Starting phenix.real_space_refine on Wed Sep 17 08:11:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b0l_44046/09_2025/9b0l_44046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b0l_44046/09_2025/9b0l_44046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b0l_44046/09_2025/9b0l_44046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b0l_44046/09_2025/9b0l_44046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b0l_44046/09_2025/9b0l_44046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b0l_44046/09_2025/9b0l_44046.map" } resolution = 2.99 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= 0.025 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 155 5.49 5 Mg 1 5.21 5 S 21 5.16 5 C 3903 2.51 5 N 1242 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7051 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 230 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "P" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3814 Classifications: {'peptide': 466} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 444} Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 78 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 473 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "C" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2454 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 51, 'rna3p_pyr': 56} Link IDs: {'rna2p': 10, 'rna3p': 106} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1, ' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1, ' C%rna3p_pyr:plan': 1, ' C%rna3p_pyr:plan2': 1} Unresolved non-hydrogen planarities: 30 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3703 SG CYS P 474 23.862 13.480 65.651 1.00152.90 S ATOM 3723 SG CYS P 477 23.450 10.070 67.087 1.00180.84 S ATOM 3828 SG CYS P 491 25.287 10.437 63.786 1.00167.19 S ATOM 3849 SG CYS P 494 21.568 11.179 63.853 1.00161.64 S Time building chain proxies: 1.94, per 1000 atoms: 0.28 Number of scatterers: 7051 At special positions: 0 Unit cell: (97.092, 104.4, 105.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 155 15.00 Mg 1 11.99 O 1728 8.00 N 1242 7.00 C 3903 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=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 335.0 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN P 601 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 474 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 494 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 477 " pdb="ZN ZN P 601 " - pdb=" SG CYS P 491 " Number of angles added : 6 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 906 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 6 sheets defined 47.0% alpha, 12.9% beta 66 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'P' and resid 59 through 63 Processing helix chain 'P' and resid 109 through 122 removed outlier: 3.701A pdb=" N ARG P 122 " --> pdb=" O LEU P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 171 Processing helix chain 'P' and resid 180 through 188 Processing helix chain 'P' and resid 189 through 197 Processing helix chain 'P' and resid 197 through 206 Processing helix chain 'P' and resid 213 through 237 Processing helix chain 'P' and resid 260 through 262 No H-bonds generated for 'chain 'P' and resid 260 through 262' Processing helix chain 'P' and resid 344 through 369 removed outlier: 4.702A pdb=" N ASN P 354 " --> pdb=" O ASN P 350 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU P 355 " --> pdb=" O THR P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 373 through 410 Processing helix chain 'P' and resid 419 through 425 Processing helix chain 'P' and resid 432 through 443 removed outlier: 3.915A pdb=" N LYS P 438 " --> pdb=" O ALA P 434 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER P 443 " --> pdb=" O LEU P 439 " (cutoff:3.500A) Processing helix chain 'P' and resid 443 through 458 Processing helix chain 'P' and resid 500 through 514 Processing sheet with id=AA1, first strand: chain 'P' and resid 77 through 79 removed outlier: 4.277A pdb=" N HIS P 87 " --> pdb=" O ILE P 79 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE P 413 " --> pdb=" O VAL P 463 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL P 465 " --> pdb=" O ILE P 413 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE P 415 " --> pdb=" O VAL P 465 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 101 through 105 Processing sheet with id=AA3, first strand: chain 'P' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain 'P' and resid 136 through 139 removed outlier: 4.477A pdb=" N TYR P 301 " --> pdb=" O ILE P 139 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS P 300 " --> pdb=" O ASP P 295 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR P 291 " --> pdb=" O PHE P 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 264 through 265 Processing sheet with id=AA6, first strand: chain 'P' and resid 488 through 490 206 hydrogen bonds defined for protein. 