Starting phenix.real_space_refine on Tue Mar 3 11:36:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wb5_32395/03_2026/7wb5_32395.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wb5_32395/03_2026/7wb5_32395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wb5_32395/03_2026/7wb5_32395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wb5_32395/03_2026/7wb5_32395.map" model { file = "/net/cci-nas-00/data/ceres_data/7wb5_32395/03_2026/7wb5_32395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wb5_32395/03_2026/7wb5_32395.cif" } resolution = 3.7 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= 0.022 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 2077 2.51 5 N 533 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 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: 3256 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "R" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.92, per 1000 atoms: 0.28 Number of scatterers: 3256 At special positions: 0 Unit cell: (72.36, 88.56, 72.36, 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 631 8.00 N 533 7.00 C 2077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.02 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " NAG-ASN " NAG A 1 " - " ASN R 343 " Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 109.9 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 12 sheets defined 4.4% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'R' and resid 349 through 353 Processing helix chain 'R' and resid 364 through 370 removed outlier: 4.598A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.682A pdb=" N LYS H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'H' and resid 46 through 47 removed outlier: 3.906A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51 removed outlier: 3.533A pdb=" N TRP H 50 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 68 through 70 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.846A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU L 73 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.595A pdb=" N LEU L 11 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.572A pdb=" N GLN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 354 through 358 removed outlier: 3.884A pdb=" N ILE R 434 " --> pdb=" O VAL R 511 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS R 432 " --> pdb=" O LEU R 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474 73 hydrogen bonds defined for protein. 171 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: 0.45 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 734 1.33 - 1.45: 857 1.45 - 1.57: 1735 1.57 - 1.69: 1 1.69 - 1.82: 18 Bond restraints: 3345 Sorted by residual: bond pdb=" CA SER R 438 " pdb=" CB SER R 438 " ideal model delta sigma weight residual 1.528 1.475 0.053 1.35e-02 5.49e+03 1.53e+01 bond pdb=" CA SER R 349 " pdb=" CB SER R 349 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.64e-02 3.72e+03 1.43e+01 bond pdb=" N LEU R 452 " pdb=" CA LEU R 452 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.22e-02 6.72e+03 1.23e+01 bond pdb=" N VAL R 433 " pdb=" CA VAL R 433 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.07e+01 bond pdb=" N LYS R 378 " pdb=" CA LYS R 378 " ideal model delta sigma weight residual 1.457 1.499 -0.041 1.29e-02 6.01e+03 1.03e+01 ... (remaining 3340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 4160 2.59 - 5.17: 364 5.17 - 7.76: 19 7.76 - 10.34: 3 10.34 - 12.93: 2 Bond angle restraints: 4548 Sorted by residual: angle pdb=" CA PRO L 80 " pdb=" N PRO L 80 " pdb=" CD PRO L 80 " ideal model delta sigma weight residual 112.00 99.07 12.93 1.40e+00 5.10e-01 8.52e+01 angle pdb=" CA TRP R 436 " pdb=" CB TRP R 436 " pdb=" CG TRP R 436 " ideal model delta sigma weight residual 113.60 123.83 -10.23 1.90e+00 2.77e-01 2.90e+01 angle pdb=" CA PHE R 400 " pdb=" CB PHE R 400 " pdb=" CG PHE R 400 " ideal model delta sigma weight residual 113.80 118.30 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N PRO L 80 " pdb=" CD PRO L 80 " pdb=" CG PRO L 80 " ideal model delta sigma weight residual 103.20 96.90 6.30 1.50e+00 4.44e-01 1.77e+01 angle pdb=" N LEU R 387 " pdb=" CA LEU R 387 " pdb=" C LEU R 387 " ideal model delta sigma weight residual 114.75 109.56 5.19 1.26e+00 6.30e-01 1.69e+01 ... (remaining 4543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 1718 21.52 - 43.04: 173 43.04 - 64.55: 66 64.55 - 86.07: 12 86.07 - 107.59: 12 Dihedral angle restraints: 1981 sinusoidal: 801 harmonic: 1180 Sorted by residual: dihedral pdb=" CA VAL L 29 " pdb=" C VAL L 29 " pdb=" N SER L 30 " pdb=" CA SER L 30 " ideal model delta harmonic sigma weight residual 180.00 -139.90 -40.10 