Starting phenix.real_space_refine on Fri May 9 20:37:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygu_39264/05_2025/8ygu_39264_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygu_39264/05_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_39264/05_2025/8ygu_39264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygu_39264/05_2025/8ygu_39264.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygu_39264/05_2025/8ygu_39264_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygu_39264/05_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-5687/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: 3.06, per 1000 atoms: 0.83 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: 0.80 Conformation dependent library (CDL) restraints added in 412.9 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: 0.95 Time building geometry restraints manager: 0.96 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.420 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- 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 3783 Z= 0.258 Angle : 0.923 11.923 5133 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 Details of bonding type rmsd hydrogen bonds : bond 0.29186 ( 122) hydrogen bonds : angle 9.02655 ( 354) SS BOND : bond 0.01342 ( 2) SS BOND : angle 1.48630 ( 4) covalent geometry : bond 0.00574 ( 3781) covalent geometry : angle 0.92291 ( 5129) *********************** 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 : 0.396 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: 0.1732 time to fit residues: 19.0600 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 : 0.427 ------------------------------------------------------------------------------- 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: 0.7980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.112070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.094138 restraints weight = 5743.343| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.84 r_work: 0.3010 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 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 = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3783 Z= 0.161 Angle : 0.620 6.006 5133 Z= 0.333 Chirality : 0.046 0.184 565 Planarity : 0.005 0.038 653 Dihedral : 5.754 30.696 511 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % 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: -2.23 (0.37), residues: 460 helix: -5.55 (0.21), residues: 9 sheet: -0.20 (0.36), residues: 226 loop : -2.77 (0.34), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 107 HIS 0.005 0.002 HIS B 315 PHE 0.018 0.002 PHE C 337 TYR 0.014 0.002 TYR B 305 ARG 0.004 0.001 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 122) hydrogen bonds : angle 5.57848 ( 354) SS BOND : bond 0.00939 ( 2) SS BOND : angle 1.33772 ( 4) covalent geometry : bond 0.00389 ( 3781) covalent geometry : angle 0.61942 ( 5129) *********************** 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 79 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8115 (t0) cc_final: 0.7799 (t0) REVERT: H 4 LEU cc_start: 0.7923 (mp) cc_final: 0.7667 (mt) REVERT: H 50 MET cc_start: 0.8414 (ttt) cc_final: 0.8193 (ttp) REVERT: H 105 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: H 112 THR cc_start: 0.8410 (t) cc_final: 0.8015 (m) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 0.1411 time to fit residues: 13.1070 Evaluate side-chains 68 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 B 414 GLN L 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091172 restraints weight = 5735.784| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.88 r_work: 0.2955 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3783 Z= 0.161 Angle : 0.598 4.945 5133 Z= 0.321 Chirality : 0.046 0.146 565 Planarity : 0.004 0.035 653 Dihedral : 5.513 29.691 511 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.42 % Allowed : 8.31 % Favored : 88.26 % 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: -1.71 (0.37), residues: 460 helix: None (None), residues: 0 sheet: 0.11 (0.34), residues: 230 loop : -2.57 (0.35), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 356 HIS 0.004 0.002 HIS L 91 PHE 0.017 0.002 PHE C 337 TYR 0.014 0.002 TYR B 305 ARG 0.003 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 122) hydrogen bonds : angle 5.18072 ( 354) SS BOND : bond 0.00860 ( 2) SS BOND : angle 1.22665 ( 4) covalent geometry : bond 0.00388 ( 3781) covalent geometry : angle 0.59701 ( 5129) *********************** 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 : 0.408 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8087 (t0) cc_final: 0.7608 (t0) REVERT: B 377 SER cc_start: 0.8556 (p) cc_final: 0.8339 (m) REVERT: B 388 SER cc_start: 0.8786 (t) cc_final: 0.8500 (p) REVERT: B 414 GLN cc_start: 0.8387 (tt0) cc_final: 0.8164 (tt0) REVERT: H 4 LEU cc_start: 0.7910 (mp) cc_final: 0.7639 (mt) REVERT: H 50 MET cc_start: 0.8405 (ttt) cc_final: 0.8122 (ttp) REVERT: H 80 LEU cc_start: 0.7172 (tt) cc_final: 0.6954 (tp) REVERT: H 105 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7880 (m-30) REVERT: H 112 THR cc_start: 0.8319 (t) cc_final: 0.7918 (m) REVERT: L 45 LYS cc_start: 0.7425 (mmtp) cc_final: 0.7112 (mmtp) REVERT: L 90 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.7496 (pp30) outliers start: 14 outliers final: 11 residues processed: 73 average time/residue: 0.1477 time to fit residues: 13.5735 Evaluate side-chains 78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 67 LEU Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain L residue 90 GLN 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: 1.