Starting phenix.real_space_refine on Fri Oct 10 12:36:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iva_35755/10_2025/8iva_35755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iva_35755/10_2025/8iva_35755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iva_35755/10_2025/8iva_35755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iva_35755/10_2025/8iva_35755.map" model { file = "/net/cci-nas-00/data/ceres_data/8iva_35755/10_2025/8iva_35755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iva_35755/10_2025/8iva_35755.cif" } resolution = 3.95 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= 0.010 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 26 5.16 5 C 3182 2.51 5 N 827 2.21 5 O 994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5029 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.12, per 1000 atoms: 0.22 Number of scatterers: 5029 At special positions: 0 Unit cell: (80.912, 77.8, 108.142, 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 26 16.00 O 994 8.00 N 827 7.00 C 3182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.28 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " 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 G 343 " Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 165.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 15 sheets defined 5.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.529A pdb=" N ALA G 352 " --> pdb=" O SER G 349 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 349 through 353' Processing helix chain 'G' and resid 364 through 370 removed outlier: 3.868A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.130A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.695A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.669A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.140A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 50 removed outlier: 4.834A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS C 35 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.617A pdb=" N THR E 72 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 11 removed outlier: 4.037A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 44 through 46 Processing sheet with id=AA7, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.696A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'L' and resid 19 through 29 removed outlier: 3.829A pdb=" N VAL L 25 " --> pdb=" O THR L 68 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR L 68 " --> pdb=" O VAL L 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.789A pdb=" N TRP L 34 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.124A pdb=" N MET H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER H 25 " --> pdb=" O MET H 3 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR H 80 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.595A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.595A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 324 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: 0.73 Time building geometry restraints manager: 0.42 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: 1558 1.34 - 1.46: 1395 1.46 - 1.58: 2165 1.58 - 1.71: 0 1.71 - 1.83: 36 Bond restraints: 5154 Sorted by residual: bond pdb=" CA ALA G 475 " pdb=" C ALA G 475 " ideal model delta sigma weight residual 1.522 1.571 -0.049 9.30e-03 1.16e+04 2.75e+01 bond pdb=" N ASP G 442 " pdb=" CA ASP G 442 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.16e-02 7.43e+03 1.04e+01 bond pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.24e+00 bond pdb=" N GLN G 474 " pdb=" CA GLN G 474 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.29e-02 6.01e+03 9.15e+00 bond pdb=" N ALA G 475 " pdb=" CA ALA G 475 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.09e+00 ... (remaining 5149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 6902 3.00 - 5.99: 84 5.99 - 8.99: 11 8.99 - 11.99: 2 11.99 - 14.98: 2 Bond angle restraints: 7001 Sorted by residual: angle pdb=" C LEU G 335 " pdb=" N CYS G 336 " pdb=" CA CYS G 336 " ideal model delta sigma weight residual 120.49 135.47 -14.98 