cc_final: 0.7794 (t0) REVERT: B 388 SER cc_start: 0.8785 (t) cc_final: 0.8529 (p) REVERT: B 427 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8167 (ttp-170) REVERT: H 50 MET cc_start: 0.8440 (ttt) cc_final: 0.8192 (ttp) REVERT: H 112 THR cc_start: 0.8281 (t) cc_final: 0.7955 (m) outliers start: 14 outliers final: 13 residues processed: 69 average time/residue: 0.1552 time to fit residues: 13.3918 Evaluate side-chains 74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN L 90 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.090136 restraints weight = 5764.824| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.91 r_work: 0.2938 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3781 Z= 0.353 Angle : 0.664 7.625 5129 Z= 0.348 Chirality : 0.048 0.160 565 Planarity : 0.004 0.040 653 Dihedral : 5.506 32.485 511 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.91 % Allowed : 9.78 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.08 (0.38), residues: 460 helix: None (None), residues: 0 sheet: 0.71 (0.33), residues: 229 loop : -2.36 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 356 HIS 0.005 0.002 HIS L 8 PHE 0.015 0.002 PHE L 73 TYR 0.016 0.002 TYR B 462 ARG 0.004 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: B 312 VAL cc_start: 0.8283 (m) cc_final: 0.8061 (t) REVERT: B 388 SER cc_start: 0.8788 (t) cc_final: 0.8531 (p) REVERT: B 427 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8148 (ttp-170) REVERT: H 112 THR cc_start: 0.8257 (t) cc_final: 0.7950 (m) REVERT: L 90 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7842 (pp30) outliers start: 16 outliers final: 14 residues processed: 72 average time/residue: 0.1544 time to fit residues: 14.0170 Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 460 GLU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 14 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 23 optimal weight: 0.0010 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN L 90 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.092151 restraints weight = 5664.298| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.91 r_work: 0.2973 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3781 Z= 0.183 Angle : 0.582 7.776 5129 Z= 0.305 Chirality : 0.044 0.149 565 Planarity : 0.004 0.033 653 Dihedral : 5.136 30.032 511 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.18 % Allowed : 10.76 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.04 (0.38), residues: 460 helix: None (None), residues: 0 sheet: 0.72 (0.34), residues: 220 loop : -2.20 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 356 HIS 0.005 0.002 HIS L 91 PHE 0.015 0.002 PHE B 437 TYR 0.012 0.001 TYR B 305 ARG 0.003 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: B 388 SER cc_start: 0.8761 (t) cc_final: 0.8517 (p) REVERT: B 427 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8154 (ttp-170) REVERT: H 112 THR cc_start: 0.8305 (t) cc_final: 0.7959 (m) REVERT: L 90 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7766 (pp30) outliers start: 13 outliers final: 12 residues processed: 68 average time/residue: 0.1640 time to fit residues: 14.1115 Evaluate side-chains 74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 6 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 0.0070 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN L 90 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.111086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.091826 restraints weight = 5691.146| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.90 r_work: 0.2965 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3781 Z= 0.221 Angle : 0.602 7.832 5129 Z= 0.315 Chirality : 0.045 0.148 565 Planarity : 0.004 0.033 653 Dihedral : 5.136 29.709 511 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.18 % Allowed : 11.00 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.02 (0.38), residues: 460 helix: None (None), residues: 0 sheet: 0.75 (0.34), residues: 220 loop : -2.19 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 356 HIS 0.004 0.002 HIS L 91 PHE 0.015 0.002 PHE B 437 TYR 0.013 0.002 TYR B 305 ARG 0.003 0.000 ARG L 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 388 SER cc_start: 0.8757 (t) cc_final: 0.8514 (p) REVERT: B 427 ARG cc_start: 0.8388 (ttp80) cc_final: 0.8163 (ttp-170) REVERT: H 112 THR cc_start: 0.8263 (t) cc_final: 0.7959 (m) REVERT: L 90 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7746 (pp30) outliers start: 13 outliers final: 12 residues processed: 68 average time/residue: 0.1590 time to fit residues: 13.5067 Evaluate side-chains 73 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain L residue 90 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 39 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 0.3980 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN L 90 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.091820 restraints weight = 5677.538| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.90 r_work: 0.2966 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3781 Z= 0.220 Angle : 0.600 7.934 5129 Z= 0.314 Chirality : 0.045 0.148 565 Planarity : 0.004 0.033 653 Dihedral : 5.136 29.433 511 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.42 % Allowed : 11.00 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.96 (0.38), residues: 460 helix: None (None), residues: 0 sheet: 0.83 (0.33), residues: 229 loop : -2.32 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 356 HIS 0.004 0.002 HIS L 91 PHE 0.015 0.002 PHE B 437 TYR 0.013 0.002 TYR B 305 ARG 0.003 0.000 ARG L 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2598.54 seconds wall clock time: 45 minutes 13.68 seconds (2713.68 seconds total)