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 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 = 0.3333 r_free = 0.3333 target = 0.109158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.089782 restraints weight = 5724.070| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.97 r_work: 0.2925 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3783 Z= 0.216 Angle : 0.655 5.455 5133 Z= 0.351 Chirality : 0.048 0.150 565 Planarity : 0.005 0.041 653 Dihedral : 5.729 32.592 511 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.91 % Allowed : 8.31 % Favored : 87.78 % 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: -1.51 (0.37), residues: 460 helix: None (None), residues: 0 sheet: 0.31 (0.33), residues: 235 loop : -2.58 (0.35), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 356 HIS 0.005 0.002 HIS L 8 PHE 0.021 0.002 PHE C 337 TYR 0.018 0.002 TYR L 86 ARG 0.003 0.001 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.04894 ( 122) hydrogen bonds : angle 5.13191 ( 354) SS BOND : bond 0.00878 ( 2) SS BOND : angle 1.30458 ( 4) covalent geometry : bond 0.00534 ( 3781) covalent geometry : angle 0.65438 ( 5129) *********************** 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 82 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8098 (t0) cc_final: 0.7679 (t0) REVERT: B 388 SER cc_start: 0.8797 (t) cc_final: 0.8551 (p) REVERT: H 50 MET cc_start: 0.8484 (ttt) cc_final: 0.8212 (ttp) REVERT: H 80 LEU cc_start: 0.7299 (tt) cc_final: 0.7056 (tp) REVERT: H 112 THR cc_start: 0.8308 (t) cc_final: 0.7952 (m) REVERT: L 45 LYS cc_start: 0.7497 (mmtp) cc_final: 0.7212 (mmtp) outliers start: 16 outliers final: 12 residues processed: 74 average time/residue: 0.1496 time to fit residues: 13.8911 Evaluate side-chains 76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 B residue 456 ASN 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 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: 2.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 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 = 0.3341 r_free = 0.3341 target = 0.109472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.090206 restraints weight = 5826.314| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.92 r_work: 0.2939 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 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 = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3783 Z= 0.209 Angle : 0.654 7.205 5133 Z= 0.347 Chirality : 0.048 0.149 565 Planarity : 0.004 0.038 653 Dihedral : 5.700 33.559 511 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.72 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: -1.30 (0.37), residues: 460 helix: None (None), residues: 0 sheet: 0.48 (0.32), residues: 239 loop : -2.53 (0.36), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 356 HIS 0.005 0.002 HIS L 8 PHE 0.017 0.002 PHE C 337 TYR 0.016 0.002 TYR B 462 ARG 0.003 0.001 ARG B 427 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 122) hydrogen bonds : angle 5.07328 ( 354) SS BOND : bond 0.00928 ( 2) SS BOND : angle 1.35473 ( 4) covalent geometry : bond 0.00518 ( 3781) covalent geometry : angle 0.65349 ( 5129) *********************** 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 79 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8056 (t0) cc_final: 0.7710 (t0) REVERT: B 388 SER cc_start: 0.8784 (t) cc_final: 0.8533 (p) REVERT: B 427 ARG cc_start: 0.8401 (ttp80) cc_final: 0.8149 (ttp-170) REVERT: H 50 MET cc_start: 0.8477 (ttt) cc_final: 0.8210 (ttp) REVERT: H 112 THR cc_start: 0.8269 (t) cc_final: 0.7920 (m) REVERT: L 45 LYS cc_start: 0.7471 (mmtp) cc_final: 0.7190 (mmtp) outliers start: 15 outliers final: 13 residues processed: 72 average time/residue: 0.1579 time to fit residues: 14.3072 Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 456 ASN 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 67 LEU Chi-restraints excluded: chain H residue 68 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 43 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 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 = 0.3351 r_free = 0.3351 target = 0.110120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.090816 restraints weight = 5804.686| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.93 r_work: 0.2948 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- 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 = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3783 Z= 0.171 Angle : 0.619 7.493 5133 Z= 0.327 Chirality : 0.046 0.147 565 Planarity : 0.004 0.036 653 Dihedral : 5.543 33.019 511 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.42 % Allowed : 9.54 % 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: -1.20 (0.37), residues: 460 helix: None (None), residues: 0 sheet: 0.61 (0.33), residues: 233 loop : -2.47 (0.36), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 356 HIS 0.006 0.002 HIS L 91 PHE 0.016 0.002 PHE B 437 TYR 0.014 0.002 TYR B 305 ARG 0.003 