Starting phenix.real_space_refine on Tue Mar 11 15:24:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ug7_42216/03_2025/8ug7_42216.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ug7_42216/03_2025/8ug7_42216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ug7_42216/03_2025/8ug7_42216.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ug7_42216/03_2025/8ug7_42216.map" model { file = "/net/cci-nas-00/data/ceres_data/8ug7_42216/03_2025/8ug7_42216.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ug7_42216/03_2025/8ug7_42216.cif" } resolution = 2.95 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= 0.003 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 42 5.16 5 C 4156 2.51 5 N 1006 2.21 5 O 1038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6242 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3121 Classifications: {'peptide': 393} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 383} Chain breaks: 7 Restraints were copied for chains: B Time building chain proxies: 5.20, per 1000 atoms: 0.83 Number of scatterers: 6242 At special positions: 0 Unit cell: (87.15, 98.77, 70.55, 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 42 16.00 O 1038 8.00 N 1006 7.00 C 4156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 28 through 53 removed outlier: 3.540A pdb=" N ASN A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 85 Processing helix chain 'A' and resid 101 through 128 removed outlier: 4.304A pdb=" N GLY A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 156 Proline residue: A 140 - end of helix Processing helix chain 'A' and resid 165 through 194 Processing helix chain 'A' and resid 247 through 265 Processing helix chain 'A' and resid 292 through 312 Processing helix chain 'A' and resid 322 through 353 removed outlier: 3.562A pdb=" N PHE A 353 " --> pdb=" O VAL A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 393 removed outlier: 4.506A pdb=" N GLY A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 429 removed outlier: 3.564A pdb=" N GLY A 429 " --> pdb=" O SER A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 508 removed outlier: 3.572A pdb=" N ASP A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 515 Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 530 through 563 Proline residue: A 543 - end of helix removed outlier: 3.500A pdb=" N ILE A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 53 removed outlier: 3.539A pdb=" N ASN B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 85 Processing helix chain 'B' and resid 101 through 128 removed outlier: 4.304A pdb=" N GLY B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 156 Proline residue: B 140 - end of helix Processing helix chain 'B' and resid 165 through 194 Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 292 through 312 Processing helix chain 'B' and resid 322 through 353 removed outlier: 3.562A pdb=" N PHE B 353 " --> pdb=" O VAL B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 393 removed outlier: 4.505A pdb=" N GLY B 379 " --> pdb=" O GLY B 375 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 429 removed outlier: 3.564A pdb=" N GLY B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 508 removed outlier: 3.573A pdb=" N ASP B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 515 Processing helix chain 'B' and resid 522 through 530 Processing helix chain 'B' and resid 530 through 563 Proline residue: B 543 - end of helix removed outlier: 3.500A pdb=" N ILE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1584 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1267 1.33 - 1.45: 1564 1.45 - 1.57: 3499 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 6396 Sorted by residual: bond pdb=" CA SER B 256 " pdb=" CB SER B 256 " ideal model delta sigma weight residual 1.528 1.467 0.061 1.56e-02 4.11e+03 1.54e+01 bond pdb=" CA SER A 256 " pdb=" CB SER A 256 " ideal model delta sigma weight residual 1.528 1.468 0.060 1.56e-02 4.11e+03 1.50e+01 bond pdb=" CA SER B 346 " pdb=" CB SER B 346 " ideal model delta sigma weight residual 1.528 1.479 0.049 1.56e-02 4.11e+03 9.99e+00 bond pdb=" CA SER A 346 " pdb=" CB SER A 346 " ideal model delta sigma weight residual 1.528 1.480 0.049 1.56e-02 4.11e+03 9.85e+00 bond pdb=" N VAL A 307 " pdb=" CA VAL A 307 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.78e+00 ... (remaining 6391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 8335 1.53 - 3.06: 290 3.06 - 4.60: 57 4.60 - 6.13: 12 6.13 - 7.66: 4 Bond angle restraints: 8698 Sorted by residual: angle pdb=" N TYR B 124 " pdb=" CA TYR B 124 " pdb=" C TYR B 124 " ideal model delta sigma weight residual 111.40 106.84 4.56 1.22e+00 6.72e-01 1.40e+01 angle pdb=" N TYR A 124 " pdb=" CA TYR A 124 " pdb=" C TYR A 124 " ideal model delta sigma weight residual 111.40 106.86 