Starting phenix.real_space_refine on Sat May 10 05:03:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iva_35755/05_2025/8iva_35755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iva_35755/05_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_35755/05_2025/8iva_35755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iva_35755/05_2025/8iva_35755.map" model { file = "/net/cci-nas-00/data/ceres_data/8iva_35755/05_2025/8iva_35755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iva_35755/05_2025/8iva_35755.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.30, per 1000 atoms: 1.65 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: 1.19 Conformation dependent library (CDL) restraints added in 604.0 milliseconds 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: 0.72 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: 1.52 Time building geometry restraints manager: 1.42 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: 30.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.480 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.450 ------------------------------------------------------------------------------- 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 : 5.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.002 TRP C 106 HIS 0.004 0.001 HIS C 35 PHE 0.022 0.002 PHE E 83 TYR 0.027 0.002 TYR E 94 ARG 0.005 0.001 ARG G 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00196 ( 1) link_NAG-ASN : angle 5.17553 ( 3) link_BETA1-4 : bond 0.00671 ( 1) link_BETA1-4 : angle 1.30442 ( 3) hydrogen bonds : bond 0.27035 ( 123) hydrogen bonds : angle 11.18507 ( 324) SS BOND : bond 0.08879 ( 8) SS BOND : angle 6.36753 ( 16) covalent geometry : bond 0.00552 ( 5154) covalent geometry : angle 0.97365 ( 7001) *********************** 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 : 0.565 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 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: 0.7319 (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: 0.7478 (tm-30) REVERT: E 90 GLN cc_start: 0.7556 (pp30) cc_final: 0.6812 (pp30) REVERT: E 93 SER cc_start: 0.8477 (m) cc_final: 0.8133 (m) REVERT: E 107 LYS cc_start: 0.4448 (tttt) cc_final: 0.3688 (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: 0.7996 (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: 0.6983 (ttpt) REVERT: L 86 TYR cc_start: 0.8370 (m-80) cc_final: 0.7987 (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: 0.1991 time to fit residues: 49.5263 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 : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.0000 chunk 57 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094966 restraints weight = 10277.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.098068 restraints weight = 5959.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100263 restraints weight = 4115.660| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5164 Z= 0.145 Angle : 0.654 7.863 7023 Z= 0.349 Chirality : 0.046 0.160 763 Planarity : 0.005 0.055 891 Dihedral : 6.067 73.538 754 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.35 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.29), residues: 638 helix: -3.43 (0.82), residues: 21 sheet: -1.91 (0.32), residues: 227 loop : -2.45 (0.27), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 106 HIS 0.003 0.001 HIS C 35 PHE 0.022 0.002 PHE G 400 TYR 0.024 0.002 TYR E 94 ARG 0.005 0.001 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00021 ( 1) link_NAG-ASN : angle 3.36190 ( 3) link_BETA1-4 : bond 0.00700 ( 1) link_BETA1-4 : angle 0.83085 ( 3) hydrogen bonds : bond 0.04143 ( 123) hydrogen bonds : angle 7.58218 ( 324) SS BOND : bond 0.00640 ( 8) SS BOND : angle 2.24764 ( 16) covalent geometry : bond 0.00332 ( 5154) covalent geometry : angle 0.64172 ( 7001) *********************** 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 191 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 LYS cc_start: 0.8746 (mmtm) cc_final: 0.8446 (mmtm) REVERT: C 94 TYR cc_start: 0.8644 (m-80) cc_final: 0.7886 (m-10) REVERT: E 89 GLN cc_start: 0.9224 (tm-30) cc_final: 0.8660 (tm-30) REVERT: E 107 LYS cc_start: 0.5125 (tttt) cc_final: 0.4423 (tptm) REVERT: G 378 LYS cc_start: 0.8836 (mttm) cc_final: 0.8342 (mtmm) REVERT: L 34 TRP cc_start: 0.8719 (m100) cc_final: 0.8288 (m100) REVERT: L 44 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8146 (ttpt) REVERT: L 78 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8156 (mm-30) REVERT: H 76 MET cc_start: 0.8212 (mpp) cc_final: 0.7910 (mtm) REVERT: H 93 MET cc_start: 0.7435 (tpp) cc_final: 0.7206 (tpp) REVERT: H 102 ASN cc_start: 0.8307 (p0) cc_final: 0.7969 (p0) outliers start: 24 outliers final: 11 residues processed: 177 average time/residue: 0.1786 time to fit residues: 39.5795 Evaluate side-chains 152 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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 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 42 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.0000 chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS C 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.113781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096718 restraints weight = 10362.