Starting phenix.real_space_refine on Wed Jul 1 22:09:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wrz_32738/07_2026/7wrz_32738.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wrz_32738/07_2026/7wrz_32738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wrz_32738/07_2026/7wrz_32738.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wrz_32738/07_2026/7wrz_32738.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wrz_32738/07_2026/7wrz_32738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wrz_32738/07_2026/7wrz_32738.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wrz_32738/07_2026/7wrz_32738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wrz_32738/07_2026/7wrz_32738.map" } resolution = 3.26 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= 0.001 sd= 0.055 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 14 5.16 5 C 2077 2.51 5 N 553 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3270 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 927 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 817 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain: "R" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1498 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.14, per 1000 atoms: 0.35 Number of scatterers: 3270 At special positions: 0 Unit cell: (84.24, 64.8, 71.28, 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 14 16.00 O 626 8.00 N 553 7.00 C 2077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 90 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN R 343 " Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 119.0 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 12.8% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.795A pdb=" N SER L 85 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.506A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 370 removed outlier: 3.567A pdb=" N TYR R 369 " --> pdb=" O TYR R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 390 removed outlier: 3.550A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN R 388 " --> pdb=" O THR R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 removed outlier: 4.622A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'R' and resid 438 through 443 Processing helix chain 'R' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.471A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N CYS H 96 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.471A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.539A pdb=" N ILE H 83 " --> pdb=" O VAL H 18 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.596A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU L 72 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.343A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 356 through 358 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 474 103 hydrogen bonds defined for protein. 243 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: 0.48 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1045 1.34 - 1.46: 834 1.46 - 1.57: 1460 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3355 Sorted by residual: bond pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.35e-02 5.49e+03 2.54e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.41e+00 bond pdb=" N ILE R 410 " pdb=" CA ILE R 410 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.22e+00 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.20e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.08e+00 ... (remaining 3350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 4498 2.18 - 4.36: 56 4.36 - 6.55: 4 6.55 - 8.73: 0 8.73 - 10.91: 1 Bond angle restraints: 4559 Sorted by residual: angle pdb=" C PRO R 373 " pdb=" N PHE R 374 " pdb=" CA PHE R 374 " ideal model delta sigma weight residual 121.72 132.63 -10.91 1.54e+00 4.22e-01 5.02e+01 angle pdb=" C VAL R 382 " pdb=" N SER R 383 " pdb=" CA SER R 383 " ideal model delta sigma weight residual 120.49 114.45 6.04 1.42e+00 4.96e-01 1.81e+01 angle pdb=" N PHE R 374 " pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " ideal model delta sigma weight residual 110.79 114.90 -4.11 1.63e+00 3.76e-01 6.35e+00 angle pdb=" CA PHE R 374 " pdb=" CB PHE R 374 " pdb=" CG PHE R 374 " ideal model delta sigma weight residual 113.80 116.26 -2.46 1.00e+00 1.00e+00 6.06e+00 angle pdb=" N TRP L 96 " pdb=" CA TRP L 96 " pdb=" C TRP L 96 " ideal model delta sigma weight residual 109.81 114.95 -5.14 2.21e+00 2.05e-01 5.42e+00 ... (remaining 4554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 1738 15.87 - 31.74: 164 31.74 - 47.61: 31 47.61 - 63.48: 9 63.48 - 79.34: 6 Dihedral angle restraints: 1948 sinusoidal: 752 harmonic: 1196 Sorted by residual: dihedral pdb=" CA TRP L 96 " pdb=" C TRP L 96 " pdb=" N PRO L 97 " pdb=" CA PRO L 97 " ideal model delta harmonic sigma weight residual 180.00 134.00 46.00 0 5.00e+00 4.00e-02 8.47e+01 dihedral pdb=" CA PRO R 373 " pdb=" C PRO R 373 " pdb=" N PHE R 374 " pdb=" CA PHE R 374 " ideal model delta harmonic sigma weight residual 180.00 159.88 20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ASP H 104 " pdb=" C ASP H 104 " pdb=" N TYR H 105 " pdb=" CA TYR H 105 " ideal model delta harmonic sigma weight residual -180.00 -164.30 -15.70 0 5.00e+00 4.00e-02 9.86e+00 ... (remaining 1945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 310 0.034 - 0.067: 124 0.067 - 0.101: 36 0.101 - 0.134: 21 0.134 - 0.168: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN R 343 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CB ILE H 34 " pdb=" CA ILE H 34 " pdb=" CG1 ILE H 34 " pdb=" CG2 ILE H 34 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL H 2 " pdb=" N VAL H 2 " pdb=" C VAL H 2 " pdb=" CB VAL H 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 489 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP L 96 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO L 97 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO L 97 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO L 97 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 41 " -0.026 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO L 42 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 42 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 42 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO L 46 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " -0.018 5.00e-02 4.00e+02 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 243 2.74 - 3.28: 3077 3.28 - 3.82: 5219 3.82 - 4.36: 6717 4.36 - 4.90: 11797 Nonbonded interactions: 27053 Sorted by model distance: nonbonded pdb=" O ASN R 439 " pdb=" OG SER R 443 " model vdw 2.201 3.040 nonbonded pdb=" NH1 ARG L 56 " pdb=" O ILE L 60 " model vdw 2.301 3.120 nonbonded pdb=" OD1 ASP R 442 " pdb=" OH TYR R 451 " model vdw 2.312 3.040 nonbonded pdb=" OH TYR R 369 " pdb=" O PRO R 384 " model vdw 2.314 3.040 nonbonded pdb=" O ASP R 442 " pdb=" ND2 ASN R 448 " model vdw 2.367 3.120 ... (remaining 27048 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: 4.100 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: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.410 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.004 0.029 3363 Z= 0.169 Angle : 0.619 10.910 4577 Z= 0.355 Chirality : 0.044 0.168 492 Planarity : 0.005 0.066 587 Dihedral : 13.698 79.345 1170 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.03 (0.40), residues: 406 helix: -3.69 (0.60), residues: 27 sheet: -0.30 (0.41), residues: 152 loop : -0.47 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 357 TYR 0.015 0.001 TYR L 93 PHE 0.012 0.001 PHE R 347 TRP 0.006 0.001 TRP R 436 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 3355) covalent geometry : angle 0.61825 / 0.36 ( 4559) SS BOND : bond 0.00122 / 0.06 ( 6) SS BOND : angle 0.37689 / 0.19 ( 12) hydrogen bonds : bond 0.24946 / 17.03 ( 99) hydrogen bonds : angle 11.75452 / 8.16 ( 243) link_BETA1-4 : bond 0.00073 / 0.04 ( 1) link_BETA1-4 : angle 1.24355 / 0.64 ( 3) link_NAG-ASN : bond 0.00197 / 0.10 ( 1) link_NAG-ASN : angle 1.24696 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 GLU cc_start: 0.7412 (pm20) cc_final: 0.7186 (pm20) REVERT: L 84 ASP cc_start: 0.8096 (m-30) cc_final: 0.7859 (m-30) REVERT: R 340 GLU cc_start: 0.8305 (mp0) cc_final: 0.8014 (mm-30) REVERT: R 356 LYS cc_start: 0.9212 (mttp) cc_final: 0.8991 (mttm) REVERT: R 369 TYR cc_start: 0.7160 (m-80) cc_final: 0.6940 (m-80) REVERT: R 483 VAL cc_start: 0.7956 (t) cc_final: 0.7741 (m) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0950 time to fit residues: 8.0624 Evaluate side-chains 62 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 95 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 = 0.3145 r_free = 0.3145 target = 0.106033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.088378 restraints weight = 4857.548| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.86 r_work: 0.3143 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3363 Z= 0.195 Angle : 0.581 5.724 4577 Z= 0.306 Chirality : 0.046 0.158 492 Planarity : 0.005 0.067 587 Dihedral : 5.070 44.989 460 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 1.44 % Allowed : 9.48 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.14 (0.39), residues: 406 helix: -3.56 (0.56), residues: 33 sheet: -0.42 (0.39), residues: 154 loop : -0.43 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 357 TYR 0.015 0.001 TYR L 93 PHE 0.016 0.001 PHE R 347 TRP 0.012 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 3355) covalent geometry : angle 0.57969 / 0.31 ( 4559) SS BOND : bond 0.00254 / 0.13 ( 6) SS BOND : angle 0.66174 / 0.34 ( 12) hydrogen bonds : bond 0.04329 / 2.77 ( 99) hydrogen bonds : angle 7.57259 / 5.24 ( 243) link_BETA1-4 : bond 0.00205 / 0.11 ( 1) link_BETA1-4 : angle 1.04528 / 0.58 ( 3) link_NAG-ASN : bond 0.00072 / 0.04 ( 1) link_NAG-ASN : angle 1.28000 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: R 420 ASP cc_start: 0.8941 (m-30) cc_final: 0.8535 (m-30) outliers start: 5 outliers final: 5 residues processed: 67 average time/residue: 0.0727 time to fit residues: 5.6669 Evaluate side-chains 68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 445 VAL Chi-restraints excluded: chain R residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 95 ASN R 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.104326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.087102 restraints weight = 4766.715| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.83 r_work: 0.2759 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3363 Z= 0.193 Angle : 0.562 5.984 4577 Z= 0.293 Chirality : 0.046 0.151 492 Planarity : 0.005 0.067 587 Dihedral : 5.045 45.272 460 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.67 % Favored : 94.09 % Rotamer: Outliers : 1.72 % Allowed : 13.79 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.26 (0.40), residues: 406 helix: -3.80 (0.49), residues: 33 sheet: -0.59 (0.39), residues: 153 loop : -0.40 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.012 0.001 PHE R 347 TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 ( 3355) covalent geometry : angle 0.56059 / 0.29 ( 4559) SS BOND : bond 0.00231 / 0.11 ( 6) SS BOND : angle 0.65978 / 0.33 ( 12) hydrogen bonds : bond 0.03860 / 2.49 ( 99) hydrogen bonds : angle 7.04083 / 4.84 ( 243) link_BETA1-4 : bond 0.00209 / 0.11 ( 1) link_BETA1-4 : angle 1.26334 / 0.67 ( 3) link_NAG-ASN : bond 0.00093 / 0.05 ( 1) link_NAG-ASN : angle 1.18657 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8579 (mp10) cc_final: 0.7724 (mp10) REVERT: R 420 ASP cc_start: 0.8985 (m-30) cc_final: 0.8415 (m-30) REVERT: R 478 LYS cc_start: 0.7465 (mmtt) cc_final: 0.7263 (mmtp) outliers start: 6 outliers final: 5 residues processed: 66 average time/residue: 0.0942 time to fit residues: 7.2864 Evaluate side-chains 65 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 445 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 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3125 r_free = 0.3125 target = 0.104929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.087776 restraints weight = 4693.671| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.84 r_work: 0.2776 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3363 Z= 0.151 Angle : 0.529 6.183 4577 Z= 0.275 Chirality : 0.044 0.145 492 Planarity : 0.005 0.067 587 Dihedral : 4.913 44.288 460 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.19 % Favored : 95.57 % Rotamer: Outliers : 2.87 % Allowed : 14.37 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.14 (0.40), residues: 406 helix: -3.80 (0.47), residues: 33 sheet: -0.52 (0.40), residues: 152 loop : -0.30 