4.54 1.22e+00 6.72e-01 1.39e+01 angle pdb=" C GLN A 238 " pdb=" N GLN A 239 " pdb=" CA GLN A 239 " ideal model delta sigma weight residual 120.71 114.71 6.00 1.67e+00 3.59e-01 1.29e+01 angle pdb=" C GLN B 238 " pdb=" N GLN B 239 " pdb=" CA GLN B 239 " ideal model delta sigma weight residual 120.71 114.73 5.98 1.67e+00 3.59e-01 1.28e+01 angle pdb=" CA ARG B 366 " pdb=" C ARG B 366 " pdb=" O ARG B 366 " ideal model delta sigma weight residual 122.41 118.12 4.29 1.21e+00 6.83e-01 1.26e+01 ... (remaining 8693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.55: 2886 12.55 - 25.10: 454 25.10 - 37.66: 198 37.66 - 50.21: 78 50.21 - 62.76: 22 Dihedral angle restraints: 3638 sinusoidal: 1358 harmonic: 2280 Sorted by residual: dihedral pdb=" CD ARG B 366 " pdb=" NE ARG B 366 " pdb=" CZ ARG B 366 " pdb=" NH1 ARG B 366 " ideal model delta sinusoidal sigma weight residual 0.00 -30.55 30.55 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CD ARG A 366 " pdb=" NE ARG A 366 " pdb=" CZ ARG A 366 " pdb=" NH1 ARG A 366 " ideal model delta sinusoidal sigma weight residual 0.00 -30.49 30.49 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CG ARG B 104 " pdb=" CD ARG B 104 " pdb=" NE ARG B 104 " pdb=" CZ ARG B 104 " ideal model delta sinusoidal sigma weight residual 90.00 134.89 -44.89 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 3635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 995 0.090 - 0.179: 28 0.179 - 0.269: 7 0.269 - 0.359: 0 0.359 - 0.448: 2 Chirality restraints: 1032 Sorted by residual: chirality pdb=" CB VAL B 389 " pdb=" CA VAL B 389 " pdb=" CG1 VAL B 389 " pdb=" CG2 VAL B 389 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CB VAL A 389 " pdb=" CA VAL A 389 " pdb=" CG1 VAL A 389 " pdb=" CG2 VAL A 389 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA ILE A 546 " pdb=" N ILE A 546 " pdb=" C ILE A 546 " pdb=" CB ILE A 546 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1029 not shown) Planarity restraints: 1042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 366 " 0.544 9.50e-02 1.11e+02 2.44e-01 3.64e+01 pdb=" NE ARG B 366 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG B 366 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG B 366 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 366 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 366 " -0.544 9.50e-02 1.11e+02 2.44e-01 3.63e+01 pdb=" NE ARG A 366 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 366 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 366 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 366 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 293 " -0.038 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO A 294 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " -0.032 5.00e-02 4.00e+02 ... (remaining 1039 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 964 2.75 - 3.29: 6261 3.29 - 3.83: 11054 3.83 - 4.36: 12647 4.36 - 4.90: 22100 Nonbonded interactions: 53026 Sorted by model distance: nonbonded pdb=" O PHE B 421 " pdb=" OG SER B 425 " model vdw 2.215 3.040 nonbonded pdb=" O PHE A 421 " pdb=" OG SER A 425 " model vdw 2.215 3.040 nonbonded pdb=" O ASN A 248 " pdb=" OG SER A 252 " model vdw 2.243 3.040 nonbonded pdb=" O ASN B 248 " pdb=" OG SER B 252 " model vdw 2.244 3.040 nonbonded pdb=" O VAL A 147 " pdb=" OG1 THR A 151 " model vdw 2.272 3.040 ... (remaining 53021 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.880 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 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 : 0.005 0.073 6396 Z= 0.320 Angle : 0.664 7.660 8698 Z= 0.436 Chirality : 0.046 0.448 1032 Planarity : 0.012 0.244 1042 Dihedral : 16.571 62.762 2170 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 29.55 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.30), residues: 754 helix: 1.80 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -1.92 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 509 HIS 0.003 0.001 HIS A 519 PHE 0.009 0.001 PHE A 110 TYR 0.024 0.002 TYR B 560 ARG 0.004 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.635 Fit side-chains REVERT: A 124 TYR cc_start: 0.7932 (t80) cc_final: 0.7683 (t80) REVERT: A 366 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7949 (mtp180) REVERT: A 563 SER cc_start: 0.7427 (t) cc_final: 0.7200 (m) REVERT: B 124 TYR cc_start: 0.7934 (t80) cc_final: 0.7691 (t80) REVERT: B 366 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7948 (mtp180) REVERT: B 563 SER cc_start: 0.7396 (t) cc_final: 0.7164 (m) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.9408 time to fit residues: 89.2095 Evaluate side-chains 80 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 404 ASN B 53 ASN B 404 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.086978 restraints weight = 