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099813 restraints weight = 5866.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101997 restraints weight = 3995.376| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 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 = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5164 Z= 0.123 Angle : 0.628 8.687 7023 Z= 0.332 Chirality : 0.046 0.165 763 Planarity : 0.005 0.053 891 Dihedral : 5.738 72.340 754 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.30), residues: 638 helix: -3.19 (0.90), residues: 21 sheet: -1.64 (0.34), residues: 225 loop : -2.19 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.002 0.000 HIS C 35 PHE 0.019 0.002 PHE G 347 TYR 0.020 0.002 TYR G 473 ARG 0.006 0.001 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 3.03322 ( 3) link_BETA1-4 : bond 0.00396 ( 1) link_BETA1-4 : angle 0.84080 ( 3) hydrogen bonds : bond 0.03718 ( 123) hydrogen bonds : angle 6.83417 ( 324) SS BOND : bond 0.00335 ( 8) SS BOND : angle 1.75584 ( 16) covalent geometry : bond 0.00290 ( 5154) covalent geometry : angle 0.62000 ( 7001) *********************** 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 170 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: C 76 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8553 (mmtm) REVERT: C 83 MET cc_start: 0.7794 (mtt) cc_final: 0.7506 (mtt) REVERT: C 89 GLU cc_start: 0.7680 (mp0) cc_final: 0.7234 (mp0) REVERT: E 89 GLN cc_start: 0.9234 (tm-30) cc_final: 0.8711 (tm-30) REVERT: E 107 LYS cc_start: 0.5154 (tttt) cc_final: 0.4437 (tptm) REVERT: L 78 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8044 (mm-30) REVERT: L 90 TRP cc_start: 0.8896 (t60) cc_final: 0.8684 (t60) REVERT: H 73 ASP cc_start: 0.7337 (t0) cc_final: 0.6218 (t0) REVERT: H 102 ASN cc_start: 0.8288 (p0) cc_final: 0.7986 (p0) outliers start: 24 outliers final: 16 residues processed: 161 average time/residue: 0.1726 time to fit residues: 35.1874 Evaluate side-chains 149 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.541 ------------------------------------------------------------------------------- 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 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 494 SER 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 49 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 0.0170 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 0.0040 chunk 15 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 overall best weight: 0.3430 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.115127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.097932 restraints weight = 10411.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101152 restraints weight = 5835.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103371 restraints weight = 3929.498| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 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 = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3066 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= 0.109 Angle : 0.620 8.306 7023 Z= 0.325 Chirality : 0.044 0.156 763 Planarity : 0.005 0.050 891 Dihedral : 5.497 71.389 754 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.17 % Allowed : 21.56 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.31), residues: 638 helix: -3.64 (0.75), residues: 27 sheet: -1.31 (0.34), residues: 227 loop : -2.10 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 106 HIS 0.004 0.001 HIS C 35 PHE 0.019 0.002 PHE G 347 TYR 0.021 0.001 TYR G 473 ARG 0.004 0.001 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 2.86418 ( 3) link_BETA1-4 : bond 0.00369 ( 1) link_BETA1-4 : angle 0.83384 ( 3) hydrogen bonds : bond 0.03475 ( 123) hydrogen bonds : angle 6.54646 ( 324) SS BOND : bond 0.00532 ( 8) SS BOND : angle 2.62550 ( 16) covalent geometry : bond 0.00252 ( 5154) covalent geometry : angle 0.60520 ( 7001) *********************** 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 166 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9362 (mmmt) cc_final: 0.9103 (mmtm) REVERT: C 83 MET cc_start: 0.8067 (mtt) cc_final: 0.7831 (mtt) REVERT: C 89 GLU cc_start: 0.7630 (mp0) cc_final: 0.7237 (mp0) REVERT: E 89 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8737 (tm-30) REVERT: E 107 LYS cc_start: 0.5066 (tttt) cc_final: 0.4385 (tptm) REVERT: G 340 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8216 (mp0) REVERT: L 78 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8025 (mm-30) REVERT: L 90 TRP cc_start: 0.8836 (t60) cc_final: 0.8483 (t60) REVERT: H 73 ASP cc_start: 0.7037 (t0) cc_final: 0.6704 (t0) REVERT: H 102 ASN cc_start: 0.8285 (p0) cc_final: 0.8005 (p0) outliers start: 23 outliers final: 18 residues processed: 156 average time/residue: 0.1662 time to fit residues: 33.0086 Evaluate side-chains 150 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 104 LEU 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 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 25 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** C 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.092519 restraints weight = 10622.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.095610 restraints weight = 6104.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097716 restraints weight = 4180.031| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 5164 Z= 0.228 Angle : 0.703 9.152 7023 Z= 0.368 Chirality : 0.047 0.175 763 Planarity : 0.005 0.055 891 Dihedral : 5.912 76.387 754 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.71 % Allowed : 21.74 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.31), residues: 638 helix: -3.66 (0.73), residues: 27 sheet: -1.26 (0.35), residues: 222 loop : -2.05 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 106 HIS 0.002 0.001 HIS L 88 PHE 0.025 0.002 PHE G 347 TYR 0.022 0.002 TYR E 94 ARG 0.005 0.001 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 1) link_NAG-ASN : angle 3.11220 ( 3) link_BETA1-4 : bond 0.00007 ( 1) link_BETA1-4 : angle 1.03216 ( 3) hydrogen bonds : bond 0.04050 ( 123) hydrogen bonds : angle 6.64273 ( 324) SS BOND : bond 0.00553 ( 8) SS BOND : angle 2.47131 ( 16) covalent geometry : bond 0.00530 ( 5154) covalent geometry : angle 0.69040 ( 7001) *********************** 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 163 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 60 TYR cc_start: 0.9539 (OUTLIER) cc_final: 0.9255 (m-80) REVERT: C 73 ASP cc_start: 0.8437 (t70) cc_final: 0.7066 (t0) REVERT: C 76 LYS cc_start: 0.8582 (mmtm) cc_final: 0.8223 (mmtm) REVERT: C 89 GLU cc_start: 0.7666 (mp0) cc_final: 0.7241 (mp0) REVERT: C 98 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8248 (tttm) REVERT: E 89 GLN cc_start: 0.9249 (tm-30) cc_final: 0.8753 (tm-30) REVERT: G 340 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8332 (mp0) REVERT: G 378 LYS cc_start: 0.8947 (mttm) cc_final: 0.8362 (mtmm) REVERT: L 32 MET cc_start: 0.8739 (mmt) cc_final: 0.8535 (mmm) REVERT: H 73 ASP cc_start: 0.7220 (t0) cc_final: 0.6864 (t0) REVERT: H 79 LEU cc_start: 0.7893 (tp) cc_final: 0.7571 (tp) outliers start: 26 outliers final: 19 residues processed: 152 average time/residue: 0.1682 time to fit residues: 32.5771 Evaluate side-chains 153 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 60 TYR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 105 LEU 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 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 48 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 0.0050 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094980 restraints weight = 10455.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098123 restraints weight = 5940.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100301 restraints weight = 4038.480| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5164 Z= 0.141 Angle : 0.638 8.504 7023 Z= 0.335 Chirality : 0.045 0.156 763 Planarity : 0.005 0.053 891 Dihedral : 5.614 76.002 754 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.89 % Allowed : 22.46 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.31), residues: 638 helix: -3.66 (0.74), residues: 27 sheet: -1.20 (0.34), residues: 234 loop : -1.98 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 106 HIS 0.003 0.001 HIS C 35 PHE 0.018 0.002 PHE G 347 TYR 0.019 0.002 TYR E 94 ARG 0.005 0.001 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 1) link_NAG-ASN : angle 2.84498 ( 3) link_BETA1-4 : bond 0.00321 ( 1) link_BETA1-4 : angle 0.94304 ( 3) hydrogen bonds : bond 0.03589 ( 123) hydrogen bonds : angle 6.48263 ( 324) SS BOND : bond 0.00514 ( 8) SS BOND : angle 2.19351 ( 16) covalent geometry : bond 0.00329 ( 5154) covalent geometry : angle 0.62682 ( 7001) *********************** 