1.42e+00 4.96e-01 1.11e+02 angle pdb=" N ALA G 475 " pdb=" CA ALA G 475 " pdb=" C ALA G 475 " ideal model delta sigma weight residual 112.12 124.69 -12.57 1.34e+00 5.57e-01 8.80e+01 angle pdb=" N SER G 477 " pdb=" CA SER G 477 " pdb=" C SER G 477 " ideal model delta sigma weight residual 112.38 123.66 -11.28 1.22e+00 6.72e-01 8.55e+01 angle pdb=" N CYS G 480 " pdb=" CA CYS G 480 " pdb=" C CYS G 480 " ideal model delta sigma weight residual 112.45 121.62 -9.17 1.39e+00 5.18e-01 4.35e+01 angle pdb=" N LEU G 441 " pdb=" CA LEU G 441 " pdb=" C LEU G 441 " ideal model delta sigma weight residual 111.36 117.78 -6.42 1.09e+00 8.42e-01 3.47e+01 ... (remaining 6996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 2735 17.75 - 35.50: 250 35.50 - 53.25: 46 53.25 - 71.00: 4 71.00 - 88.75: 5 Dihedral angle restraints: 3040 sinusoidal: 1179 harmonic: 1861 Sorted by residual: dihedral pdb=" CB CYS G 391 " pdb=" SG CYS G 391 " pdb=" SG CYS G 525 " pdb=" CB CYS G 525 " ideal model delta sinusoidal sigma weight residual 93.00 46.06 46.94 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CA LEU G 461 " pdb=" C LEU G 461 " pdb=" N LYS G 462 " pdb=" CA LYS G 462 " ideal model delta harmonic sigma weight residual 180.00 157.06 22.94 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TRP L 90 " pdb=" C TRP L 90 " pdb=" N SER L 91 " pdb=" CA SER L 91 " ideal model delta harmonic sigma weight residual -180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 3037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 654 0.086 - 0.172: 94 0.172 - 0.258: 10 0.258 - 0.343: 2 0.343 - 0.429: 3 Chirality restraints: 763 Sorted by residual: chirality pdb=" CA ALA G 475 " pdb=" N ALA G 475 " pdb=" C ALA G 475 " pdb=" CB ALA G 475 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA CYS G 480 " pdb=" N CYS G 480 " pdb=" C CYS G 480 " pdb=" CB CYS G 480 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA SER G 477 " pdb=" N SER G 477 " pdb=" C SER G 477 " pdb=" CB SER G 477 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 760 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 94 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO E 95 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 472 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C ILE G 472 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE G 472 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR G 473 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR H 40 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO H 41 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.036 5.00e-02 4.00e+02 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1604 2.82 - 3.34: 4003 3.34 - 3.86: 8000 3.86 - 4.38: 8740 4.38 - 4.90: 15568 Nonbonded interactions: 37915 Sorted by model distance: nonbonded pdb=" O TYR E 49 " pdb=" OG SER E 53 " model vdw 2.302 3.040 nonbonded pdb=" O VAL L 29 " pdb=" OH TYR L 70 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR L 86 " pdb=" O LYS H 43 " model vdw 2.349 3.040 nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.355 3.040 nonbonded pdb=" NE2 GLN E 6 " pdb=" OG1 THR E 102 " model vdw 2.378 3.120 ... (remaining 37910 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=0.50 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: 16.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.740 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 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 : 0.007 0.250 5164 Z= 0.346 Angle : 1.024 24.285 7023 Z= 0.618 Chirality : 0.066 0.429 763 Planarity : 0.007 0.071 891 Dihedral : 13.804 88.750 1840 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.54 % Allowed : 7.43 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -4.03 (0.28), residues: 638 helix: -5.15 (0.31), residues: 14 sheet: -2.71 (0.30), residues: 223 loop : -2.65 (0.26), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 457 TYR 0.027 0.002 TYR E 94 PHE 0.022 0.002 PHE E 83 TRP 0.023 0.002 TRP C 106 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00552 ( 5154) covalent geometry : angle 0.97365 ( 7001) SS BOND : bond 0.08879 ( 8) SS BOND : angle 6.36753 ( 16) hydrogen bonds : bond 0.27035 ( 123) hydrogen bonds : angle 11.18507 ( 324) link_BETA1-4 : bond 0.00671 ( 1) link_BETA1-4 : angle 1.30442 ( 3) link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 5.17553 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7986 (ptm-80) REVERT: C 59 TYR cc_start: 0.8333 (t80) cc_final: 0.8079 (t80) REVERT: C 97 VAL cc_start: 0.8206 (m) cc_final: 0.7978 (m) REVERT: E 23 CYS cc_start: 0.7962 (t) cc_final: 0.7397 (t) REVERT: E 24 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7403 (ttm110) REVERT: E 27 GLN cc_start: 0.8312 (tt0) cc_final: 0.7881 (mp10) REVERT: E 42 LYS cc_start: 0.8276 (pttm) cc_final: 0.7935 (mtpt) REVERT: E 61 ARG cc_start: 0.7920 (ptt-90) cc_final: 0.7318 (ptt90) REVERT: E 82 ASP cc_start: 0.8556 (m-30) cc_final: 0.7458 (m-30) REVERT: E 89 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7480 (tm-30) REVERT: E 90 GLN cc_start: 0.7556 (pp30) cc_final: 0.6810 (pp30) REVERT: E 93 SER cc_start: 0.8477 (m) cc_final: 0.8136 (m) REVERT: E 107 LYS cc_start: 0.4448 (tttt) cc_final: 0.3687 (tptm) REVERT: G 335 LEU cc_start: 0.8075 (mp) cc_final: 0.7866 (mt) REVERT: G 369 TYR cc_start: 0.9026 (t80) cc_final: 0.8627 (t80) REVERT: G 378 LYS cc_start: 0.6890 (mttm) cc_final: 0.6514 (mtmm) REVERT: G 442 ASP cc_start: 0.8632 (m-30) cc_final: 0.8398 (m-30) REVERT: G 465 GLU cc_start: 0.8580 (tt0) cc_final: 0.8214 (tt0) REVERT: G 471 GLU cc_start: 0.8086 (tt0) cc_final: 0.7696 (pt0) REVERT: L 1 GLN cc_start: 0.8967 (pt0) cc_final: 0.8651 (pp30) REVERT: L 31 ASP cc_start: 0.7177 (p0) cc_final: 0.6598 (p0) REVERT: L 32 MET cc_start: 0.8278 (tpp) cc_final: 0.7995 (mmm) REVERT: L 34 TRP cc_start: 0.8514 (m100) cc_final: 0.7779 (m100) REVERT: L 44 LYS cc_start: 0.7328 (mtmm) cc_final: 0.6966 (ttpt) REVERT: L 86 TYR cc_start: 0.8370 (m-80) cc_final: 0.7988 (m-10) REVERT: H 19 LYS cc_start: 0.8173 (tttt) cc_final: 0.7585 (ptmt) REVERT: H 73 ASP cc_start: 0.7287 (t0) cc_final: 0.6969 (t0) REVERT: H 76 MET cc_start: 0.7944 (mpp) cc_final: 0.7696 (mtm) REVERT: H 93 MET cc_start: 0.6600 (tpp) cc_final: 0.6290 (tpp) REVERT: H 102 ASN cc_start: 0.8301 (p0) cc_final: 0.8001 (p0) REVERT: H 107 VAL cc_start: 0.8477 (p) cc_final: 0.8157 (t) outliers start: 3 outliers final: 0 residues processed: 204 average time/residue: 0.0889 time to fit residues: 22.2944 Evaluate side-chains 159 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.093590 restraints weight = 10504.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.096681 restraints weight = 6042.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.098876 restraints weight = 4162.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100359 restraints weight = 3191.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101500 restraints weight = 2624.582| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5164 Z= 0.170 Angle : 0.669 7.938 7023 Z= 0.358 Chirality : 0.046 0.170 763 Planarity : 0.005 0.056 891 Dihedral : 6.178 74.409 754 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.71 % Allowed : 16.30 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -3.39 (0.29), residues: 638 helix: -3.49 (0.81), residues: 21 sheet: -1.90 (0.33), residues: 222 loop : -2.48 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 18 TYR 0.025 0.002 TYR E 94 PHE 0.022 0.002 PHE G 400 TRP 0.019 0.002 TRP C 106 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5154) covalent geometry : angle 0.65738 ( 7001) SS BOND : bond 0.00681 ( 8) SS BOND : angle 2.28122 ( 16) hydrogen bonds : bond 0.04400 ( 123) hydrogen bonds : angle 7.68598 ( 324) link_BETA1-4 : bond 0.00286 ( 1) link_BETA1-4 : angle 1.02107 ( 3) link_NAG-ASN : bond 0.00218 ( 1) link_NAG-ASN : angle 3.36416 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 LYS cc_start: 0.8719 (mmtm) cc_final: 0.8435 (mmtm) REVERT: E 89 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8662 (tm-30) REVERT: E 107 LYS cc_start: 0.5168 (tttt) cc_final: 0.4671 (tptm) REVERT: G 378 LYS cc_start: 0.8840 (mttm) cc_final: 0.8354 (mtmm) REVERT: L 34 TRP cc_start: 0.8742 (m100) cc_final: 0.8286 (m100) REVERT: L 44 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8142 (ttpt) REVERT: L 61 PHE cc_start: 0.8700 (m-80) cc_final: 0.8497 (m-80) REVERT: H 76 MET cc_start: 0.8175 (mpp) cc_final: 0.7744 (mtm) REVERT: H 93 MET cc_start: 0.7528 (tpp) cc_final: 0.7299 (tpp) outliers start: 26 outliers final: 14 residues processed: 175 average time/residue: 0.0744 time to fit residues: 16.3976 Evaluate side-chains 152 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.110716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.093560 restraints weight = 10510.