Starting phenix.real_space_refine on Thu Jul 24 04:24:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iva_35755/07_2025/8iva_35755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iva_35755/07_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_35755/07_2025/8iva_35755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iva_35755/07_2025/8iva_35755.map" model { file = "/net/cci-nas-00/data/ceres_data/8iva_35755/07_2025/8iva_35755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iva_35755/07_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-5711/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: 5.45, per 1000 atoms: 1.08 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: 1.17 Conformation dependent library (CDL) restraints added in 609.8 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: 0.65 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: 1.22 Time building geometry restraints manager: 1.41 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: 30.190 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.810 Find NCS groups from input model: 0.070 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.430 ------------------------------------------------------------------------------- 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 : 0.531 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: 0.1966 time to fit residues: 49.1225 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 : 0.463 ------------------------------------------------------------------------------- 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 = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094964 restraints weight = 10277.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.098062 restraints weight = 5959.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100261 restraints weight = 4117.723| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 LYS cc_start: 0.8738 (mmtm) cc_final: 0.8439 (mmtm) REVERT: C 94 TYR cc_start: 0.8643 (m-80) cc_final: 0.7892 (m-10) REVERT: E 89 GLN cc_start: 0.9220 (tm-30) cc_final: 0.8669 (tm-30) REVERT: E 107 LYS cc_start: 0.5131 (tttt) cc_final: 0.4434 (tptm) REVERT: G 378 LYS cc_start: 0.8849 (mttm) cc_final: 0.8371 (mtmm) REVERT: L 34 TRP cc_start: 0.8711 (m100) cc_final: 0.8294 (m100) REVERT: L 44 LYS cc_start: 0.8376 (mtmm) cc_final: 0.8171 (ttpt) REVERT: L 78 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8139 (mm-30) REVERT: H 76 MET cc_start: 0.8202 (mpp) cc_final: 0.7894 (mtm) REVERT: H 93 MET cc_start: 0.7445 (tpp) cc_final: 0.7229 (tpp) REVERT: H 102 ASN cc_start: 0.8296 (p0) cc_final: 0.7959 (p0) outliers start: 24 outliers final: 11 residues processed: 177 average time/residue: 0.2643 time to fit residues: 59.5361 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 : 0.791 ------------------------------------------------------------------------------- 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: 0.0770 chunk 22 optimal weight: 0.0000 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 overall best weight: 0.3342 ------------------------------------------------------------------------------- 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 = 0.3495 r_free = 0.3495 target = 0.117867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100488 restraints weight = 10525.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103631 restraints weight = 6190.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105827 restraints weight = 4305.778| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5164 Z= 0.113 Angle : 0.619 8.668 7023 Z= 0.327 Chirality : 0.045 0.164 763 Planarity : 0.005 0.053 891 Dihedral : 5.645 71.214 754 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.62 % Allowed : 20.47 % 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: -2.98 (0.30), residues: 638 helix: -3.20 (0.90), residues: 21 sheet: -1.62 (0.33), residues: 225 loop : -2.20 (0.28), residues: 392 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 0.016 0.001 PHE G 400 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 0.00061 ( 1) link_NAG-ASN : angle 2.97062 ( 3) link_BETA1-4 : bond 0.00500 ( 1) link_BETA1-4 : angle 0.86979 ( 3) hydrogen bonds : bond 0.03638 ( 123) hydrogen bonds : angle 6.81438 ( 324) SS BOND : bond 0.00399 ( 8) SS BOND : angle 1.68170 ( 16) covalent geometry : bond 0.00266 ( 5154) covalent geometry : angle 0.61164 ( 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 168 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: C 82 GLN cc_start: 0.7828 (tp40) cc_final: 0.7619 (mm110) REVERT: C 83 MET cc_start: 0.7681 (mtt) cc_final: 0.7374 (mtt) REVERT: C 89 GLU cc_start: 0.7617 (mp0) cc_final: 0.7203 (mp0) REVERT: E 89 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8718 (tm-30) REVERT: E 107 LYS cc_start: 0.5136 (tttt) cc_final: 0.4424 (tptm) REVERT: G 340 