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: 27 poor density : 141 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 34 MET cc_start: 0.8052 (mtm) cc_final: 0.7780 (ptp) REVERT: C 43 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8970 (mmtm) REVERT: C 73 ASP cc_start: 0.8478 (t70) cc_final: 0.7221 (t70) REVERT: C 76 LYS cc_start: 0.8685 (mmtm) cc_final: 0.8407 (mmtm) REVERT: C 81 LEU cc_start: 0.7565 (tt) cc_final: 0.7119 (tt) REVERT: C 89 GLU cc_start: 0.7614 (mp0) cc_final: 0.7232 (mp0) REVERT: C 98 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8404 (tttm) REVERT: G 340 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8229 (mp0) REVERT: G 353 TRP cc_start: 0.8840 (p-90) cc_final: 0.8565 (p-90) REVERT: G 378 LYS cc_start: 0.8940 (mttm) cc_final: 0.8340 (mtmm) REVERT: L 2 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8803 (mt) REVERT: L 90 TRP cc_start: 0.8941 (t60) cc_final: 0.8719 (t60) REVERT: H 73 ASP cc_start: 0.7178 (t0) cc_final: 0.6850 (t0) outliers start: 27 outliers final: 23 residues processed: 157 average time/residue: 0.2290 time to fit residues: 47.5887 Evaluate side-chains 159 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 64 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 98 LYS 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 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 427 ASP 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 9 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 388 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 = 0.3382 r_free = 0.3382 target = 0.110658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.093381 restraints weight = 10316.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.096499 restraints weight = 5847.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.098674 restraints weight = 3980.850| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5164 Z= 0.155 Angle : 0.665 8.959 7023 Z= 0.346 Chirality : 0.045 0.158 763 Planarity : 0.005 0.054 891 Dihedral : 5.676 75.477 754 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.25 % Allowed : 23.73 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.31), residues: 638 helix: -3.59 (0.75), residues: 27 sheet: -1.12 (0.34), residues: 233 loop : -1.98 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.002 0.001 HIS C 35 PHE 0.018 0.002 PHE G 347 TYR 0.019 0.002 TYR E 94 ARG 0.006 0.001 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 2.91437 ( 3) link_BETA1-4 : bond 0.00134 ( 1) link_BETA1-4 : angle 0.86083 ( 3) hydrogen bonds : bond 0.03571 ( 123) hydrogen bonds : angle 6.50613 ( 324) SS BOND : bond 0.00981 ( 8) SS BOND : angle 1.65502 ( 16) covalent geometry : bond 0.00357 ( 5154) covalent geometry : angle 0.65793 ( 7001) *********************** 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 168 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9277 (mmmt) cc_final: 0.9039 (mmtm) REVERT: C 73 ASP cc_start: 0.8496 (t70) cc_final: 0.7239 (t70) REVERT: C 76 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8465 (mmtm) REVERT: C 81 LEU cc_start: 0.7623 (tt) cc_final: 0.7236 (tt) REVERT: C 89 GLU cc_start: 0.7674 (mp0) cc_final: 0.7283 (mp0) REVERT: E 89 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8905 (tm-30) REVERT: G 340 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8269 (mp0) REVERT: G 353 TRP cc_start: 0.8861 (p-90) cc_final: 0.8568 (p-90) REVERT: G 385 THR cc_start: 0.8562 (p) cc_final: 0.8227 (m) REVERT: L 2 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8826 (mt) REVERT: H 73 ASP cc_start: 0.7321 (t0) cc_final: 0.6945 (t0) outliers start: 29 outliers final: 23 residues processed: 154 average time/residue: 0.1624 time to fit residues: 32.1762 Evaluate side-chains 161 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 64 VAL Chi-restraints excluded: chain C residue 88 VAL 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 47 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 89 GLN 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 427 ASP Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 45 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 51 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 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 = 0.3394 r_free = 0.3394 target = 0.111402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.094108 restraints weight = 10554.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097190 restraints weight = 5973.