Starting phenix.real_space_refine on Fri Oct 10 12:36:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iv4_35740/10_2025/8iv4_35740.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iv4_35740/10_2025/8iv4_35740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iv4_35740/10_2025/8iv4_35740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iv4_35740/10_2025/8iv4_35740.map" model { file = "/net/cci-nas-00/data/ceres_data/8iv4_35740/10_2025/8iv4_35740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iv4_35740/10_2025/8iv4_35740.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 33 5.16 5 C 3173 2.51 5 N 841 2.21 5 O 980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5027 Number of models: 1 Model: "" Number of chains: 6 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: "B" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "A" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 921 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.54, per 1000 atoms: 0.31 Number of scatterers: 5027 At special positions: 0 Unit cell: (86.358, 66.908, 109.698, 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 33 16.00 O 980 8.00 N 841 7.00 C 3173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 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 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 98 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " 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 C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN G 343 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 176.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1172 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 12 sheets defined 6.2% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.002A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.801A pdb=" N ASP B 82 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 83 " --> pdb=" O CYS B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.918A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 370 removed outlier: 3.923A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.482A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 410 " --> pdb=" O VAL G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 removed outlier: 3.698A pdb=" N TYR G 421 " --> pdb=" O LYS G 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.745A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N THR L 68 " --> pdb=" O VAL L 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.532A pdb=" N GLU L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.560A pdb=" N TYR L 48 " --> pdb=" O ASN L 52 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLN L 36 " --> pdb=" O VAL L 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.521A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.535A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR H 94 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.535A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 115 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR H 94 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.565A pdb=" N GLU B 105 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 49 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP B 35 " --> pdb=" O MET B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.519A pdb=" N GLY A 10 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET A 34 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'G' and resid 452 through 454 146 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 0.60 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: 1593 1.34 - 1.46: 1294 1.46 - 1.58: 2212 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5147 Sorted by residual: bond pdb=" C LEU G 335 " pdb=" N CYS G 336 " ideal model delta sigma weight residual 1.331 1.269 0.062 2.07e-02 2.33e+03 8.86e+00 bond pdb=" C1 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.54e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 4.97e+00 bond pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.31e+00 bond pdb=" N CYS G 488 " pdb=" CA CYS G 488 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.10e+00 ... (remaining 