Starting phenix.real_space_refine on Sat May 2 10:29:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vic_65083/05_2026/9vic_65083.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vic_65083/05_2026/9vic_65083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vic_65083/05_2026/9vic_65083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vic_65083/05_2026/9vic_65083.map" model { file = "/net/cci-nas-00/data/ceres_data/9vic_65083/05_2026/9vic_65083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vic_65083/05_2026/9vic_65083.cif" } resolution = 2.45 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= -0.001 sd= 0.092 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 12 5.16 5 C 2906 2.51 5 N 766 2.21 5 O 798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4486 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1084 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CMO': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CMO': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, D Time building chain proxies: 0.77, per 1000 atoms: 0.17 Number of scatterers: 4486 At special positions: 0 Unit cell: (70.38, 84.66, 66.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 12 16.00 O 798 8.00 N 766 7.00 C 2906 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.25 Conformation dependent library (CDL) restraints added in 91.4 milliseconds 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.641A pdb=" N TYR A 42 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.902A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.225A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 77 removed outlier: 3.504A pdb=" N LYS B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.820A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 141 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.641A pdb=" N TYR C 42 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 95 through 113 removed outlier: 3.902A pdb=" N LYS C 99 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.225A pdb=" N GLU D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER D 44 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY D 46 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 Processing helix chain 'D' and resid 57 through 77 removed outlier: 3.504A pdb=" N LYS D 61 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 100 through 119 removed outlier: 3.820A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 141 324 hydrogen bonds defined for protein. 924 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: 0.37 Time building geometry restraints manager: 0.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.39: 1826 1.39 - 1.57: 2762 1.57 - 1.76: 0 1.76 - 1.94: 22 1.94 - 2.13: 12 Bond restraints: 4622 Sorted by residual: bond pdb=" C CMO D 202 " pdb=" O CMO D 202 " ideal model delta sigma weight residual 1.141 1.280 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C CMO B 202 " pdb=" O CMO B 202 " ideal model delta sigma weight residual 1.141 1.280 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C CMO A 202 " pdb=" O CMO A 202 " ideal model delta sigma weight residual 1.141 1.251 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C CMO C 202 " pdb=" O CMO C 202 " ideal model delta sigma weight residual 1.141 1.251 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C3B HEM A 201 " pdb=" CAB HEM A 201 " ideal model delta sigma weight residual 1.544 1.442 0.102 2.00e-02 2.50e+03 2.62e+01 ... (remaining 4617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 5904 3.18 - 6.37: 392 6.37 - 9.55: 38 9.55 - 12.73: 2 12.73 - 15.91: 2 Bond angle restraints: 6338 Sorted by residual: angle pdb=" N TYR C 42 " pdb=" CA TYR C 42 " pdb=" CB TYR C 42 " ideal model delta sigma weight residual 110.46 94.55 15.91 1.57e+00 4.06e-01 1.03e+02 angle pdb=" N TYR A 42 " pdb=" CA TYR A 42 " pdb=" CB TYR A 42 " ideal model delta sigma weight residual 110.46 94.55 15.91 1.57e+00 4.06e-01 1.03e+02 angle pdb=" CA ASP A 94 " pdb=" CB ASP A 94 " pdb=" CG ASP A 94 " ideal model delta sigma weight residual 112.60 120.93 -8.33 1.00e+00 1.00e+00 6.94e+01 angle pdb=" CA ASP C 94 " pdb=" CB ASP C 94 " pdb=" CG ASP C 94 " ideal model delta sigma weight residual 112.60 120.93 -8.33 1.00e+00 1.00e+00 6.94e+01 angle pdb=" CA PHE C 43 " pdb=" CB PHE C 43 " pdb=" CG PHE C 43 " ideal model delta sigma weight residual 113.80 120.77 -6.97 1.00e+00 1.00e+00 4.86e+01 ... (remaining 6333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2344 17.88 - 35.75: 194 35.75 - 53.62: 58 53.62 - 71.50: 16 71.50 - 89.37: 10 Dihedral angle restraints: 2622 sinusoidal: 998 harmonic: 1624 Sorted by residual: dihedral pdb=" N TYR C 42 " pdb=" C TYR C 42 " pdb=" CA TYR C 42 " pdb=" CB TYR C 42 " ideal model delta harmonic sigma weight residual 122.80 106.32 16.48 0 2.50e+00 1.60e-01 4.35e+01 dihedral pdb=" N TYR A 42 " pdb=" C TYR A 42 " pdb=" CA TYR A 42 " pdb=" CB TYR A 42 " ideal model delta harmonic sigma weight residual 122.80 106.32 16.48 0 2.50e+00 1.60e-01 4.35e+01 dihedral pdb=" CD ARG C 92 " pdb=" NE ARG C 92 " pdb=" CZ ARG C 92 " pdb=" NH1 ARG C 92 " ideal model delta sinusoidal sigma weight residual 0.00 52.70 -52.70 1 1.00e+01 1.00e-02 3.78e+01 ... (remaining 2619 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.064: 412 0.064 - 0.128: 172 0.128 - 0.191: 66 0.191 - 0.254: 30 0.254 - 0.318: 10 Chirality restraints: 690 Sorted by residual: chirality pdb=" CA TYR A 140 " pdb=" N TYR A 140 " pdb=" C TYR A 140 " pdb=" CB TYR A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA TYR C 140 " pdb=" N TYR C 140 " pdb=" C TYR C 140 " pdb=" CB TYR C 140 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA PRO B 124 " pdb=" N PRO B 124 " pdb=" C PRO B 124 " pdb=" CB PRO B 124 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 687 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 92 " -0.931 9.50e-02 1.11e+02 4.18e-01 1.12e+02 pdb=" NE ARG C 92 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG C 92 " 0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG C 92 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG C 92 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 92 " 0.931 9.50e-02 1.11e+02 4.18e-01 1.12e+02 pdb=" NE ARG A 92 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 92 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 92 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 92 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 141 " 0.838 9.50e-02 1.11e+02 3.77e-01 9.80e+01 pdb=" NE ARG A 141 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 141 " -0.070 2.00e-02 2.50e+03 pdb=" NH1 ARG A 141 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 141 " 0.044 2.00e-02 2.50e+03 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 44 2.64 - 3.20: 3820 3.20 - 3.77: 7184 3.77 - 4.33: 10356 4.33 - 4.90: 16412 Nonbonded interactions: 37816 Sorted by model distance: nonbonded pdb=" O VAL C 93 " pdb=" OH TYR C 140 " model vdw 2.069 3.040 nonbonded pdb=" O VAL A 93 " pdb=" OH TYR A 140 " model vdw 2.069 3.040 nonbonded pdb=" O SER A 138 " pdb=" OG SER A 138 " model vdw 2.295 3.040 nonbonded pdb=" O SER C 138 " pdb=" OG SER C 138 " model vdw 2.295 3.040 nonbonded pdb=" O PRO C 114 " pdb=" NE2 HIS D 116 " model vdw 2.471 3.120 ... (remaining 37811 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.100 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.630 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.016 0.313 4626 Z= 0.800 Angle : 1.763 15.913 6338 Z= 1.150 Chirality : 0.092 0.318 690 Planarity : 0.031 0.418 792 Dihedral : 16.508 89.374 1570 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.43 % Favored : 97.49 % Rotamer: Outliers : 3.96 % Allowed : 6.17 % Favored : 89.87 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.28), residues: 558 helix: -1.55 (0.20), residues: 440 sheet: None (None), residues: 0 loop : -1.20 (0.49), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.013 ARG A 141 TYR 0.050 0.018 TYR C 24 PHE 0.051 0.011 PHE C 98 TRP 0.037 0.013 TRP B 37 HIS 0.032 0.006 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.01445 ( 4622) covalent geometry : angle 1.76257 ( 6338) hydrogen bonds : bond 0.21393 ( 324) hydrogen bonds : angle 6.83103 ( 924) Misc. bond : bond 0.23079 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.088 Fit side-chains REVERT: A 81 SER cc_start: 0.8038 (p) cc_final: 0.7735 (t) REVERT: A 85 ASP cc_start: 0.7845 (t70) cc_final: 0.7308 (m-30) REVERT: A 99 LYS cc_start: 0.8479 (mttm) cc_final: 0.8147 (mttt) REVERT: B 3 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5657 (mt) REVERT: B 22 GLU cc_start: 0.6956 (mt-10) cc_final: 0.5984 (mm-30) REVERT: B 26 GLU cc_start: 0.8021 (tp30) cc_final: 0.7125 (mt-10) REVERT: B 43 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: B 61 LYS cc_start: 0.8189 (tttt) cc_final: 0.7445 (mttp) REVERT: B 66 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7487 (mtmm) REVERT: B 73 ASP cc_start: 0.7400 (t0) cc_final: 0.6561 (m-30) REVERT: B 101 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7983 (tp30) REVERT: B 139 ASN cc_start: 0.7911 (t0) cc_final: 0.7670 (t0) REVERT: C 81 SER cc_start: 0.8040 (p) cc_final: 0.7736 (t) REVERT: C 85 ASP cc_start: 0.7847 (t70) cc_final: 0.7311 (m-30) REVERT: C 99 LYS cc_start: 0.8479 (mttm) cc_final: 0.8148 (mttt) REVERT: D 3 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5654 (mt) REVERT: D 22 GLU cc_start: 0.6957 (mt-10) cc_final: 0.5985 (mm-30) REVERT: D 26 GLU cc_start: 0.8021 (tp30) cc_final: 0.7123 (mt-10) REVERT: D 43 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: D 61 LYS cc_start: 0.8187 (tttt) cc_final: 0.7443 (mttp) REVERT: D 66 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7488 (mtmm) REVERT: D 73 ASP cc_start: 0.7398 (t0) cc_final: 0.6561 (m-30) REVERT: D 101 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: D 139 ASN cc_start: 0.7914 (t0) cc_final: 0.7672 (t0) outliers start: 18 outliers final: 0 residues processed: 120 average time/residue: 0.3741 time to fit residues: 46.3273 Evaluate side-chains 104 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS B 63 HIS B 131 GLN C 58 HIS C 