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099396 restraints weight = 4084.823| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5164 Z= 0.154 Angle : 0.665 8.761 7023 Z= 0.346 Chirality : 0.045 0.156 763 Planarity : 0.005 0.054 891 Dihedral : 5.724 75.805 754 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 5.62 % Allowed : 23.73 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.31), residues: 638 helix: -3.59 (0.75), residues: 27 sheet: -1.05 (0.34), residues: 233 loop : -2.00 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.002 0.001 HIS C 35 PHE 0.018 0.002 PHE G 347 TYR 0.019 0.002 TYR E 94 ARG 0.007 0.001 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 1) link_NAG-ASN : angle 2.89114 ( 3) link_BETA1-4 : bond 0.00241 ( 1) link_BETA1-4 : angle 0.91294 ( 3) hydrogen bonds : bond 0.03528 ( 123) hydrogen bonds : angle 6.52453 ( 324) SS BOND : bond 0.00553 ( 8) SS BOND : angle 1.53969 ( 16) covalent geometry : bond 0.00361 ( 5154) covalent geometry : angle 0.65889 ( 7001) *********************** 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 167 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASP cc_start: 0.8534 (t70) cc_final: 0.8222 (t70) REVERT: C 81 LEU cc_start: 0.7604 (tt) cc_final: 0.7107 (tt) REVERT: C 89 GLU cc_start: 0.7652 (mp0) cc_final: 0.7260 (mp0) REVERT: G 340 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8239 (mp0) REVERT: G 353 TRP cc_start: 0.8865 (p-90) cc_final: 0.8597 (p-90) REVERT: G 378 LYS cc_start: 0.8949 (mttm) cc_final: 0.8353 (mtmm) REVERT: G 385 THR cc_start: 0.8521 (p) cc_final: 0.8174 (m) REVERT: L 2 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8842 (mt) REVERT: H 73 ASP cc_start: 0.7317 (t0) cc_final: 0.6898 (t0) outliers start: 31 outliers final: 26 residues processed: 154 average time/residue: 0.1626 time to fit residues: 32.1870 Evaluate side-chains 160 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 64 VAL Chi-restraints excluded: chain C residue 88 VAL 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 47 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 82 ASP 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 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 57 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 388 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 = 0.3403 r_free = 0.3403 target = 0.112099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095067 restraints weight = 10355.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.098119 restraints weight = 5894.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.100314 restraints weight = 4029.299| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3769 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= 0.150 Angle : 0.690 8.838 7023 Z= 0.356 Chirality : 0.045 0.155 763 Planarity : 0.004 0.054 891 Dihedral : 5.723 75.717 754 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.07 % Allowed : 23.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.31), residues: 638 helix: -3.57 (0.75), residues: 27 sheet: -1.06 (0.34), residues: 235 loop : -2.00 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.002 0.001 HIS C 35 PHE 0.017 0.002 PHE G 347 TYR 0.019 0.002 TYR E 94 ARG 0.006 0.001 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 1) link_NAG-ASN : angle 2.88030 ( 3) link_BETA1-4 : bond 0.00214 ( 1) link_BETA1-4 : angle 0.92058 ( 3) hydrogen bonds : bond 0.03475 ( 123) hydrogen bonds : angle 6.49592 ( 324) SS BOND : bond 0.00503 ( 8) SS BOND : angle 2.62962 ( 16) covalent geometry : bond 0.00351 ( 5154) covalent geometry : angle 0.67629 ( 7001) *********************** 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 163 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9271 (mmmt) cc_final: 0.8935 (mmtm) REVERT: C 73 ASP cc_start: 0.8770 (t70) cc_final: 0.7776 (t0) REVERT: C 81 LEU cc_start: 0.7497 (tt) cc_final: 0.7126 (tt) REVERT: C 83 MET cc_start: 0.7650 (mtt) cc_final: 0.7386 (mtt) REVERT: C 89 GLU cc_start: 0.7670 (mp0) cc_final: 0.7255 (mp0) REVERT: C 98 LYS cc_start: 0.8598 (tmtt) cc_final: 0.8130 (tmtt) REVERT: C 110 ASP cc_start: 0.8223 (t0) cc_final: 0.7962 (t0) REVERT: G 340 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8245 (mp0) REVERT: G 353 TRP cc_start: 0.8871 (p-90) cc_final: 0.8593 (p-90) REVERT: G 378 LYS cc_start: 0.8920 (mttm) cc_final: 0.8295 (mtmm) REVERT: G 385 THR cc_start: 0.8522 (p) cc_final: 0.8215 (m) REVERT: L 2 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8839 (mt) REVERT: L 100 LYS cc_start: 0.8941 (tmtt) cc_final: 0.8706 (tmtt) REVERT: H 73 ASP cc_start: 0.7317 (t0) cc_final: 0.6889 (t0) outliers start: 28 outliers final: 24 residues processed: 153 average time/residue: 0.1660 time to fit residues: 32.6587 Evaluate side-chains 156 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 88 VAL 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 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 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 495 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 57 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 61 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 56 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3389 r_free = 0.3389 target = 0.111126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.094061 restraints weight = 10344.