5142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 6609 1.69 - 3.39: 323 3.39 - 5.08: 29 5.08 - 6.77: 10 6.77 - 8.47: 4 Bond angle restraints: 6975 Sorted by residual: angle pdb=" C SER L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" C SER L 92 " pdb=" N TRP L 93 " pdb=" CA TRP L 93 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N TYR B 94 " pdb=" CA TYR B 94 " pdb=" C TYR B 94 " ideal model delta sigma weight residual 109.81 118.28 -8.47 2.21e+00 2.05e-01 1.47e+01 angle pdb=" C GLN L 89 " pdb=" N TRP L 90 " pdb=" CA TRP L 90 " ideal model delta sigma weight residual 120.63 126.24 -5.61 1.61e+00 3.86e-01 1.21e+01 angle pdb=" N GLN A 111 " pdb=" CA GLN A 111 " pdb=" C GLN A 111 " ideal model delta sigma weight residual 114.56 110.26 4.30 1.27e+00 6.20e-01 1.14e+01 ... (remaining 6970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 2744 17.91 - 35.81: 253 35.81 - 53.72: 45 53.72 - 71.62: 4 71.62 - 89.53: 5 Dihedral angle restraints: 3051 sinusoidal: 1201 harmonic: 1850 Sorted by residual: dihedral pdb=" CA ASN G 487 " pdb=" C ASN G 487 " pdb=" N CYS G 488 " pdb=" CA CYS G 488 " ideal model delta harmonic sigma weight residual -180.00 -131.59 -48.41 0 5.00e+00 4.00e-02 9.38e+01 dihedral pdb=" CA CYS G 361 " pdb=" C CYS G 361 " pdb=" N VAL G 362 " pdb=" CA VAL G 362 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " pdb=" CB CYS G 361 " ideal model delta sinusoidal sigma weight residual 93.00 58.47 34.53 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 3048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 514 0.047 - 0.094: 171 0.094 - 0.141: 56 0.141 - 0.188: 9 0.188 - 0.235: 4 Chirality restraints: 754 Sorted by residual: chirality pdb=" CB VAL H 48 " pdb=" CA VAL H 48 " pdb=" CG1 VAL H 48 " pdb=" CG2 VAL H 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 28 " pdb=" CA THR A 28 " pdb=" OG1 THR A 28 " pdb=" CG2 THR A 28 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA TYR B 94 " pdb=" N TYR B 94 " pdb=" C TYR B 94 " pdb=" CB TYR B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 751 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN G 487 " 0.016 2.00e-02 2.50e+03 3.17e-02 1.01e+01 pdb=" C ASN G 487 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN G 487 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS G 488 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO B 95 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 520 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.40e+00 pdb=" N PRO G 521 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 521 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 521 " 0.035 5.00e-02 4.00e+02 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1626 2.83 - 3.35: 3861 3.35 - 3.87: 8003 3.87 - 4.38: 8760 4.38 - 4.90: 16095 Nonbonded interactions: 38345 Sorted by model distance: nonbonded pdb=" O SER G 438 " pdb=" OG SER G 438 " model vdw 2.315 3.040 nonbonded pdb=" O SER H 30 " pdb=" OG SER H 30 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.336 3.040 nonbonded pdb=" O ARG H 67 " pdb=" OG SER H 84 " model vdw 2.354 3.040 nonbonded pdb=" OG SER G 438 " pdb=" OD2 ASP G 442 " model vdw 2.361 3.040 ... (remaining 38340 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=0.83 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.190 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 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 : 0.005 0.062 5157 Z= 0.258 Angle : 0.853 8.871 6997 Z= 0.495 Chirality : 0.054 0.235 754 Planarity : 0.007 0.069 891 Dihedral : 14.005 89.529 1855 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.55 % Allowed : 6.96 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.00 (0.27), residues: 634 helix: -4.95 (0.21), residues: 21 sheet: -1.94 (0.31), residues: 250 loop : -3.14 (0.24), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 408 TYR 0.026 0.002 TYR B 94 PHE 0.022 0.002 PHE L 46 TRP 0.022 0.002 TRP H 47 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 5147) covalent geometry : angle 0.84205 ( 6975) SS BOND : bond 0.00296 ( 8) SS BOND : angle 0.84826 ( 16) hydrogen bonds : bond 0.27686 ( 144) hydrogen bonds : angle 10.62234 ( 357) link_BETA1-4 : bond 0.01097 ( 1) link_BETA1-4 : angle 1.24981 ( 3) link_NAG-ASN : bond 0.00084 ( 1) link_NAG-ASN : angle 6.51442 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 time to evaluate : 0.252 Fit side-chains REVERT: L 11 MET cc_start: 0.7400 (mtt) cc_final: 0.6839 (mtt) REVERT: L 19 ILE cc_start: 0.8245 (tt) cc_final: 0.8027 (tt) REVERT: L 32 MET cc_start: 0.7935 (tpp) cc_final: 0.7538 (tpp) REVERT: L 90 TRP cc_start: 0.7295 (t60) cc_final: 0.7029 (t60) REVERT: H 3 MET cc_start: 0.6729 (mtm) cc_final: 0.5999 (tpt) REVERT: H 19 LYS cc_start: 0.7516 (tttt) cc_final: 0.7136 (tttp) REVERT: H 82 GLN cc_start: 0.7352 (pp30) cc_final: 0.7113 (pp30) REVERT: H 93 MET cc_start: 0.6589 (ttm) cc_final: 0.6235 (ttm) REVERT: H 109 ASP cc_start: 0.8068 (m-30) cc_final: 0.7447 (m-30) REVERT: B 1 ASP cc_start: 0.7827 (p0) cc_final: 0.7625 (p0) REVERT: B 4 MET cc_start: 0.6457 (mmm) cc_final: 0.5943 (mmt) REVERT: B 47 MET cc_start: 0.7245 (mmp) cc_final: 0.6926 (mmp) REVERT: B 52 SER cc_start: 0.8365 (t) cc_final: 0.8140 (m) REVERT: B 54 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7763 (ttp80) REVERT: B 79 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7432 (mm110) REVERT: B 82 ASP cc_start: 0.8596 (m-30) cc_final: 0.8361 (m-30) REVERT: A 18 MET cc_start: 0.6312 (ttm) cc_final: 0.6019 (ttt) REVERT: A 19 LYS cc_start: 0.7633 (tttt) cc_final: 0.6873 (tttp) REVERT: A 35 ASP cc_start: 0.6952 (m-30) cc_final: 0.6540 (m-30) REVERT: A 50 GLN cc_start: 0.7547 (tt0) cc_final: 0.6930 (tt0) REVERT: A 69 ARG cc_start: 0.7395 (mtm110) cc_final: 0.7149 (mtp180) REVERT: A 108 PHE cc_start: 0.7478 (t80) cc_final: 0.7176 (t80) REVERT: G 347 PHE cc_start: 0.8147 (m-10) cc_final: 0.7860 (m-80) REVERT: G 369 TYR cc_start: 0.8841 (t80) cc_final: 0.8477 (t80) REVERT: G 442 ASP cc_start: 0.8779 (m-30) cc_final: 0.8099 (m-30) outliers start: 3 outliers final: 1 residues processed: 128 average time/residue: 0.0899 time to fit residues: 14.3257 Evaluate side-chains 103 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN G 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.125639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.105416 restraints weight = 6825.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.109017 restraints weight = 3685.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111553 restraints weight = 2442.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.113260 restraints weight = 1820.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114515 restraints weight = 1463.634| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5157 Z= 0.198 Angle : 0.632 7.731 6997 Z= 0.334 Chirality : 0.045 0.160 754 Planarity : 0.006 0.063 891 Dihedral : 6.422 68.031 752 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.04 % Favored : 91.80 % Rotamer: Outliers : 3.48 % Allowed : 10.26 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.24 (0.29), residues: 634 helix: -4.37 (0.46), residues: 15 sheet: -1.44 (0.31), residues: 252 loop : -2.66 (0.27), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 346 TYR 0.019 0.002 TYR B 94 PHE 0.016 0.001 PHE L 46 TRP 0.013 0.002 TRP G 436 HIS 0.002 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 5147) covalent geometry : angle 0.62134 ( 6975) SS BOND : bond 0.00437 ( 8) SS BOND : angle 1.01213 ( 16) hydrogen bonds : bond 0.04209 ( 144) hydrogen bonds : angle 7.06215 ( 357) link_BETA1-4 : bond 0.00977 ( 1) link_BETA1-4 : angle 0.75845 ( 3) link_NAG-ASN : bond 0.00277 ( 1) link_NAG-ASN : angle 5.38950 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: L 18 GLU cc_start: 0.7593 (pp20) cc_final: 0.7346 (pp20) REVERT: L 32 MET cc_start: 0.8618 (tpp) cc_final: 0.8073 (tpp) REVERT: L 66 SER cc_start: 0.8731 (p) cc_final: 0.8147 (m) REVERT: L 90 TRP cc_start: 0.8453 (t60) cc_final: 0.7461 (t60) REVERT: H 19 LYS cc_start: 0.8492 (tttt) cc_final: 0.8117 (tttm) REVERT: H 105 ASP cc_start: 0.8945 (p0) cc_final: 0.8554 (p0) REVERT: B 30 ARG cc_start: 0.7795 (mpt90) cc_final: 0.7497 (mmt-90) REVERT: B 42 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7926 (mt0) REVERT: A 3 LYS cc_start: 0.8602 (pptt) cc_final: 0.8215 (pttp) REVERT: A 19 LYS cc_start: 0.8530 (tttt) cc_final: 0.8135 (ttmm) REVERT: G 503 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8748 (t) outliers start: 19 outliers final: 13 residues processed: 121 average time/residue: 0.0905 time to fit residues: 13.5616 Evaluate side-chains 116 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 14 optimal weight: 0.3980 chunk 56 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS A 50 GLN G 439 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112494 restraints weight = 6751.