89 HIS D 63 HIS D 131 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.143426 restraints weight = 4407.748| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.20 r_work: 0.3492 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 4626 Z= 0.137 Angle : 0.634 5.731 6338 Z= 0.312 Chirality : 0.039 0.124 690 Planarity : 0.006 0.044 792 Dihedral : 13.111 89.808 634 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.57 % Rotamer: Outliers : 4.41 % Allowed : 9.69 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.35), residues: 558 helix: 1.45 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 0.58 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 141 TYR 0.012 0.002 TYR C 42 PHE 0.009 0.002 PHE D 118 TRP 0.014 0.002 TRP C 14 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4622) covalent geometry : angle 0.63439 ( 6338) hydrogen bonds : bond 0.03959 ( 324) hydrogen bonds : angle 3.81249 ( 924) Misc. bond : bond 0.04810 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.089 Fit side-chains REVERT: A 136 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8539 (mt) REVERT: B 3 LEU cc_start: 0.6898 (mp) cc_final: 0.6630 (mp) REVERT: B 22 GLU cc_start: 0.7542 (mt-10) cc_final: 0.6934 (mm-30) REVERT: B 43 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: B 61 LYS cc_start: 0.8275 (tttt) cc_final: 0.7897 (mttp) REVERT: B 101 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: C 136 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8547 (mt) REVERT: D 3 LEU cc_start: 0.6879 (mp) cc_final: 0.6612 (mp) REVERT: D 22 GLU cc_start: 0.7551 (mt-10) cc_final: 0.6952 (mm-30) REVERT: D 43 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: D 61 LYS cc_start: 0.8270 (tttt) cc_final: 0.7887 (mttp) REVERT: D 101 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7403 (tm-30) outliers start: 20 outliers final: 4 residues processed: 108 average time/residue: 0.3702 time to fit residues: 41.2576 Evaluate side-chains 104 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 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 39 GLN B 57 ASN D 39 GLN D 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.161256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.142000 restraints weight = 4348.059| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.18 r_work: 0.3474 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4626 Z= 0.155 Angle : 0.624 5.782 6338 Z= 0.306 Chirality : 0.041 0.126 690 Planarity : 0.007 0.049 792 Dihedral : 12.713 88.682 630 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 4.41 % Allowed : 17.18 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.36), residues: 558 helix: 2.12 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 0.73 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 40 TYR 0.010 0.002 TYR C 42 PHE 0.011 0.002 PHE D 42 TRP 0.012 0.002 TRP A 14 HIS 0.004 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 4622) covalent geometry : angle 0.62350 ( 6338) hydrogen bonds : bond 0.04339 ( 324) hydrogen bonds : angle 3.75303 ( 924) Misc. bond : bond 0.05049 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.089 Fit side-chains REVERT: A 27 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: A 136 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8635 (mt) REVERT: B 22 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6854 (mm-30) REVERT: B 43 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: B 61 LYS cc_start: 0.8341 (tttt) cc_final: 0.7887 (mttp) REVERT: B 101 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: C 27 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: C 136 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8635 (mt) REVERT: D 22 GLU cc_start: 0.7440 (mt-10) cc_final: 0.6860 (mm-30) REVERT: D 43 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: D 61 LYS cc_start: 0.8335 (tttt) cc_final: 0.7889 (mttp) REVERT: D 101 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7337 (tm-30) outliers start: 20 outliers final: 6 residues processed: 98 average time/residue: 0.3650 time to fit residues: 36.9410 Evaluate side-chains 102 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 19 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.162043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.143123 restraints weight = 4322.370| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.15 r_work: 0.3481 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4626 Z= 0.132 Angle : 0.583 5.900 6338 Z= 0.283 Chirality : 0.040 0.125 690 Planarity : 0.006 0.044 792 Dihedral : 11.819 83.620 630 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.57 % Rotamer: Outliers : 5.29 % Allowed : 18.06 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.16 (0.36), residues: 558 helix: 2.45 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 0.95 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 40 TYR 0.007 0.002 TYR B 130 PHE 0.009 0.001 PHE B 42 TRP 0.010 0.001 TRP A 14 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 4622) covalent geometry : angle 0.58318 ( 6338) hydrogen bonds : bond 