0 5.00e+00 4.00e-02 6.43e+01 dihedral pdb=" CA PHE H 106 " pdb=" C PHE H 106 " pdb=" N ASP H 107 " pdb=" CA ASP H 107 " ideal model delta harmonic sigma weight residual 180.00 -146.68 -33.32 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 136.78 -43.78 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 1978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 417 0.119 - 0.238: 63 0.238 - 0.356: 5 0.356 - 0.475: 0 0.475 - 0.593: 2 Chirality restraints: 487 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.89e+01 chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.29e+01 chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN R 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.81e+00 ... (remaining 484 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.304 2.00e-02 2.50e+03 2.62e-01 8.61e+02 pdb=" C7 NAG A 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " 0.009 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.453 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " -0.292 2.00e-02 2.50e+03 2.51e-01 7.91e+02 pdb=" C7 NAG A 1 " 0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " 0.443 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN L 79 " -0.111 5.00e-02 4.00e+02 1.57e-01 3.92e+01 pdb=" N PRO L 80 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO L 80 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO L 80 " -0.076 5.00e-02 4.00e+02 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 281 2.73 - 3.27: 3255 3.27 - 3.82: 5356 3.82 - 4.36: 6706 4.36 - 4.90: 11080 Nonbonded interactions: 26678 Sorted by model distance: nonbonded pdb=" O ILE L 21 " pdb=" OG1 THR L 72 " model vdw 2.188 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.216 3.040 nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 113 " model vdw 2.319 3.040 nonbonded pdb=" OG SER L 26 " pdb=" OE1 GLN L 27 " model vdw 2.405 3.040 nonbonded pdb=" O VAL H 76 " pdb=" OG SER H 77 " model vdw 2.421 3.040 ... (remaining 26673 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 group one per residue 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: 5.910 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.920 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.011 0.132 3353 Z= 0.659 Angle : 1.420 12.925 4567 Z= 0.928 Chirality : 0.090 0.593 487 Planarity : 0.018 0.262 581 Dihedral : 21.949 107.591 1220 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 2.24 % Allowed : 18.16 % Favored : 79.60 % Rotamer: Outliers : 14.00 % Allowed : 7.43 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % 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: -4.90 (0.36), residues: 402 helix: -4.22 (0.64), residues: 21 sheet: -3.58 (0.39), residues: 121 loop : -3.14 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 61 TYR 0.024 0.003 TYR L 49 PHE 0.023 0.003 PHE R 400 TRP 0.092 0.006 TRP H 109 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.01062 ( 3345) covalent geometry : angle 1.40708 ( 4548) SS BOND : bond 0.00729 ( 5) SS BOND : angle 2.86471 ( 10) hydrogen bonds : bond 0.24913 ( 63) hydrogen bonds : angle 11.58444 ( 171) link_BETA1-4 : bond 0.00673 ( 2) link_BETA1-4 : angle 4.14677 ( 6) link_NAG-ASN : bond 0.02467 ( 1) link_NAG-ASN : angle 2.58754 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.124 Fit side-chains revert: symmetry clash REVERT: H 83 ILE cc_start: 0.9173 (tt) cc_final: 0.8932 (tt) REVERT: L 74 THR cc_start: 0.7091 (m) cc_final: 0.6571 (m) REVERT: L 79 GLN cc_start: 0.8296 (mp10) cc_final: 0.7806 (mp10) REVERT: R 369 TYR cc_start: 0.7979 (t80) cc_final: 0.7755 (t80) REVERT: R 387 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8498 (tt) REVERT: R 454 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7653 (mtp-110) REVERT: R 493 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7989 (tm-30) outliers start: 49 outliers final: 12 residues processed: 150 average time/residue: 0.0754 time to fit residues: 13.2896 Evaluate side-chains 120 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 422 ASN Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 454 ARG Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 493 GLN Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.139006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115464 restraints weight = 5182.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.118186 restraints weight = 3271.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.119987 restraints weight = 2405.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121271 restraints weight = 1958.