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116155 restraints weight = 3797.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.118735 restraints weight = 2582.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120365 restraints weight = 1939.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.121628 restraints weight = 1583.578| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5157 Z= 0.175 Angle : 0.596 8.490 6997 Z= 0.311 Chirality : 0.045 0.162 754 Planarity : 0.005 0.057 891 Dihedral : 5.998 57.675 752 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 5.31 % Allowed : 13.19 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.30), residues: 634 helix: -3.83 (0.64), residues: 15 sheet: -0.94 (0.32), residues: 245 loop : -2.31 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 346 TYR 0.017 0.002 TYR B 94 PHE 0.010 0.001 PHE L 46 TRP 0.010 0.002 TRP L 90 HIS 0.002 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 5147) covalent geometry : angle 0.58839 ( 6975) SS BOND : bond 0.00257 ( 8) SS BOND : angle 0.98560 ( 16) hydrogen bonds : bond 0.03576 ( 144) hydrogen bonds : angle 6.32448 ( 357) link_BETA1-4 : bond 0.00677 ( 1) link_BETA1-4 : angle 0.73488 ( 3) link_NAG-ASN : bond 0.00201 ( 1) link_NAG-ASN : angle 4.23234 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: L 18 GLU cc_start: 0.7652 (pp20) cc_final: 0.7402 (pp20) REVERT: L 32 MET cc_start: 0.8620 (tpp) cc_final: 0.8070 (tpp) REVERT: L 66 SER cc_start: 0.8753 (p) cc_final: 0.8202 (m) REVERT: H 19 LYS cc_start: 0.8488 (tttt) cc_final: 0.8095 (tttm) REVERT: H 91 THR cc_start: 0.9119 (m) cc_final: 0.8915 (t) REVERT: B 42 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7971 (mt0) REVERT: A 3 LYS cc_start: 0.8448 (pptt) cc_final: 0.8175 (pttp) REVERT: A 19 LYS cc_start: 0.8602 (tttt) cc_final: 0.8173 (ttmm) REVERT: G 369 TYR cc_start: 0.8634 (t80) cc_final: 0.8400 (t80) REVERT: G 498 GLN cc_start: 0.8734 (mt0) cc_final: 0.8407 (mt0) REVERT: G 503 VAL cc_start: 0.9312 (OUTLIER) cc_final: 0.8956 (t) outliers start: 29 outliers final: 23 residues processed: 126 average time/residue: 0.0806 time to fit residues: 12.7696 Evaluate side-chains 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.120537 restraints weight = 6675.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124034 restraints weight = 3884.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126423 restraints weight = 2698.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128131 restraints weight = 2062.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129315 restraints weight = 1674.634| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5157 Z= 0.181 Angle : 0.592 7.278 6997 Z= 0.311 Chirality : 0.045 0.164 754 Planarity : 0.005 0.059 891 Dihedral : 5.788 50.505 752 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 6.04 % Allowed : 15.20 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.31), residues: 634 helix: -3.17 (0.89), residues: 15 sheet: -0.75 (0.32), residues: 257 loop : -2.15 (0.30), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 346 TYR 0.026 0.002 TYR H 32 PHE 0.010 0.001 PHE A 70 TRP 0.011 0.002 TRP A 33 HIS 0.004 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 5147) covalent geometry : angle 0.58407 ( 6975) SS BOND : bond 0.00241 ( 8) SS BOND : angle 1.01369 ( 16) hydrogen bonds : bond 0.03258 ( 144) hydrogen bonds : angle 5.99939 ( 357) link_BETA1-4 : bond 0.00698 ( 1) link_BETA1-4 : angle 0.72745 ( 3) link_NAG-ASN : bond 0.00131 ( 1) link_NAG-ASN : angle 4.39538 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: L 32 MET cc_start: 0.8606 (tpp) cc_final: 0.8063 (tpp) REVERT: L 66 SER cc_start: 0.8759 (p) cc_final: 0.8186 (m) REVERT: H 19 LYS