Starting phenix.real_space_refine on Wed Jun 4 14:24:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcu_32429/06_2025/7wcu_32429.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcu_32429/06_2025/7wcu_32429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wcu_32429/06_2025/7wcu_32429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcu_32429/06_2025/7wcu_32429.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcu_32429/06_2025/7wcu_32429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcu_32429/06_2025/7wcu_32429.cif" } resolution = 3.09 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= 0.038 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 15 5.16 5 C 2053 2.51 5 N 553 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3248 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1496 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain breaks: 1 Time building chain proxies: 3.49, per 1000 atoms: 1.07 Number of scatterers: 3248 At special positions: 0 Unit cell: (85.32, 63.72, 87.48, 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 15 16.00 O 627 8.00 N 553 7.00 C 2053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.06 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 394.5 milliseconds 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 11.8% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.561A pdb=" N ARG A 31 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.864A pdb=" N THR A 90 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.505A pdb=" N ASP B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 83 " --> pdb=" O SER B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 365 through 370 Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.107A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 422 Processing helix chain 'R' and resid 438 through 443 removed outlier: 3.609A pdb=" N SER R 443 " --> pdb=" O ASN R 439 " (cutoff:3.500A) Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 4.022A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 80 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.296A pdb=" N TYR A 33 " --> pdb=" O ASP A 98 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET A 34 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N VAL A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 11 through 12 removed outlier: 7.067A pdb=" N CYS A 95 " --> pdb=" O TRP A 107 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TRP A 107 " --> pdb=" O CYS A 95 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG A 97 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR A 103 " --> pdb=" O TYR A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 6 removed outlier: 6.813A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N GLN B 27 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 10.166A pdb=" N SER B 67 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 11.398A pdb=" N VAL B 29 " --> pdb=" O SER B 65 " (cutoff:3.500A) removed outlier: 11.419A pdb=" N SER B 65 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.894A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.596A pdb=" N GLY R 431 " --> pdb=" O TYR R 380 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR R 380 " --> pdb=" O GLY R 431 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL R 433 " --> pdb=" O LYS R 378 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS R 378 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'R' and resid 473 through 474 99 hydrogen bonds defined for protein. 240 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: 0.86 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: 1.21 - 1.34: 1053 1.34 - 1.47: 918 1.47 - 1.60: 1335 1.60 - 1.73: 0 1.73 - 1.86: 18 Bond restraints: 3324 Sorted by residual: bond pdb=" CG TYR B 91 " pdb=" CD1 TYR B 91 " ideal model delta sigma weight residual 1.389 1.317 0.072 2.10e-02 2.27e+03 1.17e+01 bond pdb=" CA THR R 430 " pdb=" CB THR R 430 " ideal model delta sigma weight residual 1.529 1.564 -0.035 1.38e-02 5.25e+03 6.41e+00 bond pdb=" CE2 TYR B 91 " pdb=" CZ TYR B 91 " ideal model delta sigma weight residual 1.378 1.335 0.043 2.40e-02 1.74e+03 3.14e+00 bond pdb=" CB GLN R 498 " pdb=" CG GLN R 498 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.14e+00 bond pdb=" CB ASP A 98 " pdb=" CG ASP A 98 " ideal model delta sigma weight residual 1.516 1.472 0.044 2.50e-02 1.60e+03 3.12e+00 ... (remaining 3319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 4352 2.74 - 5.49: 132 5.49 - 8.23: 19 8.23 - 10.98: 3 10.98 - 13.72: 3 Bond angle restraints: 4509 Sorted by residual: angle pdb=" CA CYS R 432 " pdb=" CB CYS R 432 " pdb=" SG CYS R 432 " ideal model delta sigma weight residual 114.40 128.12 -13.72 2.30e+00 1.89e-01 3.56e+01 angle pdb=" N ASP A 101 " pdb=" CA ASP A 101 " pdb=" C ASP A 101 " ideal