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.009 0.001 PHE R 347 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 3355) covalent geometry : angle 0.52732 / 0.28 ( 4559) SS BOND : bond 0.00303 / 0.11 ( 6) SS BOND : angle 0.67648 / 0.34 ( 12) hydrogen bonds : bond 0.03361 / 2.15 ( 99) hydrogen bonds : angle 6.77570 / 4.62 ( 243) link_BETA1-4 : bond 0.00309 / 0.16 ( 1) link_BETA1-4 : angle 1.32883 / 0.70 ( 3) link_NAG-ASN : bond 0.00023 / 0.01 ( 1) link_NAG-ASN : angle 1.04071 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8584 (mp10) cc_final: 0.7775 (mp10) REVERT: R 420 ASP cc_start: 0.9002 (m-30) cc_final: 0.8397 (m-30) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.0927 time to fit residues: 7.2813 Evaluate side-chains 68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 445 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 35 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3101 r_free = 0.3101 target = 0.103073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.086047 restraints weight = 4729.534| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.83 r_work: 0.2748 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3363 Z= 0.192 Angle : 0.552 6.333 4577 Z= 0.287 Chirality : 0.046 0.175 492 Planarity : 0.005 0.067 587 Dihedral : 4.976 44.995 460 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.67 % Favored : 94.09 % Rotamer: Outliers : 3.45 % Allowed : 14.94 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.16 (0.40), residues: 406 helix: -3.86 (0.46), residues: 33 sheet: -0.46 (0.40), residues: 152 loop : -0.36 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.010 0.001 PHE R 347 TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 ( 3355) covalent geometry : angle 0.54981 / 0.29 ( 4559) SS BOND : bond 0.00189 / 0.10 ( 6) SS BOND : angle 0.79561 / 0.38 ( 12) hydrogen bonds : bond 0.03440 / 2.24 ( 99) hydrogen bonds : angle 6.75893 / 4.60 ( 243) link_BETA1-4 : bond 0.00156 / 0.08 ( 1) link_BETA1-4 : angle 1.36292 / 0.72 ( 3) link_NAG-ASN : bond 0.00125 / 0.07 ( 1) link_NAG-ASN : angle 1.17719 / 0.63 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8573 (mp10) cc_final: 0.7770 (mp10) REVERT: R 369 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6591 (m-80) REVERT: R 420 ASP cc_start: 0.9016 (m-30) cc_final: 0.8392 (m-30) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.0998 time to fit residues: 7.8047 Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 445 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 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 27 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.087784 restraints weight = 4659.974| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.84 r_work: 0.2770 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3363 Z= 0.141 Angle : 0.531 6.302 4577 Z= 0.278 Chirality : 0.045 0.156 492 Planarity : 0.005 0.067 587 Dihedral : 4.864 44.622 460 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.94 % Favored : 95.81 % Rotamer: Outliers : 4.02 % Allowed : 14.94 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.04 (0.41), residues: 406 helix: -4.05 (0.51), residues: 26 sheet: -0.30 (0.41), residues: 152 loop : -0.45 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.007 0.001 PHE R 347 TRP 0.007 0.001 TRP H 50 HIS 0.001 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 3355) covalent geometry : angle 0.52874 / 0.28 ( 4559) SS BOND : bond 0.00184 / 0.08 ( 6) SS BOND : angle 0.76029 / 0.36 ( 12) hydrogen bonds : bond 0.03159 / 2.05 ( 99) hydrogen bonds : angle 6.62923 / 4.48 ( 243) link_BETA1-4 : bond 0.00238 / 0.13 ( 1) link_BETA1-4 : angle 1.37737 / 0.72 ( 3) link_NAG-ASN : bond 0.00005 / 0.00 ( 1) link_NAG-ASN : angle 1.00174 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8538 (mp10) cc_final: 0.7792 (mp10) REVERT: R 369 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6537 (m-80) REVERT: R 420 ASP cc_start: 0.9001 (m-30) cc_final: 0.8356 (m-30) outliers start: 14 outliers final: 10 residues processed: 67 average time/residue: 0.0878 time to fit residues: 6.9378 Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 445 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 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.087842 