cc_start: 0.8509 (tttt) cc_final: 0.8050 (tttm) REVERT: H 91 THR cc_start: 0.9159 (m) cc_final: 0.8915 (t) REVERT: B 4 MET cc_start: 0.8076 (mmm) cc_final: 0.7387 (mmm) REVERT: B 42 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7950 (mt0) REVERT: A 3 LYS cc_start: 0.8502 (pptt) cc_final: 0.8254 (pttp) REVERT: A 19 LYS cc_start: 0.8654 (tttt) cc_final: 0.8235 (tttp) REVERT: A 25 SER cc_start: 0.8192 (m) cc_final: 0.7902 (p) REVERT: G 369 TYR cc_start: 0.8612 (t80) cc_final: 0.8380 (t80) REVERT: G 498 GLN cc_start: 0.8729 (mt0) cc_final: 0.8505 (mt0) outliers start: 33 outliers final: 26 residues processed: 125 average time/residue: 0.0844 time to fit residues: 13.3250 Evaluate side-chains 131 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.117446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.097662 restraints weight = 7077.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.100888 restraints weight = 4171.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.103125 restraints weight = 2895.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.104743 restraints weight = 2222.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.105941 restraints weight = 1820.270| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 5157 Z= 0.251 Angle : 0.641 8.023 6997 Z= 0.336 Chirality : 0.047 0.188 754 Planarity : 0.005 0.062 891 Dihedral : 5.969 46.849 752 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 6.78 % Allowed : 15.20 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.32), residues: 634 helix: -2.88 (1.00), residues: 15 sheet: -0.79 (0.32), residues: 259 loop : -2.09 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 98 TYR 0.036 0.002 TYR H 32 PHE 0.010 0.001 PHE G 429 TRP 0.012 0.002 TRP L 90 HIS 0.006 0.002 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00593 ( 5147) covalent geometry : angle 0.63130 ( 6975) SS BOND : bond 0.00299 ( 8) SS BOND : angle 1.10553 ( 16) hydrogen bonds : bond 0.03458 ( 144) hydrogen bonds : angle 6.02177 ( 357) link_BETA1-4 : bond 0.00686 ( 1) link_BETA1-4 : angle 0.74610 ( 3) link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 4.94992 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 104 time to evaluate : 0.197 Fit side-chains REVERT: L 18 GLU cc_start: 0.7641 (pp20) cc_final: 0.7412 (pp20) REVERT: L 32 MET cc_start: 0.8583 (tpp) cc_final: 0.7997 (tpp) REVERT: L 66 SER cc_start: 0.8740 (p) cc_final: 0.8183 (m) REVERT: H 28 SER cc_start: 0.8945 (t) cc_final: 0.8588 (p) REVERT: H 91 THR cc_start: 0.9208 (m) cc_final: 0.8975 (t) REVERT: B 42 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7997 (mt0) REVERT: A 19 LYS cc_start: 0.8690 (tttt) cc_final: 0.8223 (tttp) REVERT: G 369 TYR cc_start: 0.8633 (t80) cc_final: 0.8400 (t80) REVERT: G 466 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7550 (ttp-170) outliers start: 37 outliers final: 25 residues processed: 126 average time/residue: 0.0759 time to fit residues: 12.0728 Evaluate side-chains 126 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 466 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 88 HIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.118047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.098440 restraints weight = 7020.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.101602 restraints weight = 4189.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.103872 restraints weight = 2926.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.105430 restraints weight = 2258.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.106449 restraints weight = 1852.673| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5157 Z= 0.205 Angle : 0.638 9.603 6997 Z= 0.331 Chirality : 0.046 0.196 754 Planarity : 0.005 0.056 891 Dihedral : 5.941 46.080 752 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 5.68 % Allowed : 16.48 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.32), residues: 634 helix: -2.71 (1.07), residues: 15 sheet: -0.78 (0.32), residues: 259 loop : -2.02 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.034 0.002 TYR H 32 PHE 0.009 0.001 PHE A 70 TRP 0.015 0.002 TRP L 90 HIS 0.009 0.002 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 