model delta sigma weight residual 111.81 104.16 7.65 1.54e+00 4.22e-01 2.47e+01 angle pdb=" CB MET B 4 " pdb=" CG MET B 4 " pdb=" SD MET B 4 " ideal model delta sigma weight residual 112.70 99.26 13.44 3.00e+00 1.11e-01 2.01e+01 angle pdb=" CA PRO A 14 " pdb=" N PRO A 14 " pdb=" CD PRO A 14 " ideal model delta sigma weight residual 112.00 106.09 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" CB GLN R 498 " pdb=" CG GLN R 498 " pdb=" CD GLN R 498 " ideal model delta sigma weight residual 112.60 119.40 -6.80 1.70e+00 3.46e-01 1.60e+01 ... (remaining 4504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 1691 14.69 - 29.38: 202 29.38 - 44.07: 57 44.07 - 58.75: 5 58.75 - 73.44: 5 Dihedral angle restraints: 1960 sinusoidal: 763 harmonic: 1197 Sorted by residual: dihedral pdb=" CA ASN A 73 " pdb=" C ASN A 73 " pdb=" N SER A 74 " pdb=" CA SER A 74 " ideal model delta harmonic sigma weight residual 180.00 149.82 30.18 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA TYR B 91 " pdb=" C TYR B 91 " pdb=" N ASN B 92 " pdb=" CA ASN B 92 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CB CYS R 379 " pdb=" SG CYS R 379 " pdb=" SG CYS R 432 " pdb=" CB CYS R 432 " ideal model delta sinusoidal sigma weight residual 93.00 44.38 48.62 1 1.00e+01 1.00e-02 3.25e+01 ... (remaining 1957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 320 0.057 - 0.115: 122 0.115 - 0.172: 31 0.172 - 0.229: 5 0.229 - 0.286: 2 Chirality restraints: 480 Sorted by residual: chirality pdb=" CG LEU B 21 " pdb=" CB LEU B 21 " pdb=" CD1 LEU B 21 " pdb=" CD2 LEU B 21 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB THR B 56 " pdb=" CA THR B 56 " pdb=" OG1 THR B 56 " pdb=" CG2 THR B 56 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA CYS R 432 " pdb=" N CYS R 432 " pdb=" C CYS R 432 " pdb=" CB CYS R 432 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 477 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 52 " -0.050 5.00e-02 4.00e+02 7.71e-02 9.52e+00 pdb=" N PRO A 53 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 53 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 53 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 13 " 0.051 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO A 14 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 91 " -0.022 2.00e-02 2.50e+03 1.81e-02 6.59e+00 pdb=" CG TYR B 91 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR B 91 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 91 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 91 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 91 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 91 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 91 " -0.000 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 995 2.81 - 3.33: 2674 3.33 - 3.86: 5563 3.86 - 4.38: 6357 4.38 - 4.90: 11331 Nonbonded interactions: 26920 Sorted by model distance: nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.289 3.040 nonbonded pdb=" O ARG A 31 " pdb=" OH TYR R 473 " model vdw 2.336 3.040 nonbonded pdb=" OG SER A 35 " pdb=" O SER A 49 " model vdw 2.336 3.040 nonbonded pdb=" OH TYR A 33 " pdb=" O LEU R 455 " model vdw 2.339 3.040 nonbonded pdb=" OE2 GLU R 406 " pdb=" OH TYR R 495 " model vdw 2.352 3.040 ... (remaining 26915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.790 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 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 : 0.009 0.072 3330 Z= 0.387 Angle : 1.159 13.722 4521 Z= 0.626 Chirality : 0.064 0.286 480 Planarity : 0.007 0.077 588 Dihedral : 13.760 73.442 1186 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.29 % Allowed : 0.86 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -2.63 (0.39), residues: 408 helix: -4.49 (0.52), residues: 26 sheet: -1.34 (0.43), residues: 145 loop : -1.67 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 107 PHE 0.027 0.003 PHE A 102 TYR 0.045 0.003 TYR B 91 ARG 0.018 0.002 ARG R 454 Details of bonding type rmsd hydrogen bonds : bond 0.24917 ( 94) hydrogen bonds : angle 11.76041 ( 240) SS BOND : bond 0.01161 ( 6) SS BOND : angle 2.53304 ( 12) covalent geometry : bond 0.00880 ( 3324) covalent geometry : angle 1.15332 ( 4509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.7766 (ptm160) cc_final: 0.7031 (ptm160) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2500 time to fit residues: 25.5023 Evaluate side-chains 73 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.0970 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN R 394 ASN R 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084348 restraints weight = 7606.512| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.79 r_work: 0.3202 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3330 Z= 0.156 Angle : 0.696 7.797 4521 Z= 0.354 Chirality : 0.047 0.155 480 