0.03740 ( 324) hydrogen bonds : angle 3.64750 ( 924) Misc. bond : bond 0.03357 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.090 Fit side-chains REVERT: A 27 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: A 136 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8458 (mt) REVERT: B 3 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6743 (mt) REVERT: B 22 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6851 (mm-30) REVERT: B 43 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: B 61 LYS cc_start: 0.8274 (tttt) cc_final: 0.7867 (mttp) REVERT: B 101 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: C 27 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8531 (tt0) REVERT: C 136 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8462 (mt) REVERT: D 3 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6743 (mt) REVERT: D 22 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6857 (mm-30) REVERT: D 43 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: D 61 LYS cc_start: 0.8250 (tttt) cc_final: 0.7857 (mttp) REVERT: D 101 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7306 (tm-30) outliers start: 24 outliers final: 6 residues processed: 100 average time/residue: 0.3816 time to fit residues: 39.3614 Evaluate side-chains 104 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 127 LYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 4 optimal weight: 0.0570 chunk 17 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.2876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.165893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147133 restraints weight = 4322.970| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.17 r_work: 0.3534 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4626 Z= 0.098 Angle : 0.532 6.279 6338 Z= 0.249 Chirality : 0.036 0.116 690 Planarity : 0.006 0.042 792 Dihedral : 10.816 85.036 630 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.57 % Rotamer: Outliers : 4.41 % Allowed : 18.94 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.84 (0.36), residues: 558 helix: 2.92 (0.25), residues: 428 sheet: None (None), residues: 0 loop : 1.32 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 141 TYR 0.007 0.001 TYR D 130 PHE 0.005 0.001 PHE A 43 TRP 0.008 0.001 TRP C 14 HIS 0.003 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4622) covalent geometry : angle 0.53156 ( 6338) hydrogen bonds : bond 0.02656 ( 324) hydrogen bonds : angle 3.49158 ( 924) Misc. bond : bond 0.01084 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.089 Fit side-chains REVERT: A 27 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8558 (tt0) REVERT: B 3 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6789 (mt) REVERT: B 8 LYS cc_start: 0.7458 (mttm) cc_final: 0.7082 (mttt) REVERT: B 43 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7387 (pm20) REVERT: B 61 LYS cc_start: 0.8135 (tttt) cc_final: 0.7775 (mttp) REVERT: B 101 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: C 27 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8579 (tt0) REVERT: D 3 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6784 (mt) REVERT: D 8 LYS cc_start: 0.7435 (mttm) cc_final: 0.7056 (mttt) REVERT: D 43 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7391 (pm20) REVERT: D 61 LYS cc_start: 0.8134 (tttt) cc_final: 0.7770 (mttp) REVERT: D 101 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7306 (tm-30) outliers start: 20 outliers final: 4 residues processed: 100 average time/residue: 0.3602 time to fit residues: 37.2177 Evaluate side-chains 102 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.0010 chunk 53 optimal weight: 0.8980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS D 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145552 restraints weight = 4396.982| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.17 r_work: 0.3520 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4626 Z= 0.111 Angle : 0.564 8.325 6338 Z= 0.264 Chirality : 0.038 0.123 690 Planarity : 0.006 0.042 792 Dihedral : 10.892 83.947 630 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 4.85 % Allowed : 18.50 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.94 (0.36), residues: 558 helix: 2.98 (0.25), residues: 428 sheet: None (None), residues: 0 loop : 1.39 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 40 TYR 0.006 0.001 TYR D 130 PHE 0.008 0.001 PHE B 42 TRP 0.008 0.001 TRP A 14 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4622) covalent geometry : angle 0.56427 ( 6338) hydrogen bonds : bond 0.03129 ( 324) hydrogen bonds : angle 3.52543 ( 924) Misc. bond : bond 0.02448 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.089 Fit side-chains REVERT: A 27 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: A 64 ASP cc_start: 0.8276 (m-30) cc_final: 0.7864 (m-30) REVERT: A 139 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6277 (mttt) REVERT: B 3 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6749 (mp) REVERT: B 8 LYS cc_start: 0.7488 (mttm) cc_final: 0.7108 (mttt) REVERT: B 43 