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8249 (mp0) REVERT: L 78 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8011 (mm-30) REVERT: L 90 TRP cc_start: 0.8833 (t60) cc_final: 0.8624 (t60) REVERT: H 73 ASP cc_start: 0.7236 (t0) cc_final: 0.6189 (t0) REVERT: H 102 ASN cc_start: 0.8227 (p0) cc_final: 0.7946 (p0) outliers start: 20 outliers final: 14 residues processed: 161 average time/residue: 0.2083 time to fit residues: 43.2024 Evaluate side-chains 147 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 0.0040 chunk 55 optimal weight: 0.7980 overall best weight: 0.9194 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.112479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.095041 restraints weight = 10468.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098200 restraints weight = 5914.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100375 restraints weight = 4040.857| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5164 Z= 0.165 Angle : 0.657 8.070 7023 Z= 0.345 Chirality : 0.045 0.153 763 Planarity : 0.005 0.053 891 Dihedral : 5.649 72.954 754 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.99 % Allowed : 21.74 % 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: -2.83 (0.31), residues: 638 helix: -3.67 (0.72), residues: 27 sheet: -1.34 (0.34), residues: 227 loop : -2.14 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.015 0.003 HIS C 99 PHE 0.023 0.002 PHE G 347 TYR 0.021 0.002 TYR G 473 ARG 0.005 0.001 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00136 ( 1) link_NAG-ASN : angle 3.03420 ( 3) link_BETA1-4 : bond 0.00177 ( 1) link_BETA1-4 : angle 0.85044 ( 3) hydrogen bonds : bond 0.03773 ( 123) hydrogen bonds : angle 6.62626 ( 324) SS BOND : bond 0.00624 ( 8) SS BOND : angle 2.67461 ( 16) covalent geometry : bond 0.00387 ( 5154) covalent geometry : angle 0.64175 ( 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 161 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9378 (mmmt) cc_final: 0.9114 (mmtm) REVERT: C 76 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8392 (mmtm) REVERT: C 89 GLU cc_start: 0.7585 (mp0) cc_final: 0.7217 (mp0) REVERT: E 89 GLN cc_start: 0.9250 (tm-30) cc_final: 0.9034 (tm-30) REVERT: E 107 LYS cc_start: 0.5147 (tttt) cc_final: 0.4459 (tptm) REVERT: G 340 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8289 (mp0) REVERT: G 378 LYS cc_start: 0.8919 (mttm) cc_final: 0.8369 (mtmm) REVERT: L 32 MET cc_start: 0.8774 (mmm) cc_final: 0.8547 (mmm) REVERT: L 44 LYS cc_start: 0.8389 (mtmm) cc_final: 0.8149 (ttpt) REVERT: L 78 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8131 (mm-30) REVERT: L 90 TRP cc_start: 0.8955 (t60) cc_final: 0.8720 (t60) REVERT: H 73 ASP cc_start: 0.7115 (t0) cc_final: 0.6763 (t0) REVERT: H 102 ASN cc_start: 0.8353 (p0) cc_final: 0.8015 (p0) outliers start: 22 outliers final: 18 residues processed: 152 average time/residue: 0.1740 time to fit residues: 33.3993 Evaluate side-chains 152 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 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 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.113439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096166 restraints weight = 10501.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099330 restraints weight = 5929.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101490 restraints weight = 4028.219| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5164 Z= 0.135 Angle : 0.608 9.157 7023 Z= 0.323 Chirality : 0.044 0.156 763 Planarity : 0.005 0.052 891 Dihedral : 5.533 73.366 754 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.99 % Allowed : 21.01 % Favored : 75.00 % 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: -3.65 (0.73), residues: 27 sheet: -1.13 (0.34), residues: 224 loop : -2.03 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 106 HIS 0.001 0.001 HIS C 35 PHE 0.019 0.002 PHE G 347 TYR 0.019 0.002 TYR G 473 ARG 0.005 0.001 ARG E 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 1) link_NAG-ASN : angle 2.87184 ( 3) link_BETA1-4 : bond 0.00315 ( 1) link_BETA1-4 : angle 0.93004 ( 3) hydrogen bonds : bond 0.03543 ( 123) hydrogen bonds : angle 6.45656 ( 324) SS BOND : bond 0.00371 ( 8) SS BOND : angle 1.59636 ( 16) covalent geometry : bond 0.00313 ( 5154) covalent geometry : angle 0.60059 ( 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 156 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: C 73 ASP cc_start: 0.8482 (t70) cc_final: 0.7224 (t70) REVERT: C 76 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8428 (mmtm) REVERT: C 89 GLU cc_start: 0.7607 (mp0) cc_final: 0.7309 (mp0) REVERT: C 98 LYS cc_start: 0.8939 (tmmt) cc_final: 0.8447 (tttm) REVERT: G 340 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8248 (mp0) REVERT: G 378 LYS cc_start: 0.8935 (mttm) cc_final: 0.8352 (mtmm) REVERT: L 90 TRP cc_start: 0.8904 (t60) cc_final: 0.8665 (t60) REVERT: H 73 ASP cc_start: 0.7091 (t0) cc_final: 0.6806 (t0) outliers start: 22 outliers final: 19 residues processed: 148 average time/residue: 0.1834 time to fit residues: 34.2486 Evaluate side-chains 147 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 46 optimal weight: 0.0050 chunk 22 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS E 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.092374 restraints weight = 10536.