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122049 restraints weight = 1704.203| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3353 Z= 0.199 Angle : 0.854 8.972 4567 Z= 0.430 Chirality : 0.051 0.193 487 Planarity : 0.007 0.085 581 Dihedral : 17.915 94.171 544 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.44 % Favored : 88.06 % Rotamer: Outliers : 7.71 % Allowed : 18.29 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.50 (0.36), residues: 402 helix: -3.46 (0.76), residues: 21 sheet: -3.12 (0.43), residues: 114 loop : -3.05 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 18 TYR 0.020 0.002 TYR L 49 PHE 0.026 0.002 PHE R 515 TRP 0.050 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 3345) covalent geometry : angle 0.84070 ( 4548) SS BOND : bond 0.00445 ( 5) SS BOND : angle 1.44574 ( 10) hydrogen bonds : bond 0.04558 ( 63) hydrogen bonds : angle 7.24444 ( 171) link_BETA1-4 : bond 0.00558 ( 2) link_BETA1-4 : angle 3.85126 ( 6) link_NAG-ASN : bond 0.00229 ( 1) link_NAG-ASN : angle 1.76109 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8456 (m-80) cc_final: 0.8047 (m-10) REVERT: L 79 GLN cc_start: 0.8405 (mp10) cc_final: 0.7687 (mp10) REVERT: L 100 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7127 (tm-30) REVERT: R 387 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8385 (tt) REVERT: R 408 ARG cc_start: 0.8843 (mtm110) cc_final: 0.8132 (ptm160) REVERT: R 414 GLN cc_start: 0.7951 (tp40) cc_final: 0.7314 (tp-100) REVERT: R 493 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: R 516 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7455 (pp20) outliers start: 27 outliers final: 19 residues processed: 121 average time/residue: 0.0766 time to fit residues: 10.8159 Evaluate side-chains 120 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 422 ASN Chi-restraints excluded: chain R residue 425 LEU Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 493 GLN Chi-restraints excluded: chain R residue 495 TYR Chi-restraints excluded: chain R residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 0.0000 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 overall best weight: 0.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 82 GLN ** L 89 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.141904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.117513 restraints weight = 5005.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120449 restraints weight = 3087.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122372 restraints weight = 2250.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123721 restraints weight = 1820.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.124224 restraints weight = 1576.995| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3353 Z= 0.148 Angle : 0.756 7.846 4567 Z= 0.373 Chirality : 0.049 0.228 487 Planarity : 0.006 0.078 581 Dihedral : 14.780 80.660 538 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.45 % Favored : 89.05 % Rotamer: Outliers : 7.14 % Allowed : 19.71 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.05 (0.37), residues: 402 helix: -3.53 (0.79), residues: 21 sheet: -2.45 (0.46), residues: 111 loop : -2.90 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 408 TYR 0.020 0.001 TYR H 105 PHE 0.016 0.001 PHE R 515 TRP 0.038 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 3345) covalent geometry : angle 0.74048 ( 4548) SS BOND : bond 0.00306 ( 5) SS BOND : angle 1.09414 ( 10) hydrogen bonds : bond 0.03659 ( 63) hydrogen bonds : angle 6.56600 ( 171) link_BETA1-4 : bond 0.00953 ( 2) link_BETA1-4 : angle 4.04910 ( 6) link_NAG-ASN : bond 0.00296 ( 1) link_NAG-ASN : angle 1.40737 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8314 (m-80) cc_final: 0.8027 (m-10) REVERT: H 90 ASP cc_start: 0.7981 (m-30) cc_final: 0.7578 (m-30) REVERT: L 79 GLN cc_start: 0.8441 (mp10) cc_final: 0.8034 (mp10) REVERT: L 100 GLN cc_start: 0.7477 (tm-30) cc_final: 0.7168 (tm-30) REVERT: R 386 LYS cc_start: 0.4593 (pttt) cc_final: 0.3216 (pttt) REVERT: R 387 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8336 (tt) REVERT: R 493 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7462 (tm-30) outliers start: 25 outliers final: 19 residues processed: 123 average time/residue: 0.0696 time to fit residues: 10.2535 Evaluate side-chains 118 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 414 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.140688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116655 restraints weight = 5039.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119495 restraints weight = 3122.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121382 restraints weight = 2274.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.122569 restraints weight = 1844.