restraints weight = 4792.687| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.86 r_work: 0.2778 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3363 Z= 0.141 Angle : 0.522 6.147 4577 Z= 0.274 Chirality : 0.045 0.194 492 Planarity : 0.005 0.067 587 Dihedral : 4.806 44.416 460 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.17 % Favored : 94.58 % Rotamer: Outliers : 3.45 % Allowed : 15.52 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.01 (0.41), residues: 406 helix: -4.00 (0.52), residues: 26 sheet: -0.25 (0.42), residues: 152 loop : -0.46 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.007 0.001 PHE R 347 TRP 0.007 0.001 TRP H 50 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 3355) covalent geometry : angle 0.51999 / 0.27 ( 4559) SS BOND : bond 0.00186 / 0.08 ( 6) SS BOND : angle 0.76692 / 0.36 ( 12) hydrogen bonds : bond 0.03151 / 2.05 ( 99) hydrogen bonds : angle 6.60061 / 4.44 ( 243) link_BETA1-4 : bond 0.00227 / 0.12 ( 1) link_BETA1-4 : angle 1.38909 / 0.72 ( 3) link_NAG-ASN : bond 0.00010 / 0.01 ( 1) link_NAG-ASN : angle 0.99730 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8519 (mp10) cc_final: 0.7960 (mp10) REVERT: R 369 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6666 (m-80) REVERT: R 420 ASP cc_start: 0.8986 (m-30) cc_final: 0.8402 (m-30) REVERT: R 494 SER cc_start: 0.9094 (m) cc_final: 0.8772 (p) outliers start: 12 outliers final: 11 residues processed: 65 average time/residue: 0.0829 time to fit residues: 6.3937 Evaluate side-chains 71 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 445 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 17 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.103079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.085772 restraints weight = 4824.109| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.88 r_work: 0.2748 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3363 Z= 0.193 Angle : 0.553 6.293 4577 Z= 0.288 Chirality : 0.046 0.204 492 Planarity : 0.005 0.068 587 Dihedral : 4.912 45.160 460 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.91 % Favored : 93.84 % Rotamer: Outliers : 3.74 % Allowed : 15.80 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -1.06 (0.41), residues: 406 helix: -4.01 (0.53), residues: 26 sheet: -0.28 (0.41), residues: 152 loop : -0.49 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.009 0.001 PHE R 374 TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 ( 3355) covalent geometry : angle 0.54975 / 0.29 ( 4559) SS BOND : bond 0.00252 / 0.11 ( 6) SS BOND : angle 0.89689 / 0.42 ( 12) hydrogen bonds : bond 0.03275 / 2.14 ( 99) hydrogen bonds : angle 6.60474 / 4.44 ( 243) link_BETA1-4 : bond 0.00171 / 0.09 ( 1) link_BETA1-4 : angle 1.42999 / 0.75 ( 3) link_NAG-ASN : bond 0.00143 / 0.08 ( 1) link_NAG-ASN : angle 1.17950 / 0.64 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8521 (mp10) cc_final: 0.7966 (mp10) REVERT: R 369 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6698 (m-80) REVERT: R 420 ASP cc_start: 0.9027 (m-30) cc_final: 0.8351 (m-30) REVERT: R 494 SER cc_start: 0.9181 (m) cc_final: 0.8890 (p) outliers start: 13 outliers final: 11 residues processed: 67 average time/residue: 0.0638 time to fit residues: 5.0434 Evaluate side-chains 71 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 406 GLU Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 445 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 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.088186 restraints weight = 4748.220| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.86 r_work: 0.2778 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3363 Z= 0.129 Angle : 0.515 6.042 4577 Z= 0.269 Chirality : 0.044 0.181 492 Planarity : 0.005 0.067 587 Dihedral : 4.783 44.386 460 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.19 % Favored : 95.57 % Rotamer: Outliers : 3.16 % Allowed : 16.38 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.98 (0.41), residues: 406 helix: -3.92 (0.54), residues: 26 sheet: -0.23 (0.42), residues: 152 loop : -0.45 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.007 0.001 PHE R 347 TRP 0.006 0.001 TRP H 50 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 3355) covalent geometry : angle 0.51278 / 0.27 ( 4559) SS BOND : bond 0.00191 / 0.08 ( 6) SS BOND : angle 0.79811 / 0.38 ( 12) hydrogen bonds : bond 0.03062 / 1.98 ( 99) hydrogen bonds : angle 6.50449 / 4.37 ( 243) link_BETA1-4 : bond 0.00237 / 0.12 ( 1) link_BETA1-4 : angle 1.39730 / 0.72 ( 3) link_NAG-ASN : bond 0.00020 / 0.01 ( 1) link_NAG-ASN : angle 0.98577 / 0.