9891.350| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.04 r_work: 0.2894 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6396 Z= 0.221 Angle : 0.511 6.527 8698 Z= 0.276 Chirality : 0.038 0.126 1032 Planarity : 0.005 0.057 1042 Dihedral : 3.518 27.165 846 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.13 % Allowed : 24.33 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.20 (0.30), residues: 754 helix: 2.72 (0.19), residues: 652 sheet: None (None), residues: 0 loop : -2.28 (0.54), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 489 HIS 0.004 0.001 HIS B 551 PHE 0.012 0.001 PHE B 332 TYR 0.011 0.002 TYR B 58 ARG 0.002 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.618 Fit side-chains REVERT: A 124 TYR cc_start: 0.8276 (t80) cc_final: 0.7920 (t80) REVERT: B 124 TYR cc_start: 0.8272 (t80) cc_final: 0.7918 (t80) outliers start: 21 outliers final: 6 residues processed: 112 average time/residue: 0.8165 time to fit residues: 98.1966 Evaluate side-chains 91 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 389 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 chunk 54 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.089197 restraints weight = 10044.443| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.06 r_work: 0.2925 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6396 Z= 0.160 Angle : 0.461 5.314 8698 Z= 0.246 Chirality : 0.036 0.115 1032 Planarity : 0.004 0.056 1042 Dihedral : 3.428 24.162 846 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.49 % Allowed : 25.22 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.30), residues: 754 helix: 3.06 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -2.10 (0.54), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 489 HIS 0.003 0.001 HIS B 551 PHE 0.014 0.001 PHE A 153 TYR 0.009 0.001 TYR A 548 ARG 0.002 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.755 Fit side-chains REVERT: A 124 TYR cc_start: 0.8273 (t80) cc_final: 0.7843 (t80) REVERT: A 244 LEU cc_start: 0.8604 (mp) cc_final: 0.8366 (tt) REVERT: B 124 TYR cc_start: 0.8266 (t80) cc_final: 0.7793 (t80) REVERT: B 244 LEU cc_start: 0.8598 (mp) cc_final: 0.8375 (tt) outliers start: 10 outliers final: 2 residues processed: 103 average time/residue: 0.7876 time to fit residues: 87.3836 Evaluate side-chains 90 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 289 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.0030 chunk 77 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.086379 restraints weight = 10101.122| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.08 r_work: 0.2871 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6396 Z= 0.234 Angle : 0.498 5.638 8698 Z= 0.262 Chirality : 0.038 0.140 1032 Planarity : 0.004 0.055 1042 Dihedral : 3.483 21.437 846 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.54 % Allowed : 24.48 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.30), residues: 754 helix: 2.97 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -2.01 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 489 HIS 0.004 0.001 HIS B 551 PHE 0.014 0.001 PHE A 332 TYR 0.010 0.001 TYR B 58 ARG 0.001 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.616 Fit side-chains REVERT: A 124 TYR cc_start: 0.8294 (t80) cc_final: 0.7882 (t80) REVERT: A 244 LEU cc_start: 0.8660 (mp) cc_final: 0.8433 (tt) REVERT: A 424 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 124 TYR cc_start: 0.8306 (t80) cc_final: 0.7911 (t80) REVERT: B 244 LEU cc_start: 0.8671 (mp) cc_final: 0.8450 (tt) REVERT: B 424 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7339 (mm-30) outliers start: 17 outliers final: 6 residues processed: 99 average time/residue: 0.6386 time to fit residues: 68.8650 Evaluate side-chains 89 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 289 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 0.0470 chunk 22 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.116800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.087389 restraints weight = 10066.301| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.09 r_work: 0.2896 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6396 Z= 0.175 Angle : 0.475 7.648 8698 Z= 0.247 Chirality : 0.036 0.116 1032 Planarity : 0.004 0.053 1042 Dihedral : 3.404 19.891 846 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.18 % Allowed : 22.99 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.66 (0.30), residues: 754 helix: 3.08 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -1.92 (0.57), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.003 0.001 HIS B 551 PHE 0.012 0.001 PHE A 332 TYR 0.010 0.001 TYR A 548 ARG 0.002 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.632 Fit side-chains REVERT: A 124 TYR cc_start: 0.8247 (t80) cc_final: 0.7954 (t80) REVERT: A 128 PHE