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096670 restraints weight = 5991.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098798 restraints weight = 4082.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100246 restraints weight = 3098.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101303 restraints weight = 2537.662| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5164 Z= 0.174 Angle : 0.667 8.850 7023 Z= 0.354 Chirality : 0.046 0.168 763 Planarity : 0.005 0.054 891 Dihedral : 6.020 75.327 754 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.35 % Allowed : 19.75 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -3.09 (0.30), residues: 638 helix: -3.22 (0.90), residues: 21 sheet: -1.66 (0.34), residues: 219 loop : -2.31 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 408 TYR 0.021 0.002 TYR E 94 PHE 0.017 0.002 PHE G 347 TRP 0.017 0.001 TRP C 106 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 5154) covalent geometry : angle 0.65924 ( 7001) SS BOND : bond 0.00534 ( 8) SS BOND : angle 1.82155 ( 16) hydrogen bonds : bond 0.04008 ( 123) hydrogen bonds : angle 7.03469 ( 324) link_BETA1-4 : bond 0.00272 ( 1) link_BETA1-4 : angle 0.85639 ( 3) link_NAG-ASN : bond 0.00061 ( 1) link_NAG-ASN : angle 3.20430 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 76 LYS cc_start: 0.8783 (mmtm) cc_final: 0.8539 (mmtm) REVERT: C 83 MET cc_start: 0.7788 (mtt) cc_final: 0.7499 (mtt) REVERT: C 89 GLU cc_start: 0.7687 (mp0) cc_final: 0.7341 (mp0) REVERT: E 89 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8695 (tm-30) REVERT: G 378 LYS cc_start: 0.8887 (mttm) cc_final: 0.8340 (mtmm) REVERT: G 462 LYS cc_start: 0.9026 (pttt) cc_final: 0.8639 (pttm) REVERT: G 465 GLU cc_start: 0.8503 (tt0) cc_final: 0.8284 (tt0) REVERT: H 73 ASP cc_start: 0.7297 (t0) cc_final: 0.6171 (t0) REVERT: H 76 MET cc_start: 0.8192 (mpp) cc_final: 0.7895 (mpp) REVERT: H 95 TYR cc_start: 0.9018 (m-10) cc_final: 0.8769 (m-10) outliers start: 24 outliers final: 17 residues processed: 157 average time/residue: 0.0830 time to fit residues: 16.4549 Evaluate side-chains 146 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.094647 restraints weight = 10415.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.097787 restraints weight = 5925.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099969 restraints weight = 4032.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101496 restraints weight = 3056.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102574 restraints weight = 2485.432| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5164 Z= 0.148 Angle : 0.646 8.132 7023 Z= 0.341 Chirality : 0.045 0.161 763 Planarity : 0.005 0.052 891 Dihedral : 5.771 75.423 754 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.35 % Allowed : 21.01 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -2.88 (0.31), residues: 638 helix: -3.68 (0.73), residues: 27 sheet: -1.38 (0.34), residues: 224 loop : -2.18 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 18 TYR 0.020 0.002 TYR E 94 PHE 0.013 0.002 PHE G 400 TRP 0.015 0.001 TRP C 106 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 5154) covalent geometry : angle 0.63119 ( 7001) SS BOND : bond 0.00563 ( 8) SS BOND : angle 2.63830 ( 16) hydrogen bonds : bond 0.03740 ( 123) hydrogen bonds : angle 6.66939 ( 324) link_BETA1-4 : bond 0.00385 ( 1) link_BETA1-4 : angle 0.94274 ( 3) link_NAG-ASN : bond 0.00041 ( 1) link_NAG-ASN : angle 3.06863 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9353 (mmmt) cc_final: 