Starting phenix.real_space_refine on Tue Mar 3 11:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wcu_32429/03_2026/7wcu_32429.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wcu_32429/03_2026/7wcu_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_32429/03_2026/7wcu_32429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wcu_32429/03_2026/7wcu_32429.map" model { file = "/net/cci-nas-00/data/ceres_data/7wcu_32429/03_2026/7wcu_32429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wcu_32429/03_2026/7wcu_32429.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.76, per 1000 atoms: 0.23 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: 0.23 Conformation dependent library (CDL) restraints added in 118.8 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: 0.07 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: 0.55 Time building geometry restraints manager: 0.29 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: 4.380 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.180 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.740 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (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 ARG 0.018 0.002 ARG R 454 TYR 0.045 0.003 TYR B 91 PHE 0.027 0.003 PHE A 102 TRP 0.016 0.003 TRP A 107 Details of bonding type rmsd covalent geometry : bond 0.00880 ( 3324) covalent geometry : angle 1.15332 ( 4509) SS BOND : bond 0.01161 ( 6) SS BOND : angle 2.53304 ( 12) hydrogen bonds : bond 0.24917 ( 94) hydrogen bonds : angle 11.76041 ( 240) *********************** 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 : 0.125 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: 0.0955 time to fit residues: 9.7234 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 : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3523 r_free = 0.3523 target = 0.096901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.083870 restraints weight = 7627.539| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.75 r_work: 0.3195 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3330 Z= 0.174 Angle : 0.703 7.771 4521 Z= 0.358 Chirality : 0.047 0.152 480 Planarity : 0.005 0.059 588 Dihedral : 5.925 27.086 467 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.71 % Allowed : 11.14 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.38), residues: 408 helix: -4.39 (0.54), residues: 27 sheet: -1.34 (0.42), residues: 137 loop : -1.61 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 18 TYR 0.013 0.001 TYR A 94 PHE 0.013 0.002 PHE A 27 TRP 0.010 0.002 TRP A 107 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 3324) covalent geometry : angle 0.70071 ( 4509) SS BOND : bond 0.00653 ( 6) SS BOND : angle 1.29157 ( 12) hydrogen bonds : bond 0.03600 ( 94) hydrogen bonds : angle 8.19060 ( 240) *********************** 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 80 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.139 Fit side-chains REVERT: B 79 GLN cc_start: 0.7932 (mp10) cc_final: 0.7668 (mp10) REVERT: R 420 ASP cc_start: 0.8295 (m-30) cc_final: 0.7981 (m-30) outliers start: 6 outliers final: 5 residues processed: 78 average time/residue: 0.1008 time to fit residues: 8.9673 Evaluate side-chains 76 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.073 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.096069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083196 restraints weight = 7525.837| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.70 r_work: 0.3179 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3330 Z= 0.183 Angle : 0.671 7.637 4521 Z= 0.340 Chirality : 0.046 0.150 480 Planarity : 0.005 0.060 588 Dihedral : 5.572 28.433 467 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.57 % Allowed : 11.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.39), residues: 408 helix: -4.40 (0.54), residues: 27 sheet: -1.36 (0.42), residues: 139 loop : -1.40 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 18 TYR 0.013 0.001 TYR A 94 PHE 0.015 0.002 PHE R 377 TRP 0.010 0.002 TRP R 436 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 3324) covalent geometry : angle 0.66902 ( 4509) SS BOND : bond 0.00601 ( 6) SS BOND : angle 1.21262 ( 12) hydrogen bonds : bond 0.03290 ( 94) hydrogen bonds : angle 7.55520 ( 240) *********************** 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 91 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.084 Fit side-chains REVERT: A 98 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8089 (m-30) REVERT: R 340 GLU cc_start: 0.7260 (pm20) cc_final: 0.6994 (pm20) REVERT: R 356 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8987 (tttt) REVERT: R 420 ASP cc_start: 0.8369 (m-30) cc_final: 0.8024 (m-30) REVERT: R 478 LYS cc_start: 0.8194 (tttp) cc_final: 0.7948 (tttp) outliers start: 16 outliers final: 12 residues processed: 82 average time/residue: 0.0974 time to fit residues: 9.1071 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 : 0.074 ------------------------------------------------------------------------------- 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 63 VAL Chi-restraints excluded: chain A residue 98 ASP 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 394 ASN Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 483 VAL 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 35 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.096528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083440 restraints weight = 7554.834| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.78 r_work: 0.3181 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3330 Z= 0.161 Angle : 0.649 8.024 4521 Z= 0.331 Chirality : 0.045 0.147 480 Planarity : 0.005 0.056 588 Dihedral : 5.356 26.359 467 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.29 % Allowed : 14.