Starting phenix.real_space_refine on Wed Jul 1 22:12:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wp1_32666/07_2026/7wp1_32666.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp1_32666/07_2026/7wp1_32666.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wp1_32666/07_2026/7wp1_32666.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp1_32666/07_2026/7wp1_32666.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wp1_32666/07_2026/7wp1_32666.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wp1_32666/07_2026/7wp1_32666.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wp1_32666/07_2026/7wp1_32666.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp1_32666/07_2026/7wp1_32666.map" } resolution = 3.77 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= 0.009 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 2096 2.51 5 N 551 2.21 5 O 643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 3305 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 796 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1017 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 128} Chain: "F" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1464 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "A" 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: 0.76, per 1000 atoms: 0.23 Number of scatterers: 3305 At special positions: 0 Unit cell: (87.914, 63.018, 81.69, 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 643 8.00 N 551 7.00 C 2096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " 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 A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " Time building additional restraints: 0.16 Conformation dependent library (CDL) restraints added in 72.6 milliseconds 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 7 sheets defined 4.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.536A pdb=" N GLY L 32 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.853A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 410 removed outlier: 4.734A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.941A pdb=" N THR L 109 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY L 12 " --> pdb=" O THR L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 17 through 18 Processing sheet with id=AA3, first strand: chain 'L' and resid 47 through 50 removed outlier: 6.500A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.636A pdb=" N THR H 125 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR H 94 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 92 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 376 through 378 removed outlier: 3.575A pdb=" N THR F 376 " --> pdb=" O ALA F 435 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 435 " --> pdb=" O THR F 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 452 through 454 57 hydrogen bonds defined for protein. 123 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: 0.26 Time building geometry restraints manager: 0.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1021 1.34 - 1.46: 851 1.46 - 1.58: 1498 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3389 Sorted by residual: bond pdb=" CB ASN F 370 " pdb=" CG ASN F 370 " ideal model delta sigma weight residual 1.516 1.575 -0.059 2.50e-02 1.60e+03 5.61e+00 bond pdb=" CA ASN F 370 " pdb=" CB ASN F 370 " ideal model delta sigma weight residual 1.532 1.566 -0.034 1.43e-02 4.89e+03 5.60e+00 bond pdb=" C LEU F 425 " pdb=" N PRO F 426 " ideal model delta sigma weight residual 1.330 1.353 -0.023 1.25e-02 6.40e+03 3.51e+00 bond pdb=" C GLY L 12 " pdb=" N ALA L 13 " ideal model delta sigma weight residual 1.330 1.304 0.026 1.47e-02 4.63e+03 3.23e+00 bond pdb=" CA CYS F 336 " pdb=" C CYS F 336 " ideal model delta sigma weight residual 1.525 1.562 -0.037 2.10e-02 2.27e+03 3.10e+00 ... (remaining 3384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 4396 2.47 - 4.94: 170 4.94 - 7.41: 30 7.41 - 9.88: 6 9.88 - 12.34: 1 Bond angle restraints: 4603 Sorted by residual: angle pdb=" N VAL F 367 " pdb=" CA VAL F 367 " pdb=" C VAL F 367 " ideal model delta sigma weight residual 113.47 107.26 6.21 1.01e+00 9.80e-01 3.78e+01 angle pdb=" N ILE F 468 " pdb=" CA ILE F 468 " pdb=" C ILE F 468 " ideal