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123452 restraints weight = 1608.916| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3353 Z= 0.184 Angle : 0.757 8.292 4567 Z= 0.378 Chirality : 0.048 0.244 487 Planarity : 0.006 0.077 581 Dihedral : 12.394 67.214 524 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.70 % Favored : 90.05 % Rotamer: Outliers : 8.57 % Allowed : 22.00 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.11 (0.37), residues: 402 helix: -3.87 (0.76), residues: 21 sheet: -2.59 (0.44), residues: 125 loop : -2.82 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.021 0.002 TYR R 380 PHE 0.011 0.002 PHE R 515 TRP 0.047 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 3345) covalent geometry : angle 0.74078 ( 4548) SS BOND : bond 0.00256 ( 5) SS BOND : angle 1.26979 ( 10) hydrogen bonds : bond 0.03622 ( 63) hydrogen bonds : angle 6.13731 ( 171) link_BETA1-4 : bond 0.00983 ( 2) link_BETA1-4 : angle 4.08081 ( 6) link_NAG-ASN : bond 0.00398 ( 1) link_NAG-ASN : angle 1.03296 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.8932 (tpp) cc_final: 0.8677 (tpp) REVERT: H 60 TYR cc_start: 0.8422 (m-80) cc_final: 0.8087 (m-10) REVERT: L 62 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7030 (p90) REVERT: L 79 GLN cc_start: 0.8432 (mp10) cc_final: 0.8053 (mp10) REVERT: L 100 GLN cc_start: 0.7474 (tm-30) cc_final: 0.7177 (tm-30) REVERT: R 386 LYS cc_start: 0.4366 (pttt) cc_final: 0.3125 (pttt) REVERT: R 387 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8394 (tt) REVERT: R 408 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8359 (ptm160) REVERT: R 466 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7127 (ptm-80) REVERT: R 493 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7480 (tm-30) outliers start: 30 outliers final: 20 residues processed: 118 average time/residue: 0.0698 time to fit residues: 9.6988 Evaluate side-chains 113 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 436 TRP Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.143224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120162 restraints weight = 5070.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122634 restraints weight = 4070.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123283 restraints weight = 2838.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.124044 restraints weight = 2409.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124199 restraints weight = 2292.945| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3353 Z= 0.153 Angle : 0.750 10.967 4567 Z= 0.366 Chirality : 0.047 0.212 487 Planarity : 0.006 0.078 581 Dihedral : 10.458 50.329 523 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.46 % Favored : 91.29 % Rotamer: Outliers : 6.86 % Allowed : 25.14 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.95 (0.37), residues: 402 helix: -3.22 (0.89), residues: 19 sheet: -2.52 (0.46), residues: 115 loop : -2.77 (0.33), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 403 TYR 0.022 0.002 TYR R 380 PHE 0.021 0.002 PHE R 392 TRP 0.030 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 3345) covalent geometry : angle 0.73537 ( 4548) SS BOND : bond 0.00414 ( 5) SS BOND : angle 1.07251 ( 10) hydrogen bonds : bond 0.03389 ( 63) hydrogen bonds : angle 5.99141 ( 171) link_BETA1-4 : bond 0.00908 ( 2) link_BETA1-4 : angle 4.01251 ( 6) link_NAG-ASN : bond 0.00260 ( 1) link_NAG-ASN : angle 0.89228 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.121 Fit side-chains REVERT: H 43 GLN cc_start: 0.7091 (mp10) cc_final: 0.6681 (mp10) REVERT: H 60 TYR cc_start: 0.8387 (m-80) cc_final: 0.8126 (m-10) REVERT: L 62 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7105 (p90) REVERT: L 79 GLN cc_start: 0.8493 (mp10) cc_final: 0.8033 (mp10) REVERT: L 100 GLN cc_start: 0.7506 (tm-30) cc_final: 0.7232 (tm-30) REVERT: R 386 LYS cc_start: 0.4236 (pttt) cc_final: 0.3075 (pttt) REVERT: R 387 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8304 (tt) REVERT: R 409 GLN cc_start: 0.8418 (mt0) cc_final: 0.8177 (mt0) REVERT: R 493 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7511 (tm-30) REVERT: R 508 TYR cc_start: 0.6317 (m-80) cc_final: 0.6039 (m-80) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 0.0729 time to fit residues: 10.1074 Evaluate side-chains 113 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** 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 = 0.3803 r_free = 0.3803 target = 0.141123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.117341 restraints weight = 5088.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121052 restraints weight = 3993.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121946 restraints weight = 2434.