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.097030 restraints weight = 5911.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.099177 restraints weight = 4077.419| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5164 Z= 0.171 Angle : 0.713 8.806 7023 Z= 0.370 Chirality : 0.047 0.299 763 Planarity : 0.004 0.054 891 Dihedral : 5.803 76.653 754 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 5.07 % Allowed : 23.73 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.31), residues: 638 helix: -3.57 (0.75), residues: 27 sheet: -1.03 (0.34), residues: 230 loop : -1.96 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.002 0.001 HIS C 35 PHE 0.018 0.002 PHE G 347 TYR 0.019 0.002 TYR E 94 ARG 0.008 0.001 ARG G 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 1) link_NAG-ASN : angle 2.88101 ( 3) link_BETA1-4 : bond 0.00108 ( 1) link_BETA1-4 : angle 0.91179 ( 3) hydrogen bonds : bond 0.03600 ( 123) hydrogen bonds : angle 6.49921 ( 324) SS BOND : bond 0.00576 ( 8) SS BOND : angle 2.56556 ( 16) covalent geometry : bond 0.00401 ( 5154) covalent geometry : angle 0.70095 ( 7001) ********************** 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 160 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9293 (mmmt) cc_final: 0.8963 (mmtm) REVERT: C 73 ASP cc_start: 0.8750 (t70) cc_final: 0.7733 (t0) REVERT: C 81 LEU cc_start: 0.7350 (tt) cc_final: 0.6984 (tt) REVERT: C 89 GLU cc_start: 0.7690 (mp0) cc_final: 0.7269 (mp0) REVERT: C 98 LYS cc_start: 0.8602 (tmtt) cc_final: 0.8228 (tmtt) REVERT: G 340 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8261 (mp0) REVERT: G 353 TRP cc_start: 0.8904 (p-90) cc_final: 0.8631 (p-90) REVERT: G 378 LYS cc_start: 0.8932 (mttm) cc_final: 0.8323 (mtmm) REVERT: G 385 THR cc_start: 0.8526 (p) cc_final: 0.8234 (m) REVERT: L 2 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8906 (mt) REVERT: H 73 ASP cc_start: 0.7292 (t0) cc_final: 0.6879 (t0) outliers start: 28 outliers final: 24 residues processed: 150 average time/residue: 0.1611 time to fit residues: 31.1880 Evaluate side-chains 156 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 88 VAL 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 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 335 LEU Chi-restraints excluded: chain G residue 362 VAL 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 495 TYR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 45 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 36 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.0670 chunk 61 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 overall best weight: 0.5920 ------------------------------------------------------------------------------- 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 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3417 r_free = 0.3417 target = 0.112971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.095799 restraints weight = 10529.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098906 restraints weight = 5983.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101068 restraints weight = 4079.067| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3938 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= 0.137 Angle : 0.693 8.752 7023 Z= 0.359 Chirality : 0.046 0.238 763 Planarity : 0.005 0.054 891 Dihedral : 5.727 75.604 754 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.35 % Allowed : 25.00 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.31), residues: 638 helix: -3.56 (0.76), residues: 27 sheet: -1.00 (0.34), residues: 235 loop : -1.95 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 106 HIS 0.002 0.001 HIS C 35 PHE 0.015 0.001 PHE G 347 TYR 0.018 0.002 TYR E 94 ARG 0.006 0.001 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00101 ( 1) link_NAG-ASN : angle 2.81427 ( 3) link_BETA1-4 : bond 0.00362 ( 1) link_BETA1-4 : angle 0.93940 ( 3) hydrogen bonds : bond 0.03400 ( 123) hydrogen bonds : angle 6.35280 ( 324) SS BOND : bond 0.00542 ( 8) SS BOND : angle 2.45689 ( 16) covalent geometry : bond 0.00319 ( 5154) covalent geometry : angle 0.68137 ( 7001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2567.58 seconds wall clock time: 47 minutes 18.61 seconds (2838.61 seconds total)