model delta sigma weight residual 112.12 107.84 4.28 8.40e-01 1.42e+00 2.60e+01 angle pdb=" CA ASN F 370 " pdb=" CB ASN F 370 " pdb=" CG ASN F 370 " ideal model delta sigma weight residual 112.60 117.12 -4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" N CYS F 391 " pdb=" CA CYS F 391 " pdb=" C CYS F 391 " ideal model delta sigma weight residual 113.23 118.58 -5.35 1.22e+00 6.72e-01 1.92e+01 angle pdb=" N TYR F 473 " pdb=" CA TYR F 473 " pdb=" C TYR F 473 " ideal model delta sigma weight residual 111.69 116.53 -4.84 1.23e+00 6.61e-01 1.55e+01 ... (remaining 4598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 1719 17.43 - 34.86: 195 34.86 - 52.29: 30 52.29 - 69.72: 4 69.72 - 87.15: 2 Dihedral angle restraints: 1950 sinusoidal: 741 harmonic: 1209 Sorted by residual: dihedral pdb=" CA LEU F 390 " pdb=" C LEU F 390 " pdb=" N CYS F 391 " pdb=" CA CYS F 391 " ideal model delta harmonic sigma weight residual 180.00 145.06 34.94 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA ASP H 113 " pdb=" C ASP H 113 " pdb=" N TYR H 114 " pdb=" CA TYR H 114 " ideal model delta harmonic sigma weight residual -180.00 -146.69 -33.31 0 5.00e+00 4.00e-02 4.44e+01 dihedral pdb=" CA TYR F 380 " pdb=" C TYR F 380 " pdb=" N GLY F 381 " pdb=" CA GLY F 381 " ideal model delta harmonic sigma weight residual 180.00 -148.09 -31.91 0 5.00e+00 4.00e-02 4.07e+01 ... (remaining 1947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 474 0.138 - 0.277: 15 0.277 - 0.415: 0 0.415 - 0.553: 0 0.553 - 0.691: 1 Chirality restraints: 490 Sorted by residual: chirality pdb=" C1 NAG A 1 " pdb=" ND2 ASN F 343 " pdb=" C2 NAG A 1 " pdb=" O5 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.19e+01 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 -2.47 0.07 2.00e-02 2.50e+03 1.18e+01 chirality pdb=" CA ASN F 370 " pdb=" N ASN F 370 " pdb=" C ASN F 370 " pdb=" CB ASN F 370 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 487 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.284 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG A 1 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.172 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.421 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.274 2.00e-02 2.50e+03 2.28e-01 6.52e+02 pdb=" C7 NAG A 2 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.384 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO H 14 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " -0.036 5.00e-02 4.00e+02 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1171 2.85 - 3.36: 2769 3.36 - 3.88: 5198 3.88 - 4.39: 5643 4.39 - 4.90: 10286 Nonbonded interactions: 25067 Sorted by model distance: nonbonded pdb=" O SER F 366 " pdb=" OG SER F 366 " model vdw 2.338 3.040 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.345 3.040 nonbonded pdb=" NE2 HIS L 36 " pdb=" O ASN H 115 " model vdw 2.360 3.120 nonbonded pdb=" OG1 THR F 393 " pdb=" O GLU F 516 " model vdw 2.364 3.040 nonbonded pdb=" OH TYR L 38 " pdb=" OE1 GLN L 91 " model vdw 2.370 3.040 ... (remaining 25062 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=0.00 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: 14.330 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.280 Find NCS groups from input model: 0.010 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:0.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.006 0.059 3394 Z= 0.297 Angle : 1.181 12.344 4615 Z= 0.686 Chirality : 0.068 0.691 490 Planarity : 0.016 0.243 595 Dihedral : 14.562 87.147 1185 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.23 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 15.01 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % 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: -5.40 (0.31), residues: 417 helix: -5.32 (0.22), residues: 20 sheet: -3.25 (0.37), residues: 145 loop : -3.79 (0.28), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.018 0.002 TYR H 104 PHE 0.021 0.002 PHE F 338 TRP 0.011 0.002 TRP F 436 HIS 0.006 0.003 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.30 ( 3389) covalent geometry : angle 1.16953 / 0.68 ( 4603) SS BOND : bond 0.00338 / 0.13 ( 3) SS BOND : angle 0.79268 / 0.38 ( 6) hydrogen bonds : bond 0.27535 / 19.19 ( 57) hydrogen bonds : angle 10.86817 / 7.23 ( 123) link_BETA1-4 : bond 0.00371 / 0.20 ( 1) link_BETA1-4 : angle 3.81629 / 1.96 ( 3) link_NAG-ASN : bond 0.03583 / 1.89 ( 1) link_NAG-ASN : angle 5.53440 / 2.