0.9096 (mmtm) REVERT: C 83 MET cc_start: 0.8005 (mtt) cc_final: 0.7751 (mtt) REVERT: C 87 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7611 (mtp-110) REVERT: C 89 GLU cc_start: 0.7691 (mp0) cc_final: 0.7260 (mp0) REVERT: E 89 GLN cc_start: 0.9238 (tm-30) cc_final: 0.9033 (tm-30) REVERT: G 378 LYS cc_start: 0.8882 (mttm) cc_final: 0.8275 (mtmm) REVERT: L 61 PHE cc_start: 0.8668 (m-80) cc_final: 0.8447 (m-80) REVERT: H 73 ASP cc_start: 0.7266 (t0) cc_final: 0.6122 (t0) REVERT: H 76 MET cc_start: 0.8241 (mpp) cc_final: 0.7958 (mpp) REVERT: H 95 TYR cc_start: 0.9017 (m-10) cc_final: 0.8785 (m-10) outliers start: 24 outliers final: 18 residues processed: 151 average time/residue: 0.0702 time to fit residues: 13.6230 Evaluate side-chains 146 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.088241 restraints weight = 10925.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.091172 restraints weight = 6437.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.093209 restraints weight = 4489.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.094682 restraints weight = 3482.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.095648 restraints weight = 2890.592| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 5164 Z= 0.338 Angle : 0.781 9.404 7023 Z= 0.414 Chirality : 0.049 0.206 763 Planarity : 0.005 0.058 891 Dihedral : 6.451 81.695 754 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 5.07 % Allowed : 22.10 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -3.08 (0.30), residues: 638 helix: -3.70 (0.71), residues: 27 sheet: -1.58 (0.33), residues: 226 loop : -2.28 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 509 TYR 0.025 0.003 TYR E 94 PHE 0.021 0.002 PHE E 91 TRP 0.017 0.002 TRP C 106 HIS 0.004 0.002 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00781 ( 5154) covalent geometry : angle 0.77253 ( 7001) SS BOND : bond 0.00604 ( 8) SS BOND : angle 2.12037 ( 16) hydrogen bonds : bond 0.04493 ( 123) hydrogen bonds : angle 6.91336 ( 324) link_BETA1-4 : bond 0.00225 ( 1) link_BETA1-4 : angle 1.10049 ( 3) link_NAG-ASN : bond 0.00428 ( 1) link_NAG-ASN : angle 3.37240 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASP cc_start: 0.8639 (t70) cc_final: 0.7278 (t70) REVERT: C 87 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.7617 (mtp-110) REVERT: C 89 GLU cc_start: 0.7878 (mp0) cc_final: 0.7316 (mp0) REVERT: C 98 LYS cc_start: 0.8927 (tmmt) cc_final: 0.8358 (tttm) REVERT: E 89 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8752 (tm-30) REVERT: G 353 TRP cc_start: 0.8920 (p-90) cc_final: 0.8683 (p-90) REVERT: G 378 LYS cc_start: 0.8908 (mttm) cc_final: 0.8357 (mtmm) REVERT: L 2 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8936 (mt) REVERT: H 73 ASP cc_start: 0.7405 (t0) cc_final: 0.6572 (t0) REVERT: H 76 MET cc_start: 0.8384 (mpp) cc_final: 0.8174 (mpp) outliers start: 28 outliers final: 24 residues processed: 152 average time/residue: 0.0789 time to fit residues: 15.3780 Evaluate side-chains 151 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 9 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.108603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.090989 restraints weight = 10594.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.094081 restraints weight = 5983.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096251 restraints weight = 4079.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097747 restraints weight = 3096.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098771 restraints weight = 2534.060| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5164 Z= 0.132 Angle : 0.655 8.449 7023 Z= 0.345 Chirality : 0.045 0.163 763 Planarity : 0.005 0.052 891 Dihedral : 5.920 80.068 754 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.71 % Allowed : 23.73 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -2.79 (0.31), residues: 638 helix: -3.59 (0.76), residues: 27 sheet: -1.28 (0.35), residues: 215 loop : -2.13 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 18 TYR 0.021 0.002 TYR E 94 PHE 0.013 0.002 PHE C 27 TRP 0.017 0.002 TRP C 106 