588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 166 hydrogen bonds 308 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1583 1.33 - 1.45: 2222 1.45 - 1.57: 3363 1.57 - 1.69: 303 1.69 - 1.81: 30 Bond restraints: 7501 Sorted by residual: bond pdb=" CG HIS P 215 " pdb=" CD2 HIS P 215 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 7.74e+00 bond pdb=" N TYR P 387 " pdb=" CA TYR P 387 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.30e-02 5.92e+03 6.81e+00 bond pdb=" O5' C C-175 " pdb=" C5' C C-175 " ideal model delta sigma weight residual 1.420 1.451 -0.031 1.50e-02 4.44e+03 4.15e+00 bond pdb=" O5' G C-174 " pdb=" C5' G C-174 " ideal model delta sigma weight residual 1.420 1.450 -0.030 1.50e-02 4.44e+03 4.10e+00 bond pdb=" O5' G C-173 " pdb=" C5' G C-173 " ideal model delta sigma weight residual 1.420 1.450 -0.030 1.50e-02 4.44e+03 4.02e+00 ... (remaining 7496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 10639 1.91 - 3.82: 170 3.82 - 5.72: 12 5.72 - 7.63: 7 7.63 - 9.54: 1 Bond angle restraints: 10829 Sorted by residual: angle pdb=" CA HIS P 215 " pdb=" C HIS P 215 " pdb=" O HIS P 215 " ideal model delta sigma weight residual 119.79 113.94 5.85 1.18e+00 7.18e-01 2.46e+01 angle pdb=" CB LYS P 61 " pdb=" CG LYS P 61 " pdb=" CD LYS P 61 " ideal model delta sigma weight residual 111.30 120.84 -9.54 2.30e+00 1.89e-01 1.72e+01 angle pdb=" CA TYR P 387 " pdb=" C TYR P 387 " pdb=" O TYR P 387 " ideal model delta sigma weight residual 119.79 116.02 3.77 1.18e+00 7.18e-01 1.02e+01 angle pdb=" CA GLU P 467 " pdb=" C GLU P 467 " pdb=" O GLU P 467 " ideal model delta sigma weight residual 121.66 118.11 3.55 1.17e+00 7.31e-01 9.19e+00 angle pdb=" C HIS P 215 " pdb=" CA HIS P 215 " pdb=" CB HIS P 215 " ideal model delta sigma weight residual 110.38 116.35 -5.97 2.04e+00 2.40e-01 8.55e+00 ... (remaining 10824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.27: 4025 29.27 - 58.54: 461 58.54 - 87.80: 112 87.80 - 117.07: 7 117.07 - 146.34: 2 Dihedral angle restraints: 4607 sinusoidal: 3213 harmonic: 1394 Sorted by residual: dihedral pdb=" O4' C C-166 " pdb=" C1' C C-166 " pdb=" N1 C C-166 " pdb=" C2 C C-166 " ideal model delta sinusoidal sigma weight residual -128.00 18.34 -146.34 1 1.70e+01 3.46e-03 6.09e+01 dihedral pdb=" O4' A C-197 " pdb=" C1' A C-197 " pdb=" N9 A C-197 " pdb=" C4 A C-197 " ideal model delta sinusoidal sigma weight residual 70.00 4.34 65.66 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" C4' G C-173 " pdb=" O4' G C-173 " pdb=" C1' G C-173 " pdb=" C2' G C-173 " ideal model delta sinusoidal sigma weight residual 3.00 24.79 -21.79 1 8.00e+00 1.56e-02 1.07e+01 ... (remaining 4604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1273 0.093 - 0.187: 47 0.187 - 0.280: 0 0.280 - 0.373: 0 0.373 - 0.466: 3 Chirality restraints: 1323 Sorted by residual: chirality pdb=" P G C-174 " pdb=" OP1 G C-174 " pdb=" OP2 G C-174 " pdb=" O5' G C-174 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" P G C-173 " pdb=" OP1 G C-173 " pdb=" OP2 G C-173 " pdb=" O5' G C-173 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.36e+00 chirality pdb=" P C C-175 " pdb=" OP1 C C-175 " pdb=" OP2 C C-175 " pdb=" O5' C C-175 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.28e+00 ... (remaining 1320 not shown) Planarity restraints: 799 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C C 11 " -0.034 2.00e-02 2.50e+03 1.69e-02 6.46e+00 pdb=" N1 C C 11 " 0.034 2.00e-02 2.50e+03 pdb=" C2 C C 11 " 0.004 2.00e-02 2.50e+03 pdb=" O2 C C 11 " 0.005 2.00e-02 2.50e+03 pdb=" N3 C C 11 " -0.003 2.00e-02 2.50e+03 pdb=" C4 C C 11 " -0.006 2.00e-02 2.50e+03 pdb=" N4 C C 11 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C C 11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C C 11 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT A -7 " 0.021 2.00e-02 2.50e+03 1.01e-02 2.54e+00 pdb=" N1 DT A -7 " -0.022 2.00e-02 2.50e+03 pdb=" C2 DT A -7 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT A -7 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT A -7 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT A -7 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT A -7 