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.115 Fit side-chains REVERT: H 18 LEU cc_start: 0.6969 (tp) cc_final: 0.6738 (tp) REVERT: H 67 ARG cc_start: 0.7095 (mpt-90) cc_final: 0.6689 (mpt-90) REVERT: F 457 ARG cc_start: 0.8434 (ttt-90) cc_final: 0.7902 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.0684 time to fit residues: 6.8139 Evaluate side-chains 67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 74 ASN F 388 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.135552 restraints weight = 5294.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.138840 restraints weight = 3242.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141102 restraints weight = 2240.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142737 restraints weight = 1675.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143848 restraints weight = 1318.869| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3394 Z= 0.206 Angle : 0.770 7.468 4615 Z= 0.406 Chirality : 0.050 0.307 490 Planarity : 0.006 0.053 595 Dihedral : 7.125 33.343 474 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.71 % Favored : 87.05 % Rotamer: Outliers : 4.53 % Allowed : 17.56 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.72 (0.35), residues: 417 helix: -5.28 (0.23), residues: 20 sheet: -2.74 (0.36), residues: 166 loop : -3.29 (0.34), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 87 TYR 0.013 0.002 TYR F 421 PHE 0.018 0.002 PHE F 338 TRP 0.015 0.002 TRP F 353 HIS 0.004 0.003 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 ( 3389) covalent geometry : angle 0.76357 / 0.41 ( 4603) SS BOND : bond 0.00253 / 0.12 ( 3) SS BOND : angle 0.83927 / 0.35 ( 6) hydrogen bonds : bond 0.03789 / 2.41 ( 57) hydrogen bonds : angle 7.60394 / 5.16 ( 123) link_BETA1-4 : bond 0.00329 / 0.17 ( 1) link_BETA1-4 : angle 1.96200 / 0.99 ( 3) link_NAG-ASN : bond 0.01172 / 0.62 ( 1) link_NAG-ASN : angle 3.49832 / 1.86 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.113 Fit side-chains REVERT: L 17 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6410 (ttp-110) REVERT: L 38 TYR cc_start: 0.9336 (m-80) cc_final: 0.9107 (m-80) REVERT: L 81 GLN cc_start: 0.7951 (mp10) cc_final: 0.7737 (mp10) REVERT: H 3 GLN cc_start: 0.8327 (pt0) cc_final: 0.8120 (pt0) REVERT: F 457 ARG cc_start: 0.8440 (ttt-90) cc_final: 0.7942 (ttt-90) outliers start: 16 outliers final: 13 residues processed: 77 average time/residue: 0.0714 time to fit residues: 6.4486 Evaluate side-chains 79 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 39 GLN H 35 HIS H 115 ASN ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.148940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.132190 restraints weight = 5375.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135495 restraints weight = 3254.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137760 restraints weight = 2231.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139403 restraints weight = 1676.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140528 restraints weight = 1312.790| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 3394 Z= 0.253 Angle : 0.802 7.938 4615 Z= 0.418 Chirality : 0.051 0.268 490 Planarity : 0.006 0.063 595 Dihedral : 7.059 31.419 474 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.15 % Favored : 85.61 % Rotamer: Outliers : 7.08 % Allowed : 18.41 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.35 (0.37), residues: 417 helix: -5.28 (0.23), residues: 20 sheet: -2.50 (0.37), residues: 167 loop : -3.00 (0.37), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 19 TYR 0.020 0.002 TYR H 80 PHE 0.021 0.002 PHE F 338 TRP 0.016 0.002 TRP F 353 HIS 0.005 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00583 / 0.25 ( 3389) covalent geometry : angle 0.79523 / 0.42 ( 4603) SS BOND : bond 0.00472 / 0.21 ( 3) SS BOND : angle 0.82998 / 0.35 ( 6) hydrogen bonds : bond 0.03303 / 2.08 ( 57) hydrogen bonds : angle 7.19631 / 5.00 ( 123) link_BETA1-4 : bond 0.00339 / 0.18 ( 1) link_BETA1-4 : angle 2.34142 / 1.17 ( 3) link_NAG-ASN : bond 0.00702 / 0.37 ( 1) link_NAG-ASN : angle 3.47594 / 1.