5147) covalent geometry : angle 0.63242 ( 6975) SS BOND : bond 0.00242 ( 8) SS BOND : angle 0.94672 ( 16) hydrogen bonds : bond 0.03254 ( 144) hydrogen bonds : angle 5.91142 ( 357) link_BETA1-4 : bond 0.00645 ( 1) link_BETA1-4 : angle 0.80015 ( 3) link_NAG-ASN : bond 0.00106 ( 1) link_NAG-ASN : angle 3.69304 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.279 Fit side-chains REVERT: L 32 MET cc_start: 0.8588 (tpp) cc_final: 0.8010 (tpp) REVERT: L 66 SER cc_start: 0.8719 (p) cc_final: 0.8158 (m) REVERT: H 28 SER cc_start: 0.9015 (t) cc_final: 0.8698 (p) REVERT: H 91 THR cc_start: 0.9202 (m) cc_final: 0.8976 (t) REVERT: B 4 MET cc_start: 0.7867 (mmm) cc_final: 0.7213 (mmm) REVERT: B 42 GLN cc_start: 0.8299 (mm-40) cc_final: 0.8046 (mt0) REVERT: A 19 LYS cc_start: 0.8582 (tttt) cc_final: 0.8145 (tttp) outliers start: 31 outliers final: 25 residues processed: 121 average time/residue: 0.0842 time to fit residues: 13.1136 Evaluate side-chains 124 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.118689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.099055 restraints weight = 6969.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.102278 restraints weight = 4015.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.104576 restraints weight = 2774.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.106144 restraints weight = 2122.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.107333 restraints weight = 1738.112| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5157 Z= 0.176 Angle : 0.626 9.418 6997 Z= 0.322 Chirality : 0.046 0.204 754 Planarity : 0.005 0.057 891 Dihedral : 5.829 44.904 752 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 6.04 % Allowed : 16.85 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.32), residues: 634 helix: -2.29 (1.15), residues: 15 sheet: -0.63 (0.32), residues: 255 loop : -1.96 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.030 0.002 TYR H 32 PHE 0.007 0.001 PHE A 70 TRP 0.011 0.002 TRP H 111 HIS 0.002 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5147) covalent geometry : angle 0.61964 ( 6975) SS BOND : bond 0.00272 ( 8) SS BOND : angle 0.87014 ( 16) hydrogen bonds : bond 0.03122 ( 144) hydrogen bonds : angle 5.76281 ( 357) link_BETA1-4 : bond 0.00694 ( 1) link_BETA1-4 : angle 0.90078 ( 3) link_NAG-ASN : bond 0.00464 ( 1) link_NAG-ASN : angle 4.21863 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: L 32 MET cc_start: 0.8599 (tpp) cc_final: 0.8041 (tpp) REVERT: L 46 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7793 (t80) REVERT: L 66 SER cc_start: 0.8719 (p) cc_final: 0.8159 (m) REVERT: H 28 SER cc_start: 0.9039 (t) cc_final: 0.8781 (p) REVERT: H 91 THR cc_start: 0.9214 (m) cc_final: 0.8972 (t) REVERT: H 105 ASP cc_start: 0.9094 (p0) cc_final: 0.8860 (p0) REVERT: B 4 MET cc_start: 0.7816 (mmm) cc_final: 0.7220 (mmm) REVERT: B 42 GLN cc_start: 0.8314 (mm-40) cc_final: 0.8048 (mt0) REVERT: A 19 LYS cc_start: 0.8648 (tttt) cc_final: 0.8178 (tttp) REVERT: A 25 SER cc_start: 0.8165 (m) cc_final: 0.7852 (p) REVERT: G 466 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7371 (ttp-170) outliers start: 33 outliers final: 27 residues processed: 120 average time/residue: 0.0876 time to fit residues: 13.3848 Evaluate side-chains 125 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 466 ARG Chi-restraints excluded: chain G residue 478 THR Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.100979 restraints weight = 6997.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.104258 restraints weight = 4131.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.106601 restraints weight = 2845.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.108296 restraints weight = 2157.