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.04345 ( 122) hydrogen bonds : angle 4.95702 ( 354) SS BOND : bond 0.00847 ( 2) SS BOND : angle 1.20465 ( 4) covalent geometry : bond 0.00415 ( 3781) covalent geometry : angle 0.61841 ( 5129) *********************** 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: 14 poor density : 63 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8002 (t0) cc_final: 0.7720 (t0) REVERT: B 388 SER cc_start: 0.8780 (t) cc_final: 0.8527 (p) REVERT: B 427 ARG cc_start: 0.8383 (ttp80) cc_final: 0.8131 (ttp-170) REVERT: H 50 MET cc_start: 0.8466 (ttt) cc_final: 0.8204 (ttp) REVERT: H 80 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.7003 (tp) REVERT: H 112 THR cc_start: 0.8260 (t) cc_final: 0.7908 (m) REVERT: L 45 LYS cc_start: 0.7446 (mmtp) cc_final: 0.7187 (mmtp) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.1493 time to fit residues: 12.9294 Evaluate side-chains 75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 B residue 456 ASN 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 67 LEU Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 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 = 0.3359 r_free = 0.3359 target = 0.110701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.091479 restraints weight = 5744.355| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.91 r_work: 0.2959 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 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 = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3783 Z= 0.148 Angle : 0.596 7.633 5133 Z= 0.313 Chirality : 0.045 0.146 565 Planarity : 0.004 0.035 653 Dihedral : 5.387 31.874 511 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % 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: -1.13 (0.37), residues: 460 helix: None (None), residues: 0 sheet: 0.68 (0.32), residues: 233 loop : -2.45 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 356 HIS 0.005 0.002 HIS L 91 PHE 0.016 0.002 PHE B 437 TYR 0.013 0.001 TYR B 305 ARG 0.003 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 122) hydrogen bonds : angle 4.86078 ( 354) SS BOND : bond 0.00797 ( 2) SS BOND : angle 1.07992 ( 4) covalent geometry : bond 0.00353 ( 3781) covalent geometry : angle 0.59508 ( 5129) *********************** 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 78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: B 358 ASP cc_start: 0.8054 (t0) cc_final: 0.7789 (t0) REVERT: B 388 SER cc_start: 0.8770 (t) cc_final: 0.8513 (p) REVERT: B 427 ARG cc_start: 0.8406 (ttp80) cc_final: 0.8157 (ttp-170) REVERT: H 50 MET cc_start: 0.8460 (ttt) cc_final: 0.8198 (ttp) REVERT: H 80 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.7005 (tp) REVERT: H 112 THR cc_start: 0.8300 (t) cc_final: 0.7934 (m) REVERT: L 45 LYS cc_start: 0.7447 (mmtp) cc_final: 0.7195 (mmtp) outliers start: 14 outliers final: 12 residues processed: 70 average time/residue: 0.1465 time to fit residues: 12.8909 Evaluate side-chains 77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 67 LEU Chi-restraints excluded: chain H residue 80 LEU 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: 2.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 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 B 324 ASN ** 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 = 0.3340 r_free = 0.3340 target = 0.109304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.089786 restraints weight = 5748.612| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.96 r_work: 0.2929 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3783 Z= 0.219 Angle : 0.661 7.714 5133 Z= 0.349 Chirality : 0.048 0.169 565 Planarity : 0.004 0.040 653 Dihedral : 5.567 33.786 511 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % 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: -1.16 (0.37), residues: 460 helix: None (None), residues: 0 sheet: 0.72 (0.32), residues: 229 loop : -2.50 (0.36), residues: 231 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 0.016 0.002 PHE B 437 TYR 0.016 0.002 TYR B 462 ARG 0.003 0.001 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 122) hydrogen bonds : angle 5.00045 ( 354) SS BOND : bond 0.00940 ( 2) SS BOND : angle 1.31783 ( 4) covalent geometry : bond 0.00540 ( 3781) covalent geometry : angle 0.66049 ( 5129) *********************** 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 76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 312 VAL cc_start: 0.8277 (m) cc_final: 0.8047 (t) REVERT: B 388 SER cc_start: 0.8784 (t) cc_final: 0.8537 (p) REVERT: B 427 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8141 (ttp-170) REVERT: H 50 MET cc_start: 0.8516 (ttt) cc_final: 0.8220 (ttp) REVERT: H 80 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7048 (tp) REVERT: H 112 THR cc_start: 0.8247 (t) cc_final: 0.7917 (m) REVERT: L 45 LYS cc_start: 0.7490 (mmtp) cc_final: 0.7259 (mmtp) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.1568 time to fit residues: 13.5544 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 : 0.432 ------------------------------------------------------------------------------- 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 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 67 LEU Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.0030 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 