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.112 Fit side-chains REVERT: L 17 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6467 (ttp-110) REVERT: F 369 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7238 (t80) REVERT: F 457 ARG cc_start: 0.8462 (ttt-90) cc_final: 0.7817 (ttt-90) outliers start: 25 outliers final: 17 residues processed: 87 average time/residue: 0.0745 time to fit residues: 7.5235 Evaluate side-chains 88 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.143626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.127998 restraints weight = 5366.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130749 restraints weight = 3460.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132898 restraints weight = 2488.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.134369 restraints weight = 1886.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135450 restraints weight = 1510.307| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 3394 Z= 0.304 Angle : 0.850 9.478 4615 Z= 0.440 Chirality : 0.052 0.224 490 Planarity : 0.006 0.052 595 Dihedral : 7.263 32.489 474 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.83 % Favored : 83.93 % Rotamer: Outliers : 7.93 % Allowed : 20.11 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.28 (0.38), residues: 417 helix: -5.23 (0.26), residues: 20 sheet: -2.46 (0.38), residues: 167 loop : -2.94 (0.38), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 98 TYR 0.018 0.002 TYR H 104 PHE 0.021 0.002 PHE F 338 TRP 0.018 0.003 TRP F 353 HIS 0.005 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00699 / 0.30 ( 3389) covalent geometry : angle 0.84336 / 0.44 ( 4603) SS BOND : bond 0.00452 / 0.19 ( 3) SS BOND : angle 1.00343 / 0.44 ( 6) hydrogen bonds : bond 0.03141 / 1.99 ( 57) hydrogen bonds : angle 7.17491 / 5.00 ( 123) link_BETA1-4 : bond 0.00099 / 0.05 ( 1) link_BETA1-4 : angle 2.76450 / 1.42 ( 3) link_NAG-ASN : bond 0.00672 / 0.35 ( 1) link_NAG-ASN : angle 3.30760 / 1.80 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.068 Fit side-chains revert: symmetry clash REVERT: L 17 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6318 (ttp-110) REVERT: F 369 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7405 (t80) outliers start: 28 outliers final: 25 residues processed: 84 average time/residue: 0.0629 time to fit residues: 6.2174 Evaluate side-chains 91 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 36 HIS Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 467 ASP Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.0870 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN F 498 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.149715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132913 restraints weight = 5277.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.136233 restraints weight = 3199.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138597 restraints weight = 2187.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140186 restraints weight = 1617.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.141435 restraints weight = 1273.897| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3595 r_free = 0.3595 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3394 Z= 0.183 Angle : 0.762 7.838 4615 Z= 0.390 Chirality : 0.049 0.196 490 Planarity : 0.005 0.051 595 Dihedral : 6.767 31.888 474 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.95 % Favored : 86.81 % Rotamer: Outliers : 6.80 % Allowed : 21.81 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -4.15 (0.38), residues: 417 helix: -5.16 (0.29), residues: 20 sheet: -2.43 (0.38), residues: 169 loop : -2.79 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 98 TYR 0.014 0.002 TYR F 421 PHE 0.015 0.001 PHE F 392 TRP 0.011 0.002 TRP F 353 HIS 0.005 0.003 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 3389) covalent geometry : angle 0.75544 / 0.39 ( 4603) SS BOND : bond 0.00243 / 0.10 ( 3) SS BOND : angle 0.72284 / 0.30 ( 6) hydrogen bonds : bond 0.02729 / 1.81 ( 57) hydrogen bonds : angle 6.68949 / 4.66 ( 123) link_BETA1-4 : bond 0.00189 / 0.10 ( 1) link_BETA1-4 : angle 2.11595 / 1.08 ( 3) link_NAG-ASN : bond 0.00794 / 0.42 ( 1) link_NAG-ASN : angle 3.45508 / 1.