Planarity : 0.005 0.059 588 Dihedral : 5.922 26.919 467 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.43 % Allowed : 11.14 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.58 (0.38), residues: 408 helix: -4.42 (0.53), residues: 27 sheet: -1.33 (0.43), residues: 137 loop : -1.62 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 107 PHE 0.013 0.002 PHE A 27 TYR 0.012 0.001 TYR A 94 ARG 0.009 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 94) hydrogen bonds : angle 8.20834 ( 240) SS BOND : bond 0.00652 ( 6) SS BOND : angle 1.26624 ( 12) covalent geometry : bond 0.00354 ( 3324) covalent geometry : angle 0.69341 ( 4509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.375 Fit side-chains REVERT: B 18 ARG cc_start: 0.6891 (ttp80) cc_final: 0.6676 (ttp80) REVERT: B 79 GLN cc_start: 0.7914 (mp10) cc_final: 0.7636 (mp10) REVERT: R 420 ASP cc_start: 0.8315 (m-30) cc_final: 0.8003 (m-30) outliers start: 5 outliers final: 4 residues processed: 77 average time/residue: 0.2362 time to fit residues: 20.7764 Evaluate side-chains 74 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 0.0070 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 89 GLN ** R 394 ASN ** 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 = 0.3528 r_free = 0.3528 target = 0.097280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.084581 restraints weight = 7488.004| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.71 r_work: 0.3196 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3330 Z= 0.154 Angle : 0.644 7.397 4521 Z= 0.328 Chirality : 0.045 0.149 480 Planarity : 0.005 0.060 588 Dihedral : 5.451 27.226 467 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.43 % Allowed : 11.14 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.45 (0.39), residues: 408 helix: -4.44 (0.51), residues: 27 sheet: -1.35 (0.42), residues: 139 loop : -1.43 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 PHE 0.015 0.001 PHE R 377 TYR 0.012 0.001 TYR A 94 ARG 0.003 0.001 ARG B 18 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 94) hydrogen bonds : angle 7.46663 ( 240) SS BOND : bond 0.00578 ( 6) SS BOND : angle 1.16586 ( 12) covalent geometry : bond 0.00349 ( 3324) covalent geometry : angle 0.64208 ( 4509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.381 Fit side-chains REVERT: A 98 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: B 18 ARG cc_start: 0.7002 (ttp80) cc_final: 0.6770 (ttp80) REVERT: R 340 GLU cc_start: 0.7214 (pm20) cc_final: 0.6944 (pm20) REVERT: R 420 ASP cc_start: 0.8337 (m-30) cc_final: 0.8007 (m-30) REVERT: R 478 LYS cc_start: 0.8181 (tttp) cc_final: 0.7938 (tttp) outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.2285 time to fit residues: 21.8393 Evaluate side-chains 81 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 79 GLN R 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084470 restraints weight = 7527.768| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.76 r_work: 0.3205 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3330 Z= 0.139 Angle : 0.624 7.747 4521 Z= 0.319 Chirality : 0.045 0.146 480 Planarity : 0.004 0.056 588 Dihedral : 5.212 25.726 467 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.14 % Allowed : 13.14 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.51 (0.38), residues: 408 helix: -4.08 (0.46), residues: 34 sheet: -1.41 (0.41), residues: 139 loop : -1.41 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 PHE 0.022 0.001 PHE R 377 TYR 0.020 0.001 TYR R 369 ARG 0.003 0.001 ARG R 466 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 94) hydrogen bonds : angle 7.15434 ( 240) SS BOND : bond 0.00529 ( 6) SS BOND : angle 1.05752 ( 12) covalent geometry : bond 0.00319 ( 3324) covalent geometry : angle 0.62253 ( 4509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.341 Fit side-chains REVERT: A 31 ARG cc_start: 0.8142 (ptm160) cc_final: 0.7759 (ptm160) REVERT: A 98 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: B 18 ARG cc_start: 0.7013 (ttp80) cc_final: 0.6782 (ttp80) REVERT: R 420 ASP cc_start: 0.8222 (m-30) cc_final: 0.7930 (m-30) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.2471 time to fit residues: 22.5361 Evaluate side-chains 82 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 394 ASN Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN R 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084612 restraints weight = 7531.541| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.81 r_work: 0.3202 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3330 Z= 0.153 Angle : 0.625 7.378 4521 Z= 0.321 Chirality : 0.044 0.156 480 Planarity : 0.004 0.057 588 Dihedral : 5.167 26.758 467 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.57 % Allowed : 12.86 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.61 (0.39), residues: 