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109373 restraints weight = 1748.419| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5157 Z= 0.140 Angle : 0.594 7.861 6997 Z= 0.306 Chirality : 0.045 0.193 754 Planarity : 0.005 0.055 891 Dihedral : 5.601 43.470 752 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 5.49 % Allowed : 17.22 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.33), residues: 634 helix: -2.19 (1.22), residues: 15 sheet: -0.54 (0.33), residues: 255 loop : -1.85 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 346 TYR 0.024 0.001 TYR H 32 PHE 0.008 0.001 PHE B 62 TRP 0.010 0.001 TRP L 93 HIS 0.006 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5147) covalent geometry : angle 0.59000 ( 6975) SS BOND : bond 0.00212 ( 8) SS BOND : angle 0.74252 ( 16) hydrogen bonds : bond 0.02999 ( 144) hydrogen bonds : angle 5.61350 ( 357) link_BETA1-4 : bond 0.00681 ( 1) link_BETA1-4 : angle 0.81339 ( 3) link_NAG-ASN : bond 0.00386 ( 1) link_NAG-ASN : angle 3.30234 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.196 Fit side-chains REVERT: L 32 MET cc_start: 0.8593 (tpp) cc_final: 0.8047 (tpp) REVERT: L 46 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7779 (t80) REVERT: L 66 SER cc_start: 0.8712 (p) cc_final: 0.8135 (m) REVERT: H 28 SER cc_start: 0.9035 (t) cc_final: 0.8781 (p) REVERT: H 91 THR cc_start: 0.9209 (m) cc_final: 0.8932 (t) REVERT: B 4 MET cc_start: 0.7786 (mmm) cc_final: 0.7247 (mmm) REVERT: B 42 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8049 (mt0) REVERT: A 19 LYS cc_start: 0.8604 (tttt) cc_final: 0.8132 (tttp) REVERT: A 25 SER cc_start: 0.8141 (m) cc_final: 0.7855 (p) REVERT: G 466 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7371 (ttp-170) outliers start: 30 outliers final: 24 residues processed: 118 average time/residue: 0.0815 time to fit residues: 12.0797 Evaluate side-chains 123 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 466 ARG Chi-restraints excluded: chain G residue 478 THR Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.0050 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.117666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.098942 restraints weight = 6999.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101849 restraints weight = 4223.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.103911 restraints weight = 2985.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.105490 restraints weight = 2319.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.106562 restraints weight = 1907.517| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5157 Z= 0.185 Angle : 0.632 8.149 6997 Z= 0.327 Chirality : 0.046 0.220 754 Planarity : 0.005 0.057 891 Dihedral : 5.883 44.065 752 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 5.13 % Allowed : 17.40 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.32), residues: 634 helix: -2.19 (1.20), residues: 15 sheet: -0.50 (0.32), residues: 253 loop : -1.90 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 346 TYR 0.014 0.002 TYR L 48 PHE 0.007 0.001 PHE G 429 TRP 0.011 0.002 TRP H 111 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 5147) covalent geometry : angle 0.62439 ( 6975) SS BOND : bond 0.00250 ( 8) SS BOND : angle 0.90212 ( 16) hydrogen bonds : bond 0.03149 ( 144) hydrogen bonds : angle 5.62542 ( 357) link_BETA1-4 : bond 0.00660 ( 1) link_BETA1-4 : angle 0.93849 ( 3) link_NAG-ASN : bond 0.00693 ( 1) link_NAG-ASN : angle 4.53707 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: L 32 MET cc_start: 0.8617 (tpp) cc_final: 0.8063 (tpp) REVERT: L 46 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7749 (t80) REVERT: L 66 SER cc_start: 0.8731 (p) cc_final: 0.8150 (m) REVERT: H 28 SER cc_start: 0.9079 (t) cc_final: 0.8849 (p) REVERT: H 91 THR cc_start: 0.9220 (m) cc_final: 0.8964 (t) REVERT: B 4 MET cc_start: 0.7854 (mmm) cc_final: 0.7252 (mmm) REVERT: B 42 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8044 (mt0) REVERT: A 19 LYS cc_start: 0.8596 (tttt) cc_final: 0.8093 (tttp) REVERT: A 25 SER cc_start: 0.8182 (m) cc_final: 0.7881 (p) REVERT: G 466 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7681 (ttp-170) outliers start: 28 outliers final: 26 residues processed: 114 average time/residue: 0.0839 time to fit residues: 12.0678 Evaluate side-chains 126 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 466 ARG Chi-restraints excluded: chain G residue 478 THR Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.120105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.100545 restraints weight = 6834.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.103801 restraints weight = 4016.