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.39), residues: 408 helix: -4.03 (0.46), residues: 34 sheet: -1.42 (0.41), residues: 139 loop : -1.37 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 18 TYR 0.022 0.001 TYR R 369 PHE 0.023 0.001 PHE R 377 TRP 0.010 0.002 TRP R 436 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3324) covalent geometry : angle 0.64720 ( 4509) SS BOND : bond 0.00548 ( 6) SS BOND : angle 1.08592 ( 12) hydrogen bonds : bond 0.03018 ( 94) hydrogen bonds : angle 7.25904 ( 240) *********************** 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 92 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.123 Fit side-chains REVERT: A 31 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7710 (ptm160) REVERT: R 369 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6826 (m-10) REVERT: R 420 ASP cc_start: 0.8294 (m-30) cc_final: 0.7953 (m-30) outliers start: 15 outliers final: 11 residues processed: 83 average time/residue: 0.1076 time to fit residues: 10.1518 Evaluate side-chains 86 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 78 LEU Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ** 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 = 0.3521 r_free = 0.3521 target = 0.096910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.084007 restraints weight = 7504.246| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.72 r_work: 0.3194 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3330 Z= 0.149 Angle : 0.633 7.819 4521 Z= 0.324 Chirality : 0.045 0.143 480 Planarity : 0.005 0.058 588 Dihedral : 5.169 26.840 467 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 5.14 % Allowed : 14.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.39), residues: 408 helix: -3.88 (0.49), residues: 34 sheet: -1.41 (0.41), residues: 139 loop : -1.31 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 18 TYR 0.015 0.001 TYR R 369 PHE 0.015 0.001 PHE R 377 TRP 0.010 0.001 TRP R 436 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3324) covalent geometry : angle 0.63125 ( 4509) SS BOND : bond 0.00505 ( 6) SS BOND : angle 1.07246 ( 12) hydrogen bonds : bond 0.02820 ( 94) hydrogen bonds : angle 7.03461 ( 240) *********************** 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 96 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.081 Fit side-chains REVERT: R 420 ASP cc_start: 0.8268 (m-30) cc_final: 0.8010 (m-30) outliers start: 18 outliers final: 13 residues processed: 86 average time/residue: 0.0951 time to fit residues: 9.3826 Evaluate side-chains 89 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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 63 VAL 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 430 THR Chi-restraints excluded: chain R residue 483 VAL 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 17 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.097977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.084608 restraints weight = 7624.635| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.83 r_work: 0.3216 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3330 Z= 0.151 Angle : 0.626 7.715 4521 Z= 0.321 Chirality : 0.045 0.155 480 Planarity : 0.005 0.055 588 Dihedral : 5.082 25.707 467 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.29 % Allowed : 15.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.39), residues: 408 helix: -3.85 (0.49), residues: 40 sheet: -1.38 (0.40), residues: 139 loop : -1.36 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 18 TYR 0.021 0.001 TYR R 369 PHE 0.016 0.001 PHE R 377 TRP 0.013 0.002 TRP R 436 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 3324) covalent geometry : angle 0.62377 ( 4509) SS BOND : bond 0.00388 ( 6) SS BOND : angle 1.16653 ( 12) hydrogen bonds : bond 0.02818 ( 94) hydrogen bonds : angle 7.01437 ( 240) *********************** 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 91 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.133 Fit side-chains REVERT: A 86 ARG cc_start: 0.7155 (mmp-170) cc_final: 0.6860 (mmm160) REVERT: R 420 ASP cc_start: 0.8156 (m-30) cc_final: 0.7949 (m-30) outliers start: 15 outliers final: 14 residues processed: 83 average time/residue: 0.1078 time to fit residues: 10.1959 Evaluate side-chains 89 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 63 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 56 THR 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 23 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.0020 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.099052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.085704 restraints weight = 7737.755| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.86 r_work: 0.3237 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3330 Z= 0.122 Angle : 0.608 7.417 4521 Z= 0.312 Chirality : 0.045 0.165 480 Planarity : 0.005 0.054 588 Dihedral : 4.878 25.676 467 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.71 % Allowed : 15.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.39), residues: 408 helix: -3.91 (0.48), residues: 40 sheet: -1.32 (0.40), residues: 141 loop : -1.35 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 18 TYR 0.015 0.001 TYR R 369 PHE 0.008 0.001 PHE A 27 TRP 0.013 0.001 TRP R 436 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3324) covalent geometry : angle 0.60594 ( 4509) SS BOND : bond 0.00434 ( 6) SS BOND : angle 1.09394 ( 12) hydrogen bonds : bond 0.02804 ( 94) hydrogen bonds : angle 6.86831 ( 240) *********************** 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 90 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.119 Fit side-chains REVERT: A 86 ARG cc_start: 0.7174 (mmp-170) cc_final: 0.6829 (mmm160) outliers start: 13 outliers final: 9 residues processed: 84 average time/residue: 0.1053 time to fit residues: 10.0781 Evaluate side-chains 81 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 394 ASN Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 