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: B 61 LYS cc_start: 0.8223 (tttt) cc_final: 0.7852 (mttp) REVERT: B 90 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6816 (mt-10) REVERT: B 101 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: C 27 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: C 64 ASP cc_start: 0.8288 (m-30) cc_final: 0.7881 (m-30) REVERT: C 139 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6282 (mttt) REVERT: D 3 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6753 (mp) REVERT: D 8 LYS cc_start: 0.7485 (mttm) cc_final: 0.7110 (mttt) REVERT: D 43 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: D 61 LYS cc_start: 0.8224 (tttt) cc_final: 0.7861 (mttp) REVERT: D 90 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6829 (mt-10) REVERT: D 101 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7340 (tm-30) outliers start: 22 outliers final: 6 residues processed: 100 average time/residue: 0.3679 time to fit residues: 37.9722 Evaluate side-chains 106 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 51 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 117 HIS D 39 GLN D 117 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.164243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.145237 restraints weight = 4355.626| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.17 r_work: 0.3519 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4626 Z= 0.113 Angle : 0.563 7.242 6338 Z= 0.265 Chirality : 0.038 0.122 690 Planarity : 0.006 0.043 792 Dihedral : 10.827 83.709 630 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 4.85 % Allowed : 18.50 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.89 (0.36), residues: 558 helix: 2.95 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.33 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.007 0.001 TYR D 130 PHE 0.007 0.001 PHE D 42 TRP 0.008 0.001 TRP C 14 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 4622) covalent geometry : angle 0.56283 ( 6338) hydrogen bonds : bond 0.03186 ( 324) hydrogen bonds : angle 3.55279 ( 924) Misc. bond : bond 0.02273 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.098 Fit side-chains REVERT: A 27 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: A 139 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6270 (mttt) REVERT: B 3 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6778 (mp) REVERT: B 61 LYS cc_start: 0.8210 (tttt) cc_final: 0.7845 (mttp) REVERT: B 90 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: B 101 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: C 27 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: C 139 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6273 (mttt) REVERT: D 3 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6779 (mp) REVERT: D 61 LYS cc_start: 0.8207 (tttt) cc_final: 0.7840 (mttp) REVERT: D 90 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6867 (mt-10) REVERT: D 101 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7327 (tm-30) outliers start: 22 outliers final: 4 residues processed: 94 average time/residue: 0.3603 time to fit residues: 35.0068 Evaluate side-chains 96 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.143770 restraints weight = 4319.799| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.17 r_work: 0.3493 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4626 Z= 0.134 Angle : 0.595 6.994 6338 Z= 0.285 Chirality : 0.040 0.127 690 Planarity : 0.006 0.044 792 Dihedral : 10.675 82.117 624 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.57 % Rotamer: Outliers : 3.96 % Allowed : 18.94 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.71 (0.36), residues: 558 helix: 2.80 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.32 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 141 TYR 0.007 0.002 TYR B 130 PHE 0.007 0.001 PHE A 43 TRP 0.008 0.001 TRP C 14 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 4622) covalent geometry : angle 0.59488 ( 6338) hydrogen bonds : bond 0.03702 ( 324) hydrogen bonds : angle 3.62934 ( 924) Misc. bond : bond 0.03493 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.093 Fit side-chains REVERT: A 27 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: A 139 LYS cc_start: 0.7080 (OUTLIER) cc_final: 0.6339 (mttt) REVERT: B 3 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6691 (mp) REVERT: B 61 LYS cc_start: 0.8263 (tttt) cc_final: 0.7844 (mttp) REVERT: B 101 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: C 27 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: C 139 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6327 (mttt) REVERT: D 3 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6699 (mp) REVERT: D 61 LYS cc_start: 0.8266 (tttt) cc_final: 0.7851 (mttp) REVERT: D 90 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: D 101 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7326 (tm-30) outliers start: 18 outliers final: 4 residues processed: 94 average time/residue: 0.3531 time to fit residues: 34.3571 Evaluate side-chains 99 