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT A -7 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT A -7 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT A -7 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C -3 " 0.020 2.00e-02 2.50e+03 8.81e-03 2.33e+00 pdb=" N9 G C -3 " -0.020 2.00e-02 2.50e+03 pdb=" C8 G C -3 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G C -3 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C -3 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G C -3 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G C -3 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G C -3 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G C -3 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C -3 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G C -3 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G C -3 " -0.006 2.00e-02 2.50e+03 ... (remaining 796 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 54 2.49 - 3.09: 5098 3.09 - 3.70: 12750 3.70 - 4.30: 18307 4.30 - 4.90: 26647 Nonbonded interactions: 62856 Sorted by model distance: nonbonded pdb=" OD1 ASP P 324 " pdb="MG MG P 602 " model vdw 1.888 2.170 nonbonded pdb=" OP1 DC D 3 " pdb="MG MG P 602 " model vdw 1.924 2.170 nonbonded pdb=" N2 DG B -9 " pdb=" O2 DC A 9 " model vdw 2.064 2.496 nonbonded pdb=" O2' U C-162 " pdb=" OP1 G C-161 " model vdw 2.097 3.040 nonbonded pdb=" N GLU P 492 " pdb=" OE1 GLU P 492 " model vdw 2.103 3.120 ... (remaining 62851 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=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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.320 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 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 : 0.004 0.038 7505 Z= 0.190 Angle : 0.587 9.541 10835 Z= 0.317 Chirality : 0.043 0.466 1323 Planarity : 0.004 0.031 799 Dihedral : 21.936 146.341 3701 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.23 % Allowed : 7.76 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.24 (0.41), residues: 464 helix: 2.08 (0.35), residues: 219 sheet: -0.59 (0.82), residues: 58 loop : -0.16 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 446 TYR 0.013 0.001 TYR P 387 PHE 0.011 0.001 PHE P 444 TRP 0.003 0.001 TRP P 84 HIS 0.003 0.001 HIS P 215 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7501) covalent geometry : angle 0.58303 (10829) hydrogen bonds : bond 0.12816 ( 372) hydrogen bonds : angle 5.83987 ( 896) metal coordination : bond 0.00571 ( 4) metal coordination : angle 2.77286 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.197 Fit side-chains REVERT: P 67 LYS cc_start: 0.7933 (pttp) cc_final: 0.7580 (ptmt) REVERT: P 276 LYS cc_start: 0.8130 (ttpp) cc_final: 0.7581 (mttt) REVERT: P 298 THR cc_start: 0.7076 (m) cc_final: 0.6725 (p) REVERT: P 382 ARG cc_start: 0.6917 (ttp80) cc_final: 0.6399 (ttt-90) REVERT: P 502 GLU cc_start: 0.6641 (mm-30) cc_final: 0.6413 (mt-10) outliers start: 1 outliers final: 0 residues processed: 76 average time/residue: 0.6244 time to fit residues: 49.6880 Evaluate side-chains 50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.172786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128320 restraints weight = 8411.202| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 1.19 r_work: 0.3349 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7505 Z= 0.204 Angle : 0.596 6.394 10835 Z= 0.315 Chirality : 0.037 0.198 1323 Planarity : 0.005 0.043 799 Dihedral : 23.427 160.646 2683 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.20 % Allowed : 13.01 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.14 (0.39), residues: 464 helix: 1.99 (0.34), residues: 218 sheet: -0.06 (0.81), residues: 58 loop : -0.41 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 299 TYR 0.019 0.002 TYR P 387 PHE 0.014 0.002 PHE P 304 TRP 0.006 0.001 TRP P 68 HIS 0.002 0.001 HIS P 399 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 7501) covalent geometry : angle 0.59271 (10829) hydrogen bonds : bond 0.05086 ( 372) hydrogen bonds : angle 4.30316 ( 896) metal coordination : bond 0.00763 ( 4) metal coordination : angle 2.53922 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.201 Fit side-chains REVERT: P 276 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8360 (mttt) REVERT: P 328 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6447 (mtm110) REVERT: P 346 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: P 382 ARG cc_start: 0.8368 (ttp80) cc_final: 0.7875 (ttt-90) outliers start: 14 outliers final: 4 residues processed: 62 average