408 helix: -3.96 (0.45), residues: 40 sheet: -1.44 (0.41), residues: 139 loop : -1.44 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 436 PHE 0.018 0.001 PHE R 377 TYR 0.026 0.001 TYR R 369 ARG 0.004 0.000 ARG R 466 Details of bonding type rmsd hydrogen bonds : bond 0.02864 ( 94) hydrogen bonds : angle 7.02659 ( 240) SS BOND : bond 0.00365 ( 6) SS BOND : angle 1.04320 ( 12) covalent geometry : bond 0.00352 ( 3324) covalent geometry : angle 0.62307 ( 4509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.385 Fit side-chains REVERT: A 75 LYS cc_start: 0.7071 (pttm) cc_final: 0.6845 (pttm) REVERT: A 98 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8073 (m-30) REVERT: B 18 ARG cc_start: 0.7090 (ttp80) cc_final: 0.6856 (ttp80) REVERT: R 420 ASP cc_start: 0.8276 (m-30) cc_final: 0.7975 (m-30) outliers start: 16 outliers final: 10 residues processed: 79 average time/residue: 0.2350 time to fit residues: 21.3057 Evaluate side-chains 83 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** R 394 ASN ** 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 = 0.3565 r_free = 0.3565 target = 0.098791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.085260 restraints weight = 7811.747| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.88 r_work: 0.3229 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3330 Z= 0.131 Angle : 0.607 7.586 4521 Z= 0.313 Chirality : 0.044 0.149 480 Planarity : 0.004 0.055 588 Dihedral : 4.972 25.294 467 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.86 % Allowed : 13.43 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.51 (0.39), residues: 408 helix: -3.93 (0.47), residues: 40 sheet: -1.37 (0.40), residues: 141 loop : -1.37 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 436 PHE 0.013 0.001 PHE R 377 TYR 0.018 0.001 TYR R 369 ARG 0.004 0.001 ARG R 466 Details of bonding type rmsd hydrogen bonds : bond 0.02689 ( 94) hydrogen bonds : angle 6.87208 ( 240) SS BOND : bond 0.00413 ( 6) SS BOND : angle 1.04292 ( 12) covalent geometry : bond 0.00302 ( 3324) covalent geometry : angle 0.60541 ( 4509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.381 Fit side-chains REVERT: A 98 ASP cc_start: 0.8347 (m-30) cc_final: 0.8134 (m-30) REVERT: B 18 ARG cc_start: 0.7116 (ttp80) cc_final: 0.6888 (ttp80) REVERT: B 75 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8364 (mm) outliers start: 17 outliers final: 13 residues processed: 84 average time/residue: 0.2254 time to fit residues: 21.7160 Evaluate side-chains 85 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** R 394 ASN ** 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 = 0.3539 r_free = 0.3539 target = 0.097903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084741 restraints weight = 7584.644| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.78 r_work: 0.3201 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3330 Z= 0.163 Angle : 0.636 7.266 4521 Z= 0.328 Chirality : 0.045 0.159 480 Planarity : 0.004 0.054 588 Dihedral : 5.053 26.430 467 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.57 % Allowed : 14.29 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.46 (0.39), residues: 408 helix: -3.84 (0.50), residues: 39 sheet: -1.33 (0.41), residues: 139 loop : -1.36 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 436 PHE 0.011 0.001 PHE A 27 TYR 0.015 0.001 TYR R 369 ARG 0.004 0.000 ARG R 466 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 94) hydrogen bonds : angle 7.01775 ( 240) SS BOND : bond 0.00457 ( 6) SS BOND : angle 1.13963 ( 12) covalent geometry : bond 0.00377 ( 3324) covalent geometry : angle 0.63428 ( 4509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.406 Fit side-chains REVERT: A 86 ARG cc_start: 0.7132 (mmp-170) cc_final: 0.6731 (mmm160) REVERT: B 18 ARG cc_start: 0.7134 (ttp80) cc_final: 0.6907 (ttp80) REVERT: B 33 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8695 (tt) REVERT: B 75 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8456 (mm) outliers start: 16 outliers final: 11 residues processed: 81 average time/residue: 0.2213 time to fit residues: 20.7199 Evaluate side-chains 84 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 38 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084618 restraints weight = 7632.772| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.84 r_work: 0.3218 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3330 Z= 0.152 Angle : 0.640 7.240 4521 Z= 0.330 Chirality : 0.045 0.151 480 Planarity : 0.004 0.053 588 Dihedral : 4.977 25.649 467 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.00 % Allowed : 15.43 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.43 (0.39), residues: 408 helix: -3.80 (0.51), residues: 39 sheet: -1.27 (0.41), residues: 141 loop : -1.38 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 