cc_start: 0.7864 (p90) cc_final: 0.7066 (p90) REVERT: A 239 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6651 (pm20) REVERT: A 241 TYR cc_start: 0.3819 (OUTLIER) cc_final: 0.3573 (t80) REVERT: A 244 LEU cc_start: 0.8673 (mp) cc_final: 0.8278 (tt) REVERT: B 124 TYR cc_start: 0.8265 (t80) cc_final: 0.7877 (t80) REVERT: B 239 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: B 241 TYR cc_start: 0.3855 (OUTLIER) cc_final: 0.3603 (t80) REVERT: B 244 LEU cc_start: 0.8674 (mp) cc_final: 0.8294 (tt) outliers start: 28 outliers final: 12 residues processed: 112 average time/residue: 0.7098 time to fit residues: 85.9584 Evaluate side-chains 103 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 404 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.086886 restraints weight = 9989.174| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.08 r_work: 0.2885 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6396 Z= 0.200 Angle : 0.493 8.923 8698 Z= 0.254 Chirality : 0.037 0.119 1032 Planarity : 0.004 0.053 1042 Dihedral : 3.401 18.904 846 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.58 % Allowed : 24.18 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.64 (0.30), residues: 754 helix: 3.05 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -1.91 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 76 HIS 0.003 0.001 HIS B 551 PHE 0.013 0.001 PHE B 332 TYR 0.010 0.001 TYR A 548 ARG 0.001 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.598 Fit side-chains REVERT: A 124 TYR cc_start: 0.8270 (t80) cc_final: 0.7974 (t80) REVERT: A 128 PHE cc_start: 0.7869 (p90) cc_final: 0.6967 (p90) REVERT: A 239 GLN cc_start: 0.6909 (OUTLIER) cc_final: 0.6693 (pm20) REVERT: A 241 TYR cc_start: 0.3971 (OUTLIER) cc_final: 0.3639 (t80) REVERT: A 244 LEU cc_start: 0.8638 (mp) cc_final: 0.8286 (tt) REVERT: B 124 TYR cc_start: 0.8276 (t80) cc_final: 0.7935 (t80) REVERT: B 239 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6680 (pm20) REVERT: B 241 TYR cc_start: 0.3905 (OUTLIER) cc_final: 0.3601 (t80) REVERT: B 244 LEU cc_start: 0.8644 (mp) cc_final: 0.8299 (tt) outliers start: 24 outliers final: 13 residues processed: 105 average time/residue: 0.7802 time to fit residues: 88.6427 Evaluate side-chains 100 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 557 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087787 restraints weight = 10118.504| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.09 r_work: 0.2897 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6396 Z= 0.170 Angle : 0.481 8.262 8698 Z= 0.248 Chirality : 0.036 0.117 1032 Planarity : 0.004 0.052 1042 Dihedral : 3.380 18.514 846 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.13 % Allowed : 24.93 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.30), residues: 754 helix: 3.10 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -1.85 (0.56), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 76 HIS 0.003 0.001 HIS B 551 PHE 0.012 0.001 PHE A 332 TYR 0.009 0.001 TYR B 548 ARG 0.001 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.729 Fit side-chains REVERT: A 124 TYR cc_start: 0.8265 (t80) cc_final: 0.7979 (t80) REVERT: A 128 PHE cc_start: 0.7841 (p90) cc_final: 0.6968 (p90) REVERT: A 241 TYR cc_start: 0.3935 (OUTLIER) cc_final: 0.3658 (t80) REVERT: A 244 LEU cc_start: 0.8642 (mp) cc_final: 0.8269 (tt) REVERT: B 124 TYR cc_start: 0.8248 (t80) cc_final: 0.7946 (t80) REVERT: B 128 PHE cc_start: 0.7899 (p90) cc_final: 0.7080 (p90) REVERT: B 241 TYR cc_start: 0.3923 (OUTLIER) cc_final: 0.3651 (t80) REVERT: B 244 LEU cc_start: 0.8637 (mp) cc_final: 0.8275 (tt) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 0.8061 time to fit residues: 90.0239 Evaluate side-chains 102 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 557 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 29 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087854 restraints weight = 9995.777| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.07 r_work: 0.2898 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6396 Z= 0.177 Angle : 0.485 7.837 8698 Z= 0.250 Chirality : 0.036 0.117 1032 Planarity : 0.004 0.051 1042 Dihedral : 3.368 18.363 846 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.99 % Allowed : 25.37 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.30), residues: 754 helix: 3.09 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -1.80 (0.55), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.003 0.001 HIS B 551 PHE 0.012 0.001 PHE A 332 TYR 0.009 0.001 TYR A 548 ARG 0.001 0.000 ARG A 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.631 Fit side-chains REVERT: A 124 TYR cc_start: 0.8264 (t80) cc_final: 0.7933 (t80) REVERT: A 128 PHE cc_start: 0.7847 (p90) cc_final: 0.6976 (p90) REVERT: A 241 TYR cc_start: 0.3885 (OUTLIER) cc_final: 0.3633 (t80) REVERT: A 244 LEU cc_start: 0.8638 (mp) cc_final: 0.8270 (tt) REVERT: B 124 TYR cc_start: 0.8237 (t80) cc_final: 0.7900 (t80) REVERT: B 128 PHE cc_start: 0.7903 (p90) cc_final: 0.7019 (p90) REVERT: B 241 TYR cc_start: 0.3893 (OUTLIER) cc_final: 0.3655 (t80) REVERT: B 244 LEU cc_start: 0.8637 (mp) cc_final: 0.8284 (tt) REVERT: B 424 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7416 (mm-30) outliers start: 20 outliers final: 12 residues processed: 103 average time/residue: 0.7097 time to fit residues: 79.1281 Evaluate side-chains 99 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 54 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 51 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.089507 restraints weight = 10121.753| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.09 r_work: 0.2926 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6396 Z= 0.149 Angle : 0.479 9.152 8698 Z= 0.243 Chirality : 0.036 0.114 1032 Planarity : 0.004 0.051 1042 Dihedral : 3.300 18.676 846 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.84 % Allowed : 25.67 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.30), residues: 754 helix: 3.15 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -1.54 (0.55), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 76 HIS 0.003 0.000 HIS B 551 PHE 0.010 0.001 PHE B 332 TYR 0.008 0.001 TYR A 548 ARG 0.001 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.647 Fit side-chains REVERT: A 239 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.6647 (pm20) REVERT: A 241 TYR cc_start: 0.3849 (OUTLIER) cc_final: 0.3592 (t80) REVERT: A 244 LEU cc_start: 0.8626 (mp) cc_final: 0.8219 (tt) REVERT: A 264 LYS cc_start: 0.9158 (ttmt) cc_final: 0.8794 (tttt) REVERT: B 241 TYR cc_start: 0.3875 (OUTLIER) cc_final: 0.3604 (t80) REVERT: B 244 LEU cc_start: 0.8627 (mp) cc_final: 0.8231 (tt) REVERT: B 264 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8810 (tttt) outliers start: 19 outliers final: 12 residues processed: 108 average time/residue: 0.7430 time to fit residues: 86.5865 Evaluate side-chains 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 557 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 34 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.088571 restraints weight = 10120.929| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.08 r_work: 0.2909 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6396 Z= 0.174 Angle : 0.492 9.171 8698 Z= 0.251 Chirality : 0.036 0.119 1032 Planarity : 0.004 0.051 1042 Dihedral : 3.321 18.506 846 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.84 % Allowed : 26.42 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.30), residues: 754 helix: 3.11 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -1.50 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 76 HIS 0.003 0.001 HIS B 551 PHE 0.011 0.001 PHE A 332 TYR 0.009 0.001 TYR A 548 ARG 0.001 0.000 ARG B 517 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.695 Fit side-chains REVERT: A 241 TYR cc_start: 0.3850 (OUTLIER) cc_final: 0.3571 (t80) REVERT: A 244 LEU cc_start: 0.8631 (mp) cc_final: 0.8233 (tt) REVERT: A 264 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8801 (tttt) REVERT: B 241 TYR cc_start: 0.3823 (OUTLIER) cc_final: 0.3542 (t80) REVERT: B 244 LEU cc_start: 0.8634 (mp) cc_final: 0.8248 (tt) REVERT: B 264 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8811 (tttt) outliers start: 19 outliers final: 14 residues processed: 103 average time/residue: 0.7561 time to fit residues: 84.0155 Evaluate side-chains 104 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 241 TYR Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 241 TYR Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 404 ASN Chi-restraints excluded: chain B residue 557 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 73 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 404 ASN B 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.088334 restraints weight = 10181.635| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.09 r_work: 0.2906 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6396 Z= 0.176 Angle : 0.497 9.036 8698 Z= 0.254 Chirality : 0.036 0.120 1032 Planarity : 0.004 0.051 1042 Dihedral : 3.332 18.218 846 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.39 % Allowed : 27.16 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.30), residues: 754 helix: 3.08 (0.19), residues: 646 sheet: None (None), residues: 0 loop : -1.56 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 76 HIS 0.003 0.001 HIS B 551 PHE 0.012 0.001 PHE B 63 TYR 0.009 0.001 TYR A 548 ARG 0.001 0.000 ARG A 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4109.69 seconds wall clock time: 71 minutes 11.12 seconds (4271.12 seconds total)