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.095496 restraints weight = 6024.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097611 restraints weight = 4116.514| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 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 = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5164 Z= 0.182 Angle : 0.654 8.676 7023 Z= 0.344 Chirality : 0.045 0.159 763 Planarity : 0.005 0.055 891 Dihedral : 5.564 74.601 754 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.07 % Allowed : 21.74 % Favored : 73.19 % 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: -3.69 (0.73), residues: 27 sheet: -1.09 (0.34), residues: 231 loop : -1.95 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 106 HIS 0.004 0.001 HIS C 35 PHE 0.021 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 0.00165 ( 1) link_NAG-ASN : angle 2.96241 ( 3) link_BETA1-4 : bond 0.00239 ( 1) link_BETA1-4 : angle 1.04705 ( 3) hydrogen bonds : bond 0.03758 ( 123) hydrogen bonds : angle 6.45213 ( 324) SS BOND : bond 0.00557 ( 8) SS BOND : angle 2.32190 ( 16) covalent geometry : bond 0.00427 ( 5154) covalent geometry : angle 0.64204 ( 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 160 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9305 (mmmt) cc_final: 0.9037 (mmtm) REVERT: C 73 ASP cc_start: 0.8524 (t70) cc_final: 0.7395 (t70) REVERT: C 76 LYS cc_start: 0.8738 (mmtm) cc_final: 0.8503 (mmtm) REVERT: C 83 MET cc_start: 0.7731 (mtt) cc_final: 0.7213 (mtt) REVERT: C 89 GLU cc_start: 0.7626 (mp0) cc_final: 0.7312 (mp0) REVERT: E 89 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8893 (tm-30) REVERT: G 340 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8271 (mp0) REVERT: G 378 LYS cc_start: 0.8945 (mttm) cc_final: 0.8349 (mtmm) REVERT: L 2 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8842 (mt) REVERT: L 32 MET cc_start: 0.8635 (mmt) cc_final: 0.8427 (mmm) REVERT: H 73 ASP cc_start: 0.7174 (t0) cc_final: 0.6847 (t0) REVERT: H 78 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6469 (t) outliers start: 28 outliers final: 23 residues processed: 148 average time/residue: 0.1751 time to fit residues: 33.4704 Evaluate side-chains 155 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 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 89 GLN 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 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 78 THR 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: 1.9990 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.094810 restraints weight = 10365.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.097878 restraints weight = 5905.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099975 restraints weight = 4065.358| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 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 = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5164 Z= 0.161 Angle : 0.698 17.754 7023 Z= 0.364 Chirality : 0.047 0.263 763 Planarity : 0.005 0.054 891 Dihedral : 5.547 75.003 754 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 5.07 % Allowed : 22.83 % Favored : 72.10 % 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: -2.47 (0.31), residues: 638 helix: -3.62 (0.73), residues: 27 sheet: -1.01 (0.34), residues: 231 loop : -1.94 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 106 HIS 0.010 0.002 HIS C 99 PHE 0.019 0.002 PHE G 347 TYR 0.018 0.002 TYR E 94 ARG 0.006 0.001 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00066 ( 1) link_NAG-ASN : angle 2.87526 ( 3) link_BETA1-4 : bond 0.00225 ( 1) link_BETA1-4 : angle 0.90906 ( 3) hydrogen bonds : bond 0.03593 ( 123) hydrogen bonds : angle 6.47344 ( 324) SS BOND : bond 0.00992 ( 8) SS BOND : angle 2.30416 ( 16) covalent geometry : bond 0.00377 ( 5154) covalent geometry : angle 0.68775 ( 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 166 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9297 (mmmt) cc_final: 0.9062 (mmtm) REVERT: C 73 ASP cc_start: 0.8560 (t70) cc_final: 0.8237 (t70) REVERT: C 83 MET cc_start: 0.7713 (mtt) cc_final: 0.7251 (mtt) REVERT: C 89 GLU cc_start: 0.7614 (mp0) cc_final: 0.7313 (mp0) REVERT: G 340 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8276 (mp0) REVERT: G 378 LYS cc_start: 0.8952 (mttm) cc_final: 0.8344 (mtmm) REVERT: G 385 THR cc_start: 0.8540 (p) cc_final: 0.8191 (m) REVERT: L 2 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8841 (mt) REVERT: L 61 PHE cc_start: 0.8692 (m-80) cc_final: 0.8475 (m-80) REVERT: H 73 ASP cc_start: 0.7229 (t0) cc_final: 0.6871 (t0) REVERT: H 79 LEU cc_start: 0.8057 (tp) cc_final: 0.7584 (mp) outliers start: 28 outliers final: 24 residues processed: 155 average time/residue: 0.1713 time to fit residues: 34.0279 Evaluate side-chains 157 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 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 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 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: 0.5980 chunk 40 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 31 optimal weight: 0.0770 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 HIS ** 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 = 0.3381 r_free = 0.3381 target = 0.110766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.093176 restraints weight = 10525.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.096290 restraints weight = 5960.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098441 restraints weight = 4058.166| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5164 Z= 0.141 Angle : 0.668 10.384 7023 Z= 0.347 Chirality : 0.046 0.198 763 Planarity : 0.005 0.053 891 Dihedral : 5.544 74.455 754 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 4.89 % Allowed : 23.19 % Favored : 71.92 % 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: -2.41 (0.31), residues: 638 helix: -3.59 (0.73), residues: 27 sheet: -0.94 (0.34), residues: 225 loop : -1.91 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 353 HIS 0.002 0.001 HIS L 33 PHE 0.016 0.002 PHE G 347 TYR 0.018 0.002 TYR C 95 ARG 0.007 0.001 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 1) link_NAG-ASN : angle 2.82600 ( 3) link_BETA1-4 : bond 0.00275 ( 1) link_BETA1-4 : angle 0.95889 ( 3) hydrogen bonds : bond 0.03519 ( 123) hydrogen bonds : angle 6.37906 ( 324) SS BOND : bond 0.00865 ( 8) SS BOND : angle 1.65214 ( 16) covalent geometry : bond 0.00330 ( 5154) covalent geometry : angle 0.66151 ( 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 161 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASP cc_start: 0.8762 (t70) cc_final: 0.7784 (t0) REVERT: C 81 LEU cc_start: 0.7551 (tt) cc_final: 0.7173 (tt) REVERT: C 83 MET cc_start: 0.7799 (mtt) cc_final: 0.7449 (mtt) REVERT: C 89 GLU cc_start: 0.7573 (mp0) cc_final: 0.7296 (mp0) REVERT: C 103 GLN cc_start: 0.8745 (mp10) cc_final: 0.8237 (mp10) REVERT: G 340 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8209 (mp0) REVERT: G 385 THR cc_start: 0.8541 (p) cc_final: 0.8225 (m) REVERT: H 73 ASP cc_start: 0.7218 (t0) cc_final: 0.6866 (t0) REVERT: H 79 LEU cc_start: 0.7815 (tp) cc_final: 0.7612 (mp) outliers start: 27 outliers final: 24 residues processed: 151 average time/residue: 0.1708 time to fit residues: 32.8078 Evaluate side-chains 154 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 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 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain H residue 31 THR 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: 0.0010 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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 = 0.3363 r_free = 0.3363 target = 0.109992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.091897 restraints weight = 10515.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.094991 restraints weight = 6063.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097200 restraints weight = 4191.257| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3773 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= 0.130 Angle : 0.672 8.907 7023 Z= 0.349 Chirality : 0.045 0.187 763 Planarity : 0.005 0.052 891 Dihedral : 5.519 73.794 754 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.35 % Allowed : 24.28 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.32 (0.31), residues: 638 helix: -3.57 (0.74), residues: 27 sheet: -0.86 (0.34), residues: 225 loop : -1.86 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 353 HIS 0.003 0.001 HIS C 99 PHE 0.025 0.002 PHE L 46 TYR 0.017 0.001 TYR E 94 ARG 0.008 0.001 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 1) link_NAG-ASN : angle 2.79003 ( 3) link_BETA1-4 : bond 0.00298 ( 1) link_BETA1-4 : angle 0.90395 ( 3) hydrogen bonds : bond 0.03394 ( 123) hydrogen bonds : angle 6.35865 ( 324) SS BOND : bond 0.00713 ( 8) SS BOND : angle 1.92381 ( 16) covalent geometry : bond 0.00308 ( 5154) covalent geometry : angle 0.66389 ( 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 160 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9280 (mmmt) cc_final: 0.8945 (mmtm) REVERT: C 73 ASP cc_start: 0.8750 (t70) cc_final: 0.7738 (t0) REVERT: C 81 LEU cc_start: 0.7458 (tt) cc_final: 