40 optimal weight: 0.0980 chunk 13 optimal weight: 0.3980 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.111688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092510 restraints weight = 5664.540| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.88 r_work: 0.2977 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3783 Z= 0.120 Angle : 0.565 7.800 5133 Z= 0.298 Chirality : 0.044 0.147 565 Planarity : 0.004 0.033 653 Dihedral : 5.065 29.611 511 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.44 % Allowed : 12.22 % Favored : 85.33 % 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: -1.09 (0.37), residues: 460 helix: None (None), residues: 0 sheet: 0.71 (0.33), residues: 222 loop : -2.29 (0.36), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 356 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.002 PHE B 437 TYR 0.011 0.001 TYR B 305 ARG 0.003 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 122) hydrogen bonds : angle 4.70050 ( 354) SS BOND : bond 0.00693 ( 2) SS BOND : angle 0.88850 ( 4) covalent geometry : bond 0.00279 ( 3781) covalent geometry : angle 0.56510 ( 5129) *********************** 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 73 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 420 SER cc_start: 0.8650 (m) cc_final: 0.8432 (p) REVERT: B 388 SER cc_start: 0.8751 (t) cc_final: 0.8499 (p) REVERT: B 427 ARG cc_start: 0.8380 (ttp80) cc_final: 0.8170 (ttp-170) REVERT: H 50 MET cc_start: 0.8452 (ttt) cc_final: 0.8194 (ttp) REVERT: H 80 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6921 (tp) REVERT: H 112 THR cc_start: 0.8281 (t) cc_final: 0.7958 (m) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.1630 time to fit residues: 13.6308 Evaluate side-chains 73 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 80 LEU 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: 0.9980 chunk 7 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.0010 chunk 25 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.091133 restraints weight = 5632.245| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.95 r_work: 0.2950 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- 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: 0.7845 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3783 Z= 0.158 Angle : 0.613 7.913 5133 Z= 0.323 Chirality : 0.045 0.149 565 Planarity : 0.004 0.034 653 Dihedral : 5.226 30.204 511 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.93 % Allowed : 11.74 % Favored : 85.33 % 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: -1.00 (0.38), residues: 460 helix: None (None), residues: 0 sheet: 0.85 (0.32), residues: 230 loop : -2.44 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 356 HIS 0.004 0.002 HIS H 35 PHE 0.016 0.002 PHE B 437 TYR 0.014 0.002 TYR B 305 ARG 0.003 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 122) hydrogen bonds : angle 4.76778 ( 354) SS BOND : bond 0.00827 ( 2) SS BOND : angle 1.09922 ( 4) covalent geometry : bond 0.00379 ( 3781) covalent geometry : angle 0.61246 ( 5129) ********************** 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 75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: B 388 SER cc_start: 0.8748 (t) cc_final: 0.8509 (p) REVERT: B 427 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8133 (ttp-170) REVERT: H 50 MET cc_start: 0.8487 (ttt) cc_final: 0.8225 (ttp) REVERT: H 80 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.7004 (tp) REVERT: H 112 THR cc_start: 0.8295 (t) cc_final: 0.7989 (m) REVERT: L 45 LYS cc_start: 0.7469 (mmtp) cc_final: 0.7232 (mmtp) outliers start: 12 outliers final: 11 residues processed: 69 average time/residue: 0.1560 time to fit residues: 13.5822 Evaluate side-chains 75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 295 SER 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 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 39 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 37 optimal weight: 0.1980 chunk 1 optimal weight: 0.3980 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 302 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.092529 restraints weight = 5639.892| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.94 r_work: 0.2975 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 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 = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3783 Z= 0.116 Angle : 0.563 7.689 5133 Z= 0.297 Chirality : 0.044 0.146 565 Planarity : 0.004 0.032 653 Dihedral : 4.956 27.394 511 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.93 % Allowed : 11.74 % Favored : 85.33 % 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: -0.98 (0.38), residues: 460 helix: None (None), residues: 0 sheet: 0.72 (0.33), residues: 226 loop : -2.18 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 356 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE B 437 TYR 0.012 0.001 TYR B 305 ARG 0.003 0.000 ARG L 54 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 122) hydrogen bonds : angle 4.62644 ( 354) SS BOND : bond 0.00689 ( 2) SS BOND : angle 0.86682 ( 4) covalent geometry : bond 0.00264 ( 3781) covalent geometry : angle 0.56302 ( 5129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2599.25 seconds wall clock time: 45 minutes 50.87 seconds (2750.87 seconds total)