HIS 0.002 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 5154) covalent geometry : angle 0.64218 ( 7001) SS BOND : bond 0.00609 ( 8) SS BOND : angle 2.42155 ( 16) hydrogen bonds : bond 0.03462 ( 123) hydrogen bonds : angle 6.53404 ( 324) link_BETA1-4 : bond 0.00439 ( 1) link_BETA1-4 : angle 0.83336 ( 3) link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 2.93873 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9251 (mmmt) cc_final: 0.8943 (mmtm) REVERT: C 73 ASP cc_start: 0.8323 (t70) cc_final: 0.7123 (t0) REVERT: C 83 MET cc_start: 0.7628 (mtt) cc_final: 0.7115 (mtt) REVERT: C 89 GLU cc_start: 0.7725 (mp0) cc_final: 0.7276 (mp0) REVERT: G 353 TRP cc_start: 0.8824 (p-90) cc_final: 0.8572 (p-90) REVERT: G 378 LYS cc_start: 0.8907 (mttm) cc_final: 0.8328 (mtmm) REVERT: L 2 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8822 (mt) REVERT: H 73 ASP cc_start: 0.7304 (t0) cc_final: 0.6484 (t0) REVERT: H 76 MET cc_start: 0.8351 (mpp) cc_final: 0.8149 (mpp) REVERT: H 87 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7407 (mtt180) outliers start: 26 outliers final: 22 residues processed: 157 average time/residue: 0.0726 time to fit residues: 14.7161 Evaluate side-chains 157 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 0.0020 chunk 43 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.095398 restraints weight = 10325.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098472 restraints weight = 5876.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100612 restraints weight = 4017.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102071 restraints weight = 3053.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103131 restraints weight = 2498.698| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5164 Z= 0.124 Angle : 0.642 8.936 7023 Z= 0.337 Chirality : 0.045 0.156 763 Planarity : 0.004 0.052 891 Dihedral : 5.690 76.753 754 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.53 % Allowed : 26.09 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -2.58 (0.31), residues: 638 helix: -3.44 (0.79), residues: 27 sheet: -1.21 (0.34), residues: 227 loop : -1.94 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.020 0.001 TYR C 95 PHE 0.016 0.002 PHE L 46 TRP 0.013 0.001 TRP C 106 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5154) covalent geometry : angle 0.63300 ( 7001) SS BOND : bond 0.00418 ( 8) SS BOND : angle 1.99626 ( 16) hydrogen bonds : bond 0.03311 ( 123) hydrogen bonds : angle 6.38484 ( 324) link_BETA1-4 : bond 0.00360 ( 1) link_BETA1-4 : angle 0.88432 ( 3) link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 2.92904 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 60 TYR cc_start: 0.9402 (OUTLIER) cc_final: 0.8826 (m-10) REVERT: C 73 ASP cc_start: 0.8243 (t70) cc_final: 0.7452 (t0) REVERT: C 81 LEU cc_start: 0.7580 (tt) cc_final: 0.7201 (tt) REVERT: C 83 MET cc_start: 0.7769 (mtt) cc_final: 0.7492 (mtt) REVERT: C 89 GLU cc_start: 0.7753 (mp0) cc_final: 0.7362 (mp0) REVERT: E 89 GLN cc_start: 0.9175 (tm130) cc_final: 0.8943 (tm-30) REVERT: G 353 TRP cc_start: 0.8813 (p-90) cc_final: 0.8549 (p-90) REVERT: L 2 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8712 (mt) REVERT: L 100 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8617 (tmtt) REVERT: H 73 ASP cc_start: 0.7212 (t0) cc_final: 0.5912 (t0) REVERT: H 76 MET cc_start: 0.8348 (mpp) cc_final: 0.7942 (mpp) REVERT: H 87 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7457 (mtt180) outliers start: 25 outliers final: 22 residues processed: 156 average time/residue: 0.0734 time to fit residues: 14.7806 Evaluate side-chains 155 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.0670 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.111615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.094503 restraints weight = 10500.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097542 restraints weight = 5954.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099655 restraints weight = 4067.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.101052 restraints weight = 3096.