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.106133 restraints weight = 2771.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.107731 restraints weight = 2114.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.108798 restraints weight = 1732.155| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5157 Z= 0.157 Angle : 0.604 7.693 6997 Z= 0.313 Chirality : 0.045 0.213 754 Planarity : 0.005 0.054 891 Dihedral : 5.675 42.629 752 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.31 % Allowed : 17.40 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.32), residues: 634 helix: -2.13 (1.22), residues: 15 sheet: -0.48 (0.32), residues: 255 loop : -1.79 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 346 TYR 0.012 0.001 TYR B 49 PHE 0.008 0.001 PHE A 70 TRP 0.011 0.002 TRP H 111 HIS 0.003 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 5147) covalent geometry : angle 0.59753 ( 6975) SS BOND : bond 0.00225 ( 8) SS BOND : angle 0.78883 ( 16) hydrogen bonds : bond 0.02999 ( 144) hydrogen bonds : angle 5.53040 ( 357) link_BETA1-4 : bond 0.00597 ( 1) link_BETA1-4 : angle 0.98924 ( 3) link_NAG-ASN : bond 0.00489 ( 1) link_NAG-ASN : angle 3.88290 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1268 Ramachandran restraints generated. 634 Oldfield, 0 Emsley, 634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: L 32 MET cc_start: 0.8598 (tpp) cc_final: 0.8059 (tpp) REVERT: L 46 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7781 (t80) REVERT: L 66 SER cc_start: 0.8707 (p) cc_final: 0.8127 (m) REVERT: H 28 SER cc_start: 0.9008 (t) cc_final: 0.8785 (p) REVERT: H 91 THR cc_start: 0.9217 (m) cc_final: 0.8943 (t) REVERT: B 4 MET cc_start: 0.7821 (mmm) cc_final: 0.7296 (mmm) REVERT: B 42 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8046 (mt0) REVERT: A 19 LYS cc_start: 0.8561 (tttt) cc_final: 0.8060 (tttp) REVERT: A 25 SER cc_start: 0.8135 (m) cc_final: 0.7846 (p) REVERT: G 466 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7646 (ttp-170) outliers start: 29 outliers final: 27 residues processed: 119 average time/residue: 0.0832 time to fit residues: 12.2561 Evaluate side-chains 130 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 99 THR Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain G residue 341 VAL Chi-restraints excluded: chain G residue 353 TRP Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 442 ASP Chi-restraints excluded: chain G residue 466 ARG Chi-restraints excluded: chain G residue 478 THR Chi-restraints excluded: chain G residue 511 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 0.0470 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.120161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101430 restraints weight = 6978.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.104449 restraints weight = 4243.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.106620 restraints weight = 2983.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.108158 restraints weight = 2291.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.109207 restraints weight = 1887.178| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5157 Z= 0.142 Angle : 0.598 7.502 6997 Z= 0.311 Chirality : 0.045 0.205 754 Planarity : 0.005 0.055 891 Dihedral : 5.667 42.691 752 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 4.95 % Allowed : 18.32 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.33), residues: 634 helix: -2.07 (1.23), residues: 15 sheet: -0.45 (0.32), residues: 255 loop : -1.76 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 346 TYR 0.011 0.001 TYR B 49 PHE 0.007 0.001 PHE B 62 TRP 0.011 0.002 TRP H 111 HIS 0.003 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5147) covalent geometry : angle 0.59306 ( 6975) SS BOND : bond 0.00221 ( 8) SS BOND : angle 0.76541 ( 16) hydrogen bonds : bond 0.02937 ( 144) hydrogen bonds : angle 5.47300 ( 357) link_BETA1-4 : bond 0.00530 ( 1) link_BETA1-4 : angle 0.86559 ( 3) link_NAG-ASN : bond 0.00476 ( 1) link_NAG-ASN : angle 3.54491 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.48 seconds wall clock time: 23 minutes 55.30 seconds (1435.30 seconds total)