0.7107 (tt) REVERT: C 83 MET cc_start: 0.7778 (mtt) cc_final: 0.7431 (mtt) REVERT: C 89 GLU cc_start: 0.7548 (mp0) cc_final: 0.7301 (mp0) REVERT: C 103 GLN cc_start: 0.8708 (mp10) cc_final: 0.8157 (mp10) REVERT: G 340 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8195 (mp0) REVERT: G 385 THR cc_start: 0.8541 (p) cc_final: 0.8263 (m) REVERT: L 2 ILE cc_start: 0.9103 (mm) cc_final: 0.8878 (mt) REVERT: L 78 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8196 (mm-30) REVERT: L 100 LYS cc_start: 0.8932 (tmtt) cc_final: 0.8651 (tmtt) REVERT: H 73 ASP cc_start: 0.7301 (t0) cc_final: 0.6866 (t0) outliers start: 24 outliers final: 22 residues processed: 151 average time/residue: 0.1594 time to fit residues: 30.9678 Evaluate side-chains 151 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 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 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 61 optimal weight: 0.3980 chunk 25 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.0060 chunk 34 optimal weight: 2.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.114920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097872 restraints weight = 10435.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100921 restraints weight = 6037.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.103072 restraints weight = 4172.015| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5164 Z= 0.123 Angle : 0.687 8.674 7023 Z= 0.355 Chirality : 0.045 0.179 763 Planarity : 0.005 0.052 891 Dihedral : 5.480 72.451 754 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.17 % Allowed : 24.46 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.25 (0.32), residues: 638 helix: -3.57 (0.74), residues: 27 sheet: -0.78 (0.34), residues: 225 loop : -1.83 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 353 HIS 0.002 0.001 HIS C 99 PHE 0.013 0.001 PHE L 46 TYR 0.016 0.001 TYR E 94 ARG 0.007 0.001 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00044 ( 1) link_NAG-ASN : angle 2.77159 ( 3) link_BETA1-4 : bond 0.00419 ( 1) link_BETA1-4 : angle 0.95703 ( 3) hydrogen bonds : bond 0.03256 ( 123) hydrogen bonds : angle 6.31787 ( 324) SS BOND : bond 0.00722 ( 8) SS BOND : angle 2.59279 ( 16) covalent geometry : bond 0.00288 ( 5154) covalent geometry : angle 0.67399 ( 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: 23 poor density : 137 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9289 (mmmt) cc_final: 0.8956 (mmtm) REVERT: C 73 ASP cc_start: 0.8738 (t70) cc_final: 0.7799 (t0) REVERT: C 81 LEU cc_start: 0.7456 (tt) cc_final: 0.7086 (tt) REVERT: C 83 MET cc_start: 0.7896 (mtt) cc_final: 0.7612 (mtt) REVERT: C 98 LYS cc_start: 0.8591 (tmtt) cc_final: 0.8324 (tmtt) REVERT: E 27 GLN cc_start: 0.7848 (mp10) cc_final: 0.7450 (mp10) REVERT: G 340 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8154 (mp0) REVERT: L 78 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8091 (mm-30) REVERT: L 100 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8571 (tmtt) REVERT: H 73 ASP cc_start: 0.7211 (t0) cc_final: 0.6854 (t0) REVERT: H 87 ARG cc_start: 0.7948 (mtt180) cc_final: 0.7354 (mtt180) outliers start: 23 outliers final: 20 residues processed: 150 average time/residue: 0.1559 time to fit residues: 30.1906 Evaluate side-chains 149 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 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 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 495 TYR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.115199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098177 restraints weight = 10663.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.101303 restraints weight = 6097.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103464 restraints weight = 4169.346| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5164 Z= 0.126 Angle : 0.693 8.679 7023 Z= 0.359 Chirality : 0.045 0.181 763 Planarity : 0.005 0.051 891 Dihedral : 5.430 72.119 754 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.62 % Allowed : 25.54 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.17 (0.32), residues: 638 helix: -3.42 (0.66), residues: 33 sheet: -0.72 (0.35), residues: 225 loop : -1.75 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 353 HIS 0.002 0.001 HIS C 35 PHE 0.013 0.001 PHE G 347 TYR 0.015 0.001 TYR E 94 ARG 0.007 0.001 ARG G 408 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 2.77483 ( 3) link_BETA1-4 : bond 0.00314 ( 1) link_BETA1-4 : angle 0.93205 ( 3) hydrogen bonds : bond 0.03196 ( 123) hydrogen bonds : angle 6.22401 ( 324) SS BOND : bond 0.00617 ( 8) SS BOND : angle 2.74428 ( 16) covalent geometry : bond 0.00300 ( 5154) covalent geometry : angle 0.67884 ( 7001) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2958.38 seconds wall clock time: 54 minutes 8.29 seconds (3248.29 seconds total)