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102189 restraints weight = 2548.258| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5164 Z= 0.145 Angle : 0.678 8.725 7023 Z= 0.352 Chirality : 0.045 0.153 763 Planarity : 0.004 0.048 891 Dihedral : 5.722 76.781 754 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.07 % Allowed : 25.18 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -2.60 (0.31), residues: 638 helix: -3.52 (0.78), residues: 27 sheet: -1.18 (0.34), residues: 229 loop : -1.98 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.017 0.001 TYR E 94 PHE 0.014 0.002 PHE L 46 TRP 0.013 0.001 TRP C 106 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 5154) covalent geometry : angle 0.66083 ( 7001) SS BOND : bond 0.00554 ( 8) SS BOND : angle 2.98294 ( 16) hydrogen bonds : bond 0.03334 ( 123) hydrogen bonds : angle 6.49394 ( 324) link_BETA1-4 : bond 0.00335 ( 1) link_BETA1-4 : angle 0.93996 ( 3) link_NAG-ASN : bond 0.00070 ( 1) link_NAG-ASN : angle 2.92596 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9232 (mmmt) cc_final: 0.8902 (mmtm) REVERT: C 60 TYR cc_start: 0.9374 (OUTLIER) cc_final: 0.8959 (m-10) REVERT: C 73 ASP cc_start: 0.8394 (t70) cc_final: 0.7566 (t0) REVERT: C 81 LEU cc_start: 0.7531 (tt) cc_final: 0.7180 (tt) REVERT: C 89 GLU cc_start: 0.7767 (mp0) cc_final: 0.7371 (mp0) REVERT: G 340 GLU cc_start: 0.8619 (tp30) cc_final: 0.8145 (mp0) REVERT: G 353 TRP cc_start: 0.8823 (p-90) cc_final: 0.8593 (p-90) REVERT: L 2 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8750 (mt) REVERT: H 73 ASP cc_start: 0.7121 (t0) cc_final: 0.6444 (t0) REVERT: H 87 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7456 (mtt180) outliers start: 28 outliers final: 23 residues processed: 150 average time/residue: 0.0706 time to fit residues: 13.6374 Evaluate side-chains 152 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.091435 restraints weight = 10469.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.094474 restraints weight = 5931.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096607 restraints weight = 4073.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098076 restraints weight = 3094.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.099060 restraints weight = 2527.266| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5164 Z= 0.146 Angle : 0.672 8.869 7023 Z= 0.350 Chirality : 0.045 0.152 763 Planarity : 0.004 0.049 891 Dihedral : 5.788 76.183 754 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.71 % Allowed : 25.18 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -2.55 (0.31), residues: 638 helix: -3.49 (0.78), residues: 27 sheet: -1.08 (0.35), residues: 225 loop : -2.00 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.019 0.002 TYR C 95 PHE 0.014 0.002 PHE G 347 TRP 0.013 0.001 TRP C 106 HIS 0.002 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 5154) covalent geometry : angle 0.66348 ( 7001) SS BOND : bond 0.00816 ( 8) SS BOND : angle 1.89796 ( 16) hydrogen bonds : bond 0.03352 ( 123) hydrogen bonds : angle 6.47985 ( 324) link_BETA1-4 : bond 0.00313 ( 1) link_BETA1-4 : angle 0.93216 ( 3) link_NAG-ASN : bond 0.00094 ( 1) link_NAG-ASN : angle 2.89451 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9243 (mmmt) cc_final: 0.8943 (mmtm) REVERT: C 60 TYR cc_start: 0.9332 (OUTLIER) cc_final: 0.8773 (m-10) REVERT: C 73 ASP cc_start: 0.8403 (t70) cc_final: 0.7526 (t0) REVERT: C 81 LEU cc_start: 0.7566 (tt) cc_final: 0.7231 (tt) REVERT: C 89 GLU cc_start: 0.7783 (mp0) cc_final: 0.7370 (mp0) REVERT: C 98 LYS cc_start: 0.8745 (tmtt) cc_final: 0.8362 (tmtt) REVERT: E 89 GLN cc_start: 0.9171 (tm130) cc_final: 0.8908 (tm-30) REVERT: G 340 GLU cc_start: 0.8677 (tp30) cc_final: 0.8164 (mp0) REVERT: G 353 TRP cc_start: 0.8821 (p-90) cc_final: 0.8575 (p-90) REVERT: L 2 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8766 (mt) REVERT: L 100 LYS cc_start: 0.8916 (tmtt) cc_final: 0.8644 (tmtt) REVERT: H 73 ASP cc_start: 0.7095 (t0) cc_final: 0.6438 (t0) REVERT: H 76 MET cc_start: 0.8256 (mpp) cc_final: 0.7926 (mpp) REVERT: H 87 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7400 (mtt180) outliers start: 26 outliers final: 21 residues processed: 144 average time/residue: 0.0729 time to fit residues: 13.4368 Evaluate side-chains 151 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.093898 restraints weight = 10483.