time/residue: 0.6505 time to fit residues: 42.3252 Evaluate side-chains 49 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 199 THR Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 328 ARG Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 346 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.173974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.130757 restraints weight = 8386.425| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.16 r_work: 0.3349 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7505 Z= 0.192 Angle : 0.573 5.888 10835 Z= 0.303 Chirality : 0.037 0.211 1323 Planarity : 0.004 0.035 799 Dihedral : 23.255 160.438 2683 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.88 % Allowed : 14.61 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.97 (0.38), residues: 464 helix: 1.88 (0.34), residues: 218 sheet: -0.16 (0.76), residues: 58 loop : -0.53 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 299 TYR 0.017 0.001 TYR P 387 PHE 0.013 0.002 PHE P 156 TRP 0.008 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 7501) covalent geometry : angle 0.56908 (10829) hydrogen bonds : bond 0.04919 ( 372) hydrogen bonds : angle 4.00920 ( 896) metal coordination : bond 0.00819 ( 4) metal coordination : angle 2.83246 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.213 Fit side-chains REVERT: P 276 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8369 (mttt) REVERT: P 328 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6401 (mtm110) REVERT: P 346 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: P 382 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8130 (ttt-90) REVERT: P 421 LYS cc_start: 0.7855 (mmtp) cc_final: 0.7627 (mttm) outliers start: 17 outliers final: 4 residues processed: 65 average time/residue: 0.6160 time to fit residues: 42.2471 Evaluate side-chains 49 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 328 ARG Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 346 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 42 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 388 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.173697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129694 restraints weight = 8468.891| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.18 r_work: 0.3349 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7505 Z= 0.196 Angle : 0.579 7.680 10835 Z= 0.305 Chirality : 0.037 0.192 1323 Planarity : 0.004 0.035 799 Dihedral : 23.247 158.931 2683 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.97 % Allowed : 17.81 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.86 (0.38), residues: 464 helix: 1.80 (0.34), residues: 218 sheet: -0.13 (0.75), residues: 58 loop : -0.64 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 88 TYR 0.017 0.001 TYR P 387 PHE 0.014 0.002 PHE P 156 TRP 0.006 0.001 TRP P 68 HIS 0.003 0.001 HIS P 388 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 7501) covalent geometry : angle 0.57535 (10829) hydrogen bonds : bond 0.04896 ( 372) hydrogen bonds : angle 3.97578 ( 896) metal coordination : bond 0.00710 ( 4) metal coordination : angle 2.81841 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.208 Fit side-chains REVERT: P 328 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6400 (mtm110) REVERT: P 382 ARG cc_start: 0.8514 (ttp80) cc_final: 0.8089 (ttt-90) REVERT: P 390 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7483 (mmt90) REVERT: P 421 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7602 (mttm) outliers start: 13 outliers final: 5 residues processed: 60 average time/residue: 0.6193 time to fit residues: 39.1702 Evaluate side-chains 51 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 328 ARG Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 390 ARG Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 3 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 0.0040 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 34 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.2930 ------------------------------------------------------------------------------- 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 = 0.4126 r_free = 0.4126 target = 0.176408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131190 restraints weight = 8279.833| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.20 r_work: 0.3391 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7505 Z= 0.140 Angle : 0.531 5.595 10835 Z= 0.281 Chirality : 0.034 0.179 1323 Planarity : 0.004 0.035 799 Dihedral : 23.172 163.972 2683 