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.163734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144683 restraints weight = 4353.534| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.16 r_work: 0.3507 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4626 Z= 0.123 Angle : 0.577 6.848 6338 Z= 0.275 Chirality : 0.039 0.124 690 Planarity : 0.006 0.043 792 Dihedral : 10.561 83.111 624 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 3.74 % Allowed : 19.60 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.77 (0.36), residues: 558 helix: 2.84 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.36 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 141 TYR 0.007 0.002 TYR B 130 PHE 0.007 0.001 PHE A 43 TRP 0.007 0.001 TRP C 14 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4622) covalent geometry : angle 0.57743 ( 6338) hydrogen bonds : bond 0.03423 ( 324) hydrogen bonds : angle 3.61106 ( 924) Misc. bond : bond 0.02465 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.094 Fit side-chains REVERT: A 27 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8528 (tt0) REVERT: A 139 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6321 (mttt) REVERT: B 3 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6731 (mp) REVERT: B 61 LYS cc_start: 0.8241 (tttt) cc_final: 0.7838 (mttp) REVERT: B 101 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: C 27 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: C 139 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6298 (mttt) REVERT: D 3 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6738 (mp) REVERT: D 61 LYS cc_start: 0.8233 (tttt) cc_final: 0.7839 (mttp) REVERT: D 101 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7336 (tm-30) outliers start: 17 outliers final: 6 residues processed: 90 average time/residue: 0.3403 time to fit residues: 31.7355 Evaluate side-chains 96 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS D 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.145259 restraints weight = 4318.895| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.16 r_work: 0.3519 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4626 Z= 0.116 Angle : 0.567 6.633 6338 Z= 0.269 Chirality : 0.038 0.123 690 Planarity : 0.006 0.043 792 Dihedral : 10.499 83.613 624 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 3.08 % Allowed : 20.70 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.87 (0.36), residues: 558 helix: 2.91 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.40 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 141 TYR 0.007 0.001 TYR B 130 PHE 0.007 0.001 PHE A 43 TRP 0.006 0.001 TRP A 14 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4622) covalent geometry : angle 0.56679 ( 6338) hydrogen bonds : bond 0.03250 ( 324) hydrogen bonds : angle 3.60154 ( 924) Misc. bond : bond 0.02119 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.168 Fit side-chains REVERT: A 27 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: A 64 ASP cc_start: 0.8259 (m-30) cc_final: 0.7852 (m-30) REVERT: A 139 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6311 (mttt) REVERT: B 3 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6731 (mp) REVERT: B 61 LYS cc_start: 0.8213 (tttt) cc_final: 0.7817 (mttp) REVERT: B 101 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: C 27 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8524 (tt0) REVERT: C 64 ASP cc_start: 0.8272 (m-30) cc_final: 0.7872 (m-30) REVERT: C 139 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6304 (mttt) REVERT: D 3 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6738 (mp) REVERT: D 61 LYS cc_start: 0.8196 (tttt) cc_final: 0.7807 (mttp) REVERT: D 101 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7294 (tm-30) outliers start: 14 outliers final: 6 residues processed: 86 average time/residue: 0.3385 time to fit residues: 30.2522 Evaluate side-chains 90 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 0.0010 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.164003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.144970 restraints weight = 4346.829| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.18 r_work: 0.3513 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4626 Z= 0.117 Angle : 0.568 6.501 6338 Z= 0.270 Chirality : 0.038 0.124 690 Planarity : 0.006 0.043 792 Dihedral : 10.505 83.454 624 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 3.74 % Allowed : 19.82 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.88 (0.36), residues: 558 helix: 2.92 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.40 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 141 TYR 0.007 0.001 TYR D 130 PHE 0.007 0.001 PHE B 42 TRP 0.007 0.001 TRP A 14 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4622) covalent geometry : angle 0.56779 ( 6338) hydrogen bonds : bond 0.03324 ( 324) hydrogen bonds : angle 3.60940 ( 924) Misc. bond : bond 0.02610 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1122.72 seconds wall clock time: 30 minutes 18.73 seconds (1818.73 seconds total)