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097011 restraints weight = 6008.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099106 restraints weight = 4121.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100551 restraints weight = 3156.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101521 restraints weight = 2590.563| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5164 Z= 0.170 Angle : 0.713 8.898 7023 Z= 0.371 Chirality : 0.046 0.161 763 Planarity : 0.004 0.051 891 Dihedral : 5.902 77.155 754 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.71 % Allowed : 25.91 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -2.54 (0.31), residues: 638 helix: -3.45 (0.78), residues: 27 sheet: -1.04 (0.35), residues: 223 loop : -2.01 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.020 0.002 TYR E 94 PHE 0.014 0.002 PHE G 347 TRP 0.014 0.001 TRP C 106 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5154) covalent geometry : angle 0.70008 ( 7001) SS BOND : bond 0.00518 ( 8) SS BOND : angle 2.68418 ( 16) hydrogen bonds : bond 0.03433 ( 123) hydrogen bonds : angle 6.53654 ( 324) link_BETA1-4 : bond 0.00221 ( 1) link_BETA1-4 : angle 0.97157 ( 3) link_NAG-ASN : bond 0.00155 ( 1) link_NAG-ASN : angle 2.90086 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8965 (mmtm) REVERT: C 60 TYR cc_start: 0.9365 (OUTLIER) cc_final: 0.8939 (m-80) REVERT: C 73 ASP cc_start: 0.8485 (t70) cc_final: 0.7595 (t0) REVERT: C 89 GLU cc_start: 0.7776 (mp0) cc_final: 0.7353 (mp0) REVERT: C 98 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8350 (tmtt) REVERT: E 89 GLN cc_start: 0.9141 (tm130) cc_final: 0.8741 (pp30) REVERT: G 340 GLU cc_start: 0.8648 (tp30) cc_final: 0.8181 (mp0) REVERT: G 353 TRP cc_start: 0.8844 (p-90) cc_final: 0.8595 (p-90) REVERT: G 378 LYS cc_start: 0.8953 (mttm) cc_final: 0.8366 (mtmm) REVERT: L 2 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8822 (mt) REVERT: L 100 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8662 (tmtt) REVERT: H 73 ASP cc_start: 0.7165 (t0) cc_final: 0.6501 (t0) REVERT: H 76 MET cc_start: 0.8236 (mpp) cc_final: 0.7891 (mpp) REVERT: H 87 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7395 (mtt180) outliers start: 26 outliers final: 23 residues processed: 148 average time/residue: 0.0731 time to fit residues: 13.8840 Evaluate side-chains 155 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.094497 restraints weight = 10627.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097611 restraints weight = 6033.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.099746 restraints weight = 4127.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101225 restraints weight = 3151.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102237 restraints weight = 2574.987| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5164 Z= 0.156 Angle : 0.702 8.892 7023 Z= 0.364 Chirality : 0.045 0.159 763 Planarity : 0.004 0.051 891 Dihedral : 5.889 77.170 754 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.71 % Allowed : 26.63 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 aren not related in a simple way. whole: -2.45 (0.31), residues: 638 helix: -3.41 (0.78), residues: 27 sheet: -0.98 (0.35), residues: 223 loop : -1.95 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.020 0.002 TYR C 95 PHE 0.014 0.002 PHE G 347 TRP 0.014 0.001 TRP C 106 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5154) covalent geometry : angle 0.69008 ( 7001) SS BOND : bond 0.00509 ( 8) SS BOND : angle 2.47158 ( 16) hydrogen bonds : bond 0.03345 ( 123) hydrogen bonds : angle 6.51654 ( 324) link_BETA1-4 : bond 0.00313 ( 1) link_BETA1-4 : angle 0.95760 ( 3) link_NAG-ASN : bond 0.00138 ( 1) link_NAG-ASN : angle 2.86298 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.94 seconds wall clock time: 23 minutes 1.96 seconds (1381.96 seconds total)