PHE 0.011 0.001 PHE A 27 TYR 0.011 0.001 TYR A 94 ARG 0.005 0.000 ARG R 466 Details of bonding type rmsd hydrogen bonds : bond 0.02703 ( 94) hydrogen bonds : angle 6.93177 ( 240) SS BOND : bond 0.00457 ( 6) SS BOND : angle 1.12262 ( 12) covalent geometry : bond 0.00355 ( 3324) covalent geometry : angle 0.63829 ( 4509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.350 Fit side-chains REVERT: A 31 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7750 (ptm160) REVERT: B 18 ARG cc_start: 0.7266 (ttp80) cc_final: 0.7020 (ttp80) REVERT: B 75 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8442 (mm) outliers start: 14 outliers final: 13 residues processed: 80 average time/residue: 0.2283 time to fit residues: 21.3516 Evaluate side-chains 85 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.099650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.086472 restraints weight = 7577.494| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.80 r_work: 0.3248 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3330 Z= 0.122 Angle : 0.620 6.971 4521 Z= 0.319 Chirality : 0.044 0.143 480 Planarity : 0.004 0.053 588 Dihedral : 4.804 25.107 467 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.00 % Allowed : 15.14 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.37 (0.39), residues: 408 helix: -3.76 (0.52), residues: 39 sheet: -1.17 (0.41), residues: 141 loop : -1.38 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 436 PHE 0.009 0.001 PHE A 27 TYR 0.009 0.001 TYR A 94 ARG 0.003 0.000 ARG R 466 Details of bonding type rmsd hydrogen bonds : bond 0.02540 ( 94) hydrogen bonds : angle 6.54923 ( 240) SS BOND : bond 0.00434 ( 6) SS BOND : angle 1.07517 ( 12) covalent geometry : bond 0.00289 ( 3324) covalent geometry : angle 0.61798 ( 4509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.402 Fit side-chains REVERT: A 89 ASP cc_start: 0.8565 (m-30) cc_final: 0.8282 (m-30) REVERT: B 18 ARG cc_start: 0.7178 (ttp80) cc_final: 0.6949 (ttp80) REVERT: B 75 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8371 (mm) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.2172 time to fit residues: 20.3699 Evaluate side-chains 82 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.099018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085756 restraints weight = 7523.771| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.82 r_work: 0.3229 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3330 Z= 0.152 Angle : 0.638 7.132 4521 Z= 0.327 Chirality : 0.044 0.141 480 Planarity : 0.004 0.051 588 Dihedral : 4.882 25.610 467 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.43 % Allowed : 16.86 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.28 (0.39), residues: 408 helix: -3.71 (0.54), residues: 39 sheet: -1.05 (0.43), residues: 139 loop : -1.36 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 436 PHE 0.011 0.001 PHE A 27 TYR 0.029 0.002 TYR B 49 ARG 0.004 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.02613 ( 94) hydrogen bonds : angle 6.53314 ( 240) SS BOND : bond 0.00452 ( 6) SS BOND : angle 1.13420 ( 12) covalent geometry : bond 0.00355 ( 3324) covalent geometry : angle 0.63638 ( 4509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 816 Ramachandran restraints generated. 408 Oldfield, 0 Emsley, 408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8051 (ptm160) cc_final: 0.7785 (ptm160) REVERT: B 18 ARG cc_start: 0.7358 (ttp80) cc_final: 0.7100 (ttp80) REVERT: B 75 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8415 (mm) outliers start: 12 outliers final: 11 residues processed: 79 average time/residue: 0.2262 time to fit residues: 20.5940 Evaluate side-chains 82 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.098558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085614 restraints weight = 7501.061| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.75 r_work: 0.3223 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3330 Z= 0.160 Angle : 0.645 7.037 4521 Z= 0.331 Chirality : 0.045 0.140 480 Planarity : 0.004 0.052 588 Dihedral : 4.921 25.532 467 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.71 % Allowed : 16.29 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: -2.21 (0.40), residues: 408 helix: -3.59 (0.56), residues: 39 sheet: -0.98 (0.43), residues: 139 loop : -1.35 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 PHE 0.011 0.001 PHE A 27 TYR 0.015 0.001 TYR B 91 ARG 0.005 0.001 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.02653 ( 94) hydrogen bonds : angle 6.61423 ( 240) SS BOND : bond 0.00472 ( 6) SS BOND : angle 1.16919 ( 12) covalent geometry : bond 0.00374 ( 3324) covalent geometry : angle 0.64298 ( 4509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2153.76 seconds wall clock time: 37 minutes 52.76 seconds (2272.76 seconds total)