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122155 restraints weight = 2021.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122419 restraints weight = 2009.934| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3353 Z= 0.173 Angle : 0.751 9.822 4567 Z= 0.368 Chirality : 0.047 0.153 487 Planarity : 0.006 0.077 581 Dihedral : 9.399 52.908 521 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.96 % Favored : 90.80 % Rotamer: Outliers : 7.14 % Allowed : 24.29 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.83 (0.38), residues: 402 helix: -2.69 (1.12), residues: 18 sheet: -2.57 (0.44), residues: 121 loop : -2.63 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 403 TYR 0.022 0.002 TYR H 105 PHE 0.016 0.002 PHE R 392 TRP 0.045 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3345) covalent geometry : angle 0.73608 ( 4548) SS BOND : bond 0.00254 ( 5) SS BOND : angle 1.13795 ( 10) hydrogen bonds : bond 0.03432 ( 63) hydrogen bonds : angle 5.76789 ( 171) link_BETA1-4 : bond 0.00943 ( 2) link_BETA1-4 : angle 4.04464 ( 6) link_NAG-ASN : bond 0.00350 ( 1) link_NAG-ASN : angle 0.69338 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8433 (m-80) cc_final: 0.8036 (m-10) REVERT: H 69 VAL cc_start: 0.8350 (t) cc_final: 0.8003 (t) REVERT: H 109 TRP cc_start: 0.7506 (OUTLIER) cc_final: 0.7087 (p90) REVERT: L 62 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7172 (p90) REVERT: L 79 GLN cc_start: 0.8520 (mp10) cc_final: 0.8003 (mp10) REVERT: L 100 GLN cc_start: 0.7515 (tm-30) cc_final: 0.7243 (tm-30) REVERT: R 386 LYS cc_start: 0.4266 (pttt) cc_final: 0.3072 (pttt) REVERT: R 387 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8246 (tt) REVERT: R 408 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8290 (ptm160) REVERT: R 453 TYR cc_start: 0.8684 (p90) cc_final: 0.8288 (p90) REVERT: R 493 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7589 (tm-30) outliers start: 25 outliers final: 19 residues processed: 108 average time/residue: 0.0662 time to fit residues: 8.5702 Evaluate side-chains 108 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Chi-restraints excluded: chain R residue 495 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 409 GLN ** 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 = 0.3822 r_free = 0.3822 target = 0.142818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.119524 restraints weight = 5173.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123011 restraints weight = 4111.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123902 restraints weight = 2546.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123939 restraints weight = 2127.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.124769 restraints weight = 2103.434| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3353 Z= 0.167 Angle : 0.753 9.141 4567 Z= 0.373 Chirality : 0.047 0.144 487 Planarity : 0.006 0.076 581 Dihedral : 8.938 50.296 519 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.46 % Favored : 91.29 % Rotamer: Outliers : 8.57 % Allowed : 22.29 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.80 (0.38), residues: 402 helix: -2.89 (1.00), residues: 19 sheet: -2.62 (0.44), residues: 116 loop : -2.57 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 403 TYR 0.023 0.002 TYR H 105 PHE 0.015 0.002 PHE R 392 TRP 0.046 0.003 TRP H 109 HIS 0.001 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 3345) covalent geometry : angle 0.73793 ( 4548) SS BOND : bond 0.00201 ( 5) SS BOND : angle 1.08063 ( 10) hydrogen bonds : bond 0.03374 ( 63) hydrogen bonds : angle 5.77518 ( 171) link_BETA1-4 : bond 0.01018 ( 2) link_BETA1-4 : angle 4.11248 ( 6) link_NAG-ASN : bond 0.00283 ( 1) link_NAG-ASN : angle 0.66956 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.100 Fit side-chains REVERT: H 60 TYR cc_start: 0.8407 (m-80) cc_final: 0.8015 (m-10) REVERT: H 69 VAL cc_start: 0.8362 (t) cc_final: 0.8016 (t) REVERT: H 109 TRP cc_start: 0.7552 (OUTLIER) cc_final: 0.7193 (p90) REVERT: L 62 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7144 (p90) REVERT: L 79 GLN cc_start: 0.8488 (mp10) cc_final: 0.7984 (mp10) REVERT: L 100 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7229 (tm-30) REVERT: R 386 LYS cc_start: 0.4262 (pttt) cc_final: 0.3054 (pttt) REVERT: R 387 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8252 (tt) REVERT: R 408 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8322 (ptm160) REVERT: R 466 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6950 (ptm-80) REVERT: R 493 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7674 (tm-30) REVERT: R 508 TYR cc_start: 0.5719 (m-80) cc_final: 0.5120 (m-80) outliers start: 30 outliers final: 20 residues processed: 115 average time/residue: 0.0678 time to fit residues: 9.3022 Evaluate side-chains 118 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 345 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117346 restraints weight = 5202.