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.37 % Allowed : 20.55 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.10 (0.39), residues: 464 helix: 2.03 (0.34), residues: 218 sheet: -0.14 (0.74), residues: 58 loop : -0.52 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 88 TYR 0.013 0.001 TYR P 387 PHE 0.012 0.002 PHE P 156 TRP 0.004 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7501) covalent geometry : angle 0.52815 (10829) hydrogen bonds : bond 0.04620 ( 372) hydrogen bonds : angle 3.77096 ( 896) metal coordination : bond 0.00503 ( 4) metal coordination : angle 2.32417 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.204 Fit side-chains REVERT: P 382 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7817 (ttt-90) REVERT: P 390 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7389 (mmt90) REVERT: P 421 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7582 (mttm) outliers start: 6 outliers final: 2 residues processed: 59 average time/residue: 0.6698 time to fit residues: 41.5659 Evaluate side-chains 51 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 390 ARG Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 33 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 337 ASN P 404 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.171548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.125237 restraints weight = 8365.631| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.23 r_work: 0.3319 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7505 Z= 0.237 Angle : 0.601 6.050 10835 Z= 0.316 Chirality : 0.038 0.177 1323 Planarity : 0.004 0.037 799 Dihedral : 23.268 156.160 2683 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.97 % Allowed : 21.00 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.66 (0.38), residues: 464 helix: 1.64 (0.34), residues: 218 sheet: -0.32 (0.72), residues: 56 loop : -0.71 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 299 TYR 0.020 0.002 TYR P 387 PHE 0.016 0.003 PHE P 444 TRP 0.007 0.001 TRP P 68 HIS 0.002 0.001 HIS P 215 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 7501) covalent geometry : angle 0.59831 (10829) hydrogen bonds : bond 0.05060 ( 372) hydrogen bonds : angle 3.99065 ( 896) metal coordination : bond 0.00831 ( 4) metal coordination : angle 2.64839 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.206 Fit side-chains REVERT: P 61 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7742 (ttmm) REVERT: P 328 ARG cc_start: 0.7253 (OUTLIER) cc_final: 0.6489 (mtm110) REVERT: P 346 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: P 382 ARG cc_start: 0.8381 (ttp80) cc_final: 0.7930 (ttt-90) REVERT: P 390 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7498 (mmt90) REVERT: P 421 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7423 (mttm) outliers start: 13 outliers final: 6 residues processed: 58 average time/residue: 0.6438 time to fit residues: 39.3436 Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 296 SER Chi-restraints excluded: chain P residue 328 ARG Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 390 ARG Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 42 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 38 optimal weight: 0.4980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.174110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.128471 restraints weight = 8336.032| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.20 r_work: 0.3357 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7505 Z= 0.170 Angle : 0.557 5.779 10835 Z= 0.293 Chirality : 0.036 0.179 1323 Planarity : 0.004 0.035 799 Dihedral : 23.211 159.153 2683 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.28 % Allowed : 22.60 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.79 (0.39), residues: 464 helix: 1.77 (0.34), residues: 218 sheet: -0.25 (0.73), residues: 56 loop : -0.66 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 299 TYR 0.014 0.001 TYR P 387 PHE 0.014 0.002 PHE P 156 TRP 0.003 0.001 TRP P 68 HIS 0.003 0.001 HIS P 215 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 7501) covalent geometry : angle 0.55369 (10829) hydrogen bonds : bond 0.04728 ( 372) hydrogen bonds : angle 3.86335 ( 896) metal coordination : bond 0.00613 ( 4) metal coordination : angle 2.57142 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.211 Fit side-chains REVERT: P 61 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7731 (ttmm) REVERT: P 328 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6279 (mtm110) REVERT: P 382 ARG cc_start: 0.8374 (ttp80) cc_final: 0