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8499 (mp10) cc_final: 0.7693 (mp10) REVERT: L 84 ASP cc_start: 0.8331 (m-30) cc_final: 0.7734 (m-30) REVERT: R 369 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: R 420 ASP cc_start: 0.8977 (m-30) cc_final: 0.8329 (m-30) REVERT: R 494 SER cc_start: 0.9137 (m) cc_final: 0.8806 (p) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.0764 time to fit residues: 5.9045 Evaluate side-chains 67 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 445 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 12 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 21 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.087210 restraints weight = 4666.082| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.83 r_work: 0.2766 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3363 Z= 0.157 Angle : 0.533 6.186 4577 Z= 0.278 Chirality : 0.045 0.191 492 Planarity : 0.005 0.067 587 Dihedral : 4.799 44.653 460 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 2.87 % Allowed : 17.82 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.98 (0.41), residues: 406 helix: -3.86 (0.56), residues: 26 sheet: -0.25 (0.42), residues: 152 loop : -0.44 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.007 0.001 PHE R 374 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 3355) covalent geometry : angle 0.53101 / 0.28 ( 4559) SS BOND : bond 0.00191 / 0.09 ( 6) SS BOND : angle 0.80777 / 0.38 ( 12) hydrogen bonds : bond 0.03110 / 2.03 ( 99) hydrogen bonds : angle 6.50171 / 4.37 ( 243) link_BETA1-4 : bond 0.00210 / 0.11 ( 1) link_BETA1-4 : angle 1.42723 / 0.74 ( 3) link_NAG-ASN : bond 0.00028 / 0.01 ( 1) link_NAG-ASN : angle 1.01440 / 0.55 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: L 81 GLN cc_start: 0.8474 (mp10) cc_final: 0.7807 (mp10) REVERT: L 84 ASP cc_start: 0.8377 (m-30) cc_final: 0.7860 (m-30) REVERT: R 369 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: R 420 ASP cc_start: 0.8969 (m-30) cc_final: 0.8297 (m-30) REVERT: R 494 SER cc_start: 0.9116 (m) cc_final: 0.8796 (p) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.0855 time to fit residues: 6.4068 Evaluate side-chains 68 residues out of total 349 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain R residue 369 TYR Chi-restraints excluded: chain R residue 405 ASP Chi-restraints excluded: chain R residue 427 ASP Chi-restraints excluded: chain R residue 445 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 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.087310 restraints weight = 4753.323| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.86 r_work: 0.2773 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3363 Z= 0.162 Angle : 0.534 6.089 4577 Z= 0.278 Chirality : 0.045 0.187 492 Planarity : 0.005 0.067 587 Dihedral : 4.834 44.863 460 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.17 % Favored : 94.58 % Rotamer: Outliers : 3.16 % Allowed : 17.53 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 5.26 % 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: -0.99 (0.41), residues: 406 helix: -3.87 (0.56), residues: 26 sheet: -0.27 (0.42), residues: 152 loop : -0.44 (0.42), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 357 TYR 0.014 0.001 TYR L 93 PHE 0.007 0.001 PHE R 374 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 ( 3355) covalent geometry : angle 0.53113 / 0.28 ( 4559) SS BOND : bond 0.00207 / 0.09 ( 6) SS BOND : angle 0.80423 / 0.38 ( 12) hydrogen bonds : bond 0.03129 / 2.03 ( 99) hydrogen bonds : angle 6.50571 / 4.37 ( 243) link_BETA1-4 : bond 0.00224 / 0.12 ( 1) link_BETA1-4 : angle 1.42678 / 0.74 ( 3) link_NAG-ASN : bond 0.00053 / 0.03 ( 1) link_NAG-ASN : angle 1.05468 / 0.57 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1052.41 seconds wall clock time: 18 minutes 44.31 seconds (1124.31 seconds total)