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.120714 restraints weight = 4263.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121578 restraints weight = 2661.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121668 restraints weight = 2234.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122360 restraints weight = 2197.966| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3353 Z= 0.210 Angle : 0.794 8.916 4567 Z= 0.397 Chirality : 0.049 0.207 487 Planarity : 0.006 0.077 581 Dihedral : 8.820 49.274 519 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.20 % Favored : 89.55 % Rotamer: Outliers : 7.43 % Allowed : 23.43 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.84 (0.37), residues: 402 helix: -3.00 (0.95), residues: 18 sheet: -2.79 (0.41), residues: 124 loop : -2.48 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 403 TYR 0.022 0.002 TYR H 105 PHE 0.014 0.002 PHE R 392 TRP 0.064 0.004 TRP H 109 HIS 0.001 0.000 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 3345) covalent geometry : angle 0.77908 ( 4548) SS BOND : bond 0.00153 ( 5) SS BOND : angle 1.15586 ( 10) hydrogen bonds : bond 0.03498 ( 63) hydrogen bonds : angle 5.85518 ( 171) link_BETA1-4 : bond 0.00942 ( 2) link_BETA1-4 : angle 4.22019 ( 6) link_NAG-ASN : bond 0.00445 ( 1) link_NAG-ASN : angle 0.72032 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8445 (m-80) cc_final: 0.8035 (m-10) REVERT: H 69 VAL cc_start: 0.8406 (t) cc_final: 0.8049 (t) REVERT: H 109 TRP cc_start: 0.7397 (OUTLIER) cc_final: 0.6920 (p90) REVERT: L 62 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7261 (p90) REVERT: L 79 GLN cc_start: 0.8572 (mp10) cc_final: 0.7971 (mp10) REVERT: L 100 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7225 (tm-30) REVERT: R 386 LYS cc_start: 0.4390 (pttt) cc_final: 0.3129 (pttt) REVERT: R 387 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8278 (tt) REVERT: R 408 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8337 (ptm160) REVERT: R 453 TYR cc_start: 0.8534 (p90) cc_final: 0.8287 (p90) REVERT: R 493 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7616 (tm-30) outliers start: 26 outliers final: 22 residues processed: 114 average time/residue: 0.0721 time to fit residues: 9.7463 Evaluate side-chains 115 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 452 LEU Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.151282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127330 restraints weight = 4992.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130013 restraints weight = 3345.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.131795 restraints weight = 2553.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132990 restraints weight = 2109.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.133373 restraints weight = 1863.433| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3353 Z= 0.158 Angle : 0.775 8.516 4567 Z= 0.388 Chirality : 0.047 0.222 487 Planarity : 0.006 0.078 581 Dihedral : 8.432 51.910 519 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.71 % Favored : 91.04 % Rotamer: Outliers : 7.14 % Allowed : 24.57 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.60 (0.38), residues: 402 helix: -3.13 (0.91), residues: 18 sheet: -2.37 (0.44), residues: 114 loop : -2.47 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 18 TYR 0.025 0.002 TYR H 105 PHE 0.020 0.002 PHE H 106 TRP 0.057 0.003 TRP H 109 HIS 0.000 0.000 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 3345) covalent geometry : angle 0.75834 ( 4548) SS BOND : bond 0.00134 ( 5) SS BOND : angle 1.09081 ( 10) hydrogen bonds : bond 0.03227 ( 63) hydrogen bonds : angle 5.85897 ( 171) link_BETA1-4 : bond 0.01172 ( 2) link_BETA1-4 : angle 4.32743 ( 6) link_NAG-ASN : bond 0.00104 ( 1) link_NAG-ASN : angle 0.55355 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.8239 (m-80) cc_final: 0.7961 (m-10) REVERT: H 69 VAL cc_start: 0.8354 (t) cc_final: 0.8041 (t) REVERT: H 109 TRP cc_start: 0.7015 (OUTLIER) cc_final: 0.6765 (p90) REVERT: L 62 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7203 (p90) REVERT: L 79 GLN cc_start: 0.8477 (mp10) cc_final: 0.8036 (mp10) REVERT: R 386 LYS cc_start: 0.4451 (pttt) cc_final: 0.3132 (pttt) REVERT: R 387 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8179 (tt) REVERT: R 408 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8287 (ptm160) REVERT: R 493 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7708 (tm-30) outliers start: 25 outliers final: 18 residues processed: 112 average time/residue: 0.0680 time to fit residues: 9.0354 Evaluate side-chains 116 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 109 TRP Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 0.0000 chunk 7 optimal weight: 0.6980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** 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 = 0.3948 r_free = 0.3948 target = 0.152019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128673 restraints weight = 5000.