432 CYS Chi-restraints excluded: chain R residue 483 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 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 = 0.097635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084168 restraints weight = 7660.466| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.83 r_work: 0.3203 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3330 Z= 0.183 Angle : 0.680 7.335 4521 Z= 0.347 Chirality : 0.046 0.155 480 Planarity : 0.005 0.063 588 Dihedral : 5.040 25.800 467 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.71 % Allowed : 17.43 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.39), residues: 408 helix: -3.78 (0.49), residues: 39 sheet: -1.22 (0.41), residues: 139 loop : -1.35 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 18 TYR 0.015 0.002 TYR R 369 PHE 0.012 0.001 PHE A 27 TRP 0.010 0.002 TRP R 436 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 3324) covalent geometry : angle 0.67888 ( 4509) SS BOND : bond 0.00474 ( 6) SS BOND : angle 1.13049 ( 12) hydrogen bonds : bond 0.02830 ( 94) hydrogen bonds : angle 6.92263 ( 240) *********************** 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 88 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.133 Fit side-chains REVERT: A 31 ARG cc_start: 0.8036 (ptm160) cc_final: 0.7692 (ptm160) REVERT: A 86 ARG cc_start: 0.7139 (mmp-170) cc_final: 0.6880 (mmm160) outliers start: 13 outliers final: 13 residues processed: 83 average time/residue: 0.1052 time to fit residues: 9.9692 Evaluate side-chains 86 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 394 ASN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085511 restraints weight = 7618.412| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.82 r_work: 0.3224 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3330 Z= 0.146 Angle : 0.657 7.335 4521 Z= 0.335 Chirality : 0.045 0.146 480 Planarity : 0.005 0.070 588 Dihedral : 4.948 25.545 467 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.57 % Allowed : 18.57 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.39), residues: 408 helix: -3.73 (0.50), residues: 40 sheet: -1.21 (0.42), residues: 139 loop : -1.33 (0.41), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 18 TYR 0.012 0.001 TYR R 369 PHE 0.010 0.001 PHE A 27 TRP 0.011 0.001 TRP R 436 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3324) covalent geometry : angle 0.65557 ( 4509) SS BOND : bond 0.00468 ( 6) SS BOND : angle 1.14434 ( 12) hydrogen bonds : bond 0.02647 ( 94) hydrogen bonds : angle 6.80165 ( 240) *********************** 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 84 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.123 Fit side-chains REVERT: A 86 ARG cc_start: 0.7066 (mmp-170) cc_final: 0.6811 (mmm160) REVERT: A 89 ASP cc_start: 0.8567 (m-30) cc_final: 0.8272 (m-30) REVERT: B 4 MET cc_start: 0.8689 (mmm) cc_final: 0.7524 (mmm) outliers start: 9 outliers final: 8 residues processed: 80 average time/residue: 0.1101 time to fit residues: 10.0102 Evaluate side-chains 81 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain B residue 56 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.098764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.085303 restraints weight = 7701.007| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.88 r_work: 0.3226 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3330 Z= 0.146 Angle : 0.666 7.376 4521 Z= 0.340 Chirality : 0.045 0.143 480 Planarity : 0.005 0.086 588 Dihedral : 4.900 25.299 467 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.86 % Allowed : 18.86 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.39), residues: 408 helix: -3.66 (0.53), residues: 39 sheet: -1.12 (0.42), residues: 139 loop : -1.36 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 18 TYR 0.026 0.001 TYR B 49 PHE 0.010 0.001 PHE A 27 TRP 0.011 0.001 TRP R 436 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3324) covalent geometry : angle 0.66480 ( 4509) SS BOND : bond 0.00453 ( 6) SS BOND : angle 1.12333 ( 12) hydrogen bonds : bond 0.02586 ( 94) hydrogen bonds : angle 6.74785 ( 240) ********************** 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: 10 poor density : 74 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7782 (ptm160) REVERT: A 86 ARG cc_start: 0.7088 (mmp-170) cc_final: 0.6823 (mmm160) REVERT: A 89 ASP cc_start: 0.8580 (m-30) cc_final: 0.8281 (m-30) outliers start: 10 outliers final: 9 residues processed: 78 average time/residue: 0.1080 time to fit residues: 9.6801 Evaluate side-chains 83 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain B residue 56 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 16 optimal weight: 0.0010 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3567 r_free = 0.3567 target = 0.099054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.085664 restraints weight = 7655.616| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.85 r_work: 0.3232 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3330 Z= 0.143 Angle : 0.659 7.151 4521 Z= 0.336 Chirality : 0.045 0.141 480 Planarity : 0.005 0.085 588 Dihedral : 4.860 25.343 467 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.86 % Allowed : 18.00 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.40), residues: 408 helix: -3.51 (0.56), residues: 39 sheet: -1.05 (0.43), residues: 139 loop : -1.36 (0.40), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 18 TYR 0.011 0.001 TYR A 103 PHE 0.010 0.001 PHE A 27 TRP 0.011 0.001 TRP R 436 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 3324) covalent geometry : angle 0.65683 ( 4509) SS BOND : bond 0.00460 ( 6) SS BOND : angle 1.12773 ( 12) hydrogen bonds : bond 0.02600 ( 94) hydrogen bonds : angle 6.75408 ( 240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1004.88 seconds wall clock time: 17 minutes 50.33 seconds (1070.33 seconds total)