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: L 17 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6266 (ttp-110) REVERT: F 369 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7242 (t80) REVERT: F 457 ARG cc_start: 0.8332 (ttt-90) cc_final: 0.7818 (ttt-90) outliers start: 24 outliers final: 19 residues processed: 84 average time/residue: 0.0653 time to fit residues: 6.4052 Evaluate side-chains 85 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.133043 restraints weight = 5270.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136441 restraints weight = 3161.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.138733 restraints weight = 2150.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140426 restraints weight = 1603.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141400 restraints weight = 1250.676| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3394 Z= 0.184 Angle : 0.750 7.537 4615 Z= 0.384 Chirality : 0.048 0.196 490 Planarity : 0.005 0.049 595 Dihedral : 6.589 31.078 474 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.67 % Favored : 86.09 % Rotamer: Outliers : 6.80 % Allowed : 22.66 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.04 (0.39), residues: 417 helix: -5.05 (0.31), residues: 20 sheet: -2.40 (0.38), residues: 169 loop : -2.68 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 98 TYR 0.019 0.002 TYR H 80 PHE 0.015 0.001 PHE F 392 TRP 0.020 0.002 TRP F 353 HIS 0.005 0.003 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 3389) covalent geometry : angle 0.74291 / 0.38 ( 4603) SS BOND : bond 0.00256 / 0.10 ( 3) SS BOND : angle 0.71389 / 0.30 ( 6) hydrogen bonds : bond 0.02692 / 1.75 ( 57) hydrogen bonds : angle 6.45273 / 4.56 ( 123) link_BETA1-4 : bond 0.00316 / 0.17 ( 1) link_BETA1-4 : angle 2.44208 / 1.25 ( 3) link_NAG-ASN : bond 0.00744 / 0.39 ( 1) link_NAG-ASN : angle 3.49381 / 1.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.120 Fit side-chains revert: symmetry clash REVERT: L 17 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6244 (ttp-110) REVERT: F 369 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.7295 (t80) REVERT: F 457 ARG cc_start: 0.8342 (ttt-90) cc_final: 0.7779 (ttt-90) outliers start: 24 outliers final: 21 residues processed: 83 average time/residue: 0.0643 time to fit residues: 6.3005 Evaluate side-chains 88 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 17 ARG Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 0.0570 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.0060 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.0870 chunk 20 optimal weight: 0.3980 overall best weight: 0.2092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138079 restraints weight = 5238.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141551 restraints weight = 3094.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143969 restraints weight = 2068.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.145583 restraints weight = 1501.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146795 restraints weight = 1168.081| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3394 Z= 0.129 Angle : 0.718 8.149 4615 Z= 0.363 Chirality : 0.047 0.182 490 Planarity : 0.005 0.049 595 Dihedral : 6.110 28.314 474 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.75 % Favored : 88.01 % Rotamer: Outliers : 6.52 % Allowed : 23.23 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.39), residues: 417 helix: -4.96 (0.41), residues: 19 sheet: -2.23 (0.41), residues: 156 loop : -2.67 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 98 TYR 0.025 0.001 TYR H 80 PHE 0.011 0.001 PHE F 392 TRP 0.014 0.001 TRP F 353 HIS 0.006 0.003 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 3389) covalent geometry : angle 0.71057 / 0.36 ( 4603) SS BOND : bond 0.00185 / 0.08 ( 3) SS BOND : angle 0.68520 / 0.29 ( 6) hydrogen bonds : bond 0.02528 / 1.76 ( 57) hydrogen bonds : angle 6.09545 / 4.33 ( 123) link_BETA1-4 : bond 0.00501 / 0.26 ( 1) link_BETA1-4 : angle 1.99153 / 1.01 ( 3) link_NAG-ASN : bond 0.00832 / 0.44 ( 1) link_NAG-ASN : angle 3.51662 / 1.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: L 38 TYR cc_start: 0.9268 (m-80) cc_final: 0.8968 (m-80) REVERT: H 3 GLN cc_start: 0.8424 (pt0) cc_final: 0.8134 (pt0) REVERT: H 101 GLN cc_start: 0.7114 (tm-30) cc_final: 0.6883 (tm-30) REVERT: F 353 TRP cc_start: 0.7445 (p90) cc_final: 0.6919 (p90) REVERT: F 369 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7246 (t80) REVERT: F 457 ARG cc_start: 0.8278 (ttt-90) cc_final: 0.7831 (ttt-90) outliers start: 23 outliers final: 20 residues processed: 82 average time/residue: 0.0567 time to fit residues: 5.5216 Evaluate side-chains 87 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.0040 chunk 38 optimal weight: 0.9980 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.134608 restraints weight = 5312.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137941 restraints weight = 3194.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.140223 restraints weight = 2187.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.141913 restraints weight = 1637.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143036 restraints weight = 1289.277| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3599 r_free = 0.3599 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3394 Z= 0.186 Angle : 0.753 7.335 4615 Z= 0.384 Chirality : 0.048 0.195 490 Planarity : 0.005 0.048 595 Dihedral : 6.260 28.682 474 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.23 % Favored : 87.53 % Rotamer: Outliers : 7.65 % Allowed : 21.25 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.39), residues: 417 helix: -4.82 (0.50), residues: 19 sheet: -2.30 (0.39), residues: 169 loop : -2.50 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 98 TYR 0.012 0.002 TYR H 59 PHE 0.014 0.001 PHE F 392 TRP 0.013 0.002 TRP F 353 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 3389) covalent geometry : angle 0.74461 / 0.38 ( 4603) SS BOND : bond 0.00244 / 0.10 ( 3) SS BOND : angle 0.83211 / 0.36 ( 6) hydrogen bonds : bond 0.02588 / 1.75 ( 57) hydrogen bonds : angle 6.43423 / 4.55 ( 123) link_BETA1-4 : bond 0.00292 / 0.15 ( 1) link_BETA1-4 : angle 2.66868 / 1.36 ( 3) link_NAG-ASN : bond 0.00715 / 0.38 ( 1) link_NAG-ASN : angle 3.51741 / 1.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: L 38 TYR cc_start: 0.9317 (m-80) cc_final: 0.9106 (m-80) REVERT: L 85 GLU cc_start: 0.8349 (pm20) cc_final: 0.7947 (pm20) REVERT: H 3 GLN cc_start: 0.8455 (pt0) cc_final: 0.8177 (pt0) REVERT: F 338 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6853 (p90) REVERT: F 353 TRP cc_start: 0.7566 (p90) cc_final: 0.7263 (p90) REVERT: F 369 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7317 (t80) REVERT: F 457 ARG cc_start: 0.8320 (ttt-90) cc_final: 0.7827 (ttt-90) outliers start: 27 outliers final: 20 residues processed: 87 average time/residue: 0.0585 time to fit residues: 5.9839 Evaluate side-chains 89 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 24 optimal weight: 0.0770 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.152872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135798 restraints weight = 5239.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139217 restraints weight = 3129.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141609 restraints weight = 2129.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.143270 restraints weight = 1570.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144320 restraints weight = 1234.543| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3394 Z= 0.164 Angle : 0.750 7.456 4615 Z= 0.383 Chirality : 0.048 0.191 490 Planarity : 0.005 0.049 595 Dihedral : 6.211 28.191 474 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.75 % Favored : 88.01 % Rotamer: Outliers : 6.52 % Allowed : 21.53 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.39), residues: 417 helix: -4.74 (0.57), residues: 19 sheet: -2.25 (0.39), residues: 169 loop : -2.48 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 98 TYR 0.012 0.001 TYR F 421 PHE 0.013 0.001 PHE F 392 TRP 0.013 0.002 TRP F 353 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 3389) covalent geometry : angle 0.74252 / 0.38 ( 4603) SS BOND : bond 0.00205 / 0.09 ( 3) SS BOND : angle 0.77797 / 0.33 ( 6) hydrogen bonds : bond 0.02564 / 1.75 ( 57) hydrogen bonds : angle 6.40223 / 4.53 ( 123) link_BETA1-4 : bond 0.00312 / 0.16 ( 1) link_BETA1-4 : angle 2.54867 / 1.30 ( 3) link_NAG-ASN : bond 0.00736 / 0.39 ( 1) link_NAG-ASN : angle 3.50382 / 1.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: L 38 TYR cc_start: 0.9322 (m-80) cc_final: 0.9101 (m-80) REVERT: L 85 GLU cc_start: 0.8382 (pm20) cc_final: 0.7987 (pm20) REVERT: H 3 GLN cc_start: 0.8475 (pt0) cc_final: 0.8194 (pt0) REVERT: F 369 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7422 (t80) REVERT: F 457 ARG cc_start: 0.8343 (ttt-90) cc_final: 0.7802 (ttt-90) outliers start: 23 outliers final: 19 residues processed: 80 average time/residue: 0.0627 time to fit residues: 5.9746 Evaluate side-chains 84 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 369 TYR Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132876 restraints weight = 5319.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136218 restraints weight = 3218.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138552 restraints weight = 2208.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140254 restraints weight = 1640.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.141493 restraints weight = 1290.740| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3394 Z= 0.203 Angle : 0.775 6.937 4615 Z= 0.398 Chirality : 0.049 0.201 490 Planarity : 0.005 0.048 595 Dihedral : 6.466 29.699 474 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.71 % Favored : 87.05 % Rotamer: Outliers : 6.23 % Allowed : 21.53 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.76 (0.39), residues: 417 helix: -4.68 (0.56), residues: 20 sheet: -2.19 (0.40), residues: 166 loop : -2.53 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 98 TYR 0.013 0.002 TYR H 104 PHE 0.016 0.001 PHE F 392 TRP 0.025 0.002 TRP F 353 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 ( 3389) covalent geometry : angle 0.76614 / 0.40 ( 4603) SS BOND : bond 0.00251 / 0.11 ( 3) SS BOND : angle 0.84529 / 0.36 ( 6) hydrogen bonds : bond 0.02660 / 1.75 ( 57) hydrogen bonds : angle 6.67608 / 4.73 ( 123) link_BETA1-4 : bond 0.00290 / 0.15 ( 1) link_BETA1-4 : angle 3.01468 / 1.54 ( 3) link_NAG-ASN : bond 0.00696 / 0.37 ( 1) link_NAG-ASN : angle 3.48093 / 1.91 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 834 Ramachandran restraints generated. 417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.126 Fit side-chains REVERT: L 85 GLU cc_start: 0.8376 (pm20) cc_final: 0.7984 (pm20) outliers start: 22 outliers final: 19 residues processed: 80 average time/residue: 0.0676 time to fit residues: 6.3018 Evaluate side-chains 85 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 401 VAL Chi-restraints excluded: chain F residue 402 ILE Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.131467 restraints weight = 5334.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.134806 restraints weight = 3244.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.137204 restraints weight = 2216.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138867 restraints weight = 1631.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.139970 restraints weight = 1281.788| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3394 Z= 0.228 Angle : 0.805 8.062 4615 Z= 0.413 Chirality : 0.050 0.205 490 Planarity : 0.005 0.049 595 Dihedral : 6.606 30.699 474 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.47 % Favored : 87.29 % Rotamer: Outliers : 5.95 % Allowed : 22.10 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.39), residues: 417 helix: -4.68 (0.57), residues: 20 sheet: -2.23 (0.39), residues: 167 loop : -2.53 (0.39), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 98 TYR 0.015 0.002 TYR F 421 PHE 0.016 0.002 PHE F 392 TRP 0.024 0.002 TRP F 353 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 ( 3389) covalent geometry : angle 0.79648 / 0.41 ( 4603) SS BOND : bond 0.00287 / 0.12 ( 3) SS BOND : angle 0.90429 / 0.39 ( 6) hydrogen bonds : bond 0.02728 / 1.77 ( 57) hydrogen bonds : angle 6.81618 / 4.84 ( 123) link_BETA1-4 : bond 0.00292 / 0.15 ( 1) link_BETA1-4 : angle 3.17257 / 1.62 ( 3) link_NAG-ASN : bond 0.00702 / 0.37 ( 1) link_NAG-ASN : angle 3.47349 / 1.91 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 957.72 seconds wall clock time: 17 minutes 10.45 seconds (1030.45 seconds total)