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131211 restraints weight = 3437.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132639 restraints weight = 2659.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.134039 restraints weight = 2255.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.134591 restraints weight = 1988.465| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3353 Z= 0.154 Angle : 0.780 8.123 4567 Z= 0.392 Chirality : 0.048 0.241 487 Planarity : 0.006 0.079 581 Dihedral : 7.953 51.349 517 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.21 % Favored : 91.54 % Rotamer: Outliers : 6.86 % Allowed : 24.57 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.51 (0.38), residues: 402 helix: -3.19 (0.88), residues: 18 sheet: -2.31 (0.47), residues: 108 loop : -2.40 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 454 TYR 0.025 0.002 TYR H 105 PHE 0.016 0.001 PHE R 400 TRP 0.053 0.003 TRP H 109 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3345) covalent geometry : angle 0.76268 ( 4548) SS BOND : bond 0.00174 ( 5) SS BOND : angle 1.05219 ( 10) hydrogen bonds : bond 0.03096 ( 63) hydrogen bonds : angle 5.90199 ( 171) link_BETA1-4 : bond 0.01195 ( 2) link_BETA1-4 : angle 4.47252 ( 6) link_NAG-ASN : bond 0.00029 ( 1) link_NAG-ASN : angle 0.50903 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 25 SER cc_start: 0.7578 (t) cc_final: 0.7211 (m) REVERT: H 60 TYR cc_start: 0.8223 (m-80) cc_final: 0.7899 (m-10) REVERT: L 62 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7206 (p90) REVERT: L 79 GLN cc_start: 0.8458 (mp10) cc_final: 0.8043 (mp10) REVERT: R 386 LYS cc_start: 0.4464 (pttt) cc_final: 0.3121 (pttt) REVERT: R 387 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8222 (tt) REVERT: R 408 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8297 (ptm160) REVERT: R 493 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7728 (tm-30) outliers start: 24 outliers final: 19 residues processed: 107 average time/residue: 0.0726 time to fit residues: 9.3222 Evaluate side-chains 112 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 82 GLN Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 114 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 407 VAL Chi-restraints excluded: chain R residue 408 ARG Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 443 SER Chi-restraints excluded: chain R residue 466 ARG Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain R residue 478 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.149919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.126261 restraints weight = 4973.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.127913 restraints weight = 4059.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.128951 restraints weight = 3227.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.129381 restraints weight = 2822.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129754 restraints weight = 2548.194| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3353 Z= 0.200 Angle : 0.814 8.031 4567 Z= 0.414 Chirality : 0.049 0.234 487 Planarity : 0.006 0.079 581 Dihedral : 8.047 53.570 517 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 6.86 % Allowed : 24.86 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.50 (0.38), residues: 402 helix: -3.47 (0.87), residues: 18 sheet: -2.52 (0.45), residues: 116 loop : -2.24 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 454 TYR 0.029 0.002 TYR H 105 PHE 0.025 0.002 PHE H 106 TRP 0.080 0.004 TRP H 109 HIS 0.002 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 3345) covalent geometry : angle 0.79645 ( 4548) SS BOND : bond 0.00221 ( 5) SS BOND : angle 1.61241 ( 10) hydrogen bonds : bond 0.03559 ( 63) hydrogen bonds : angle 6.08575 ( 171) link_BETA1-4 : bond 0.01033 ( 2) link_BETA1-4 : angle 4.41048 ( 6) link_NAG-ASN : bond 0.00288 ( 1) link_NAG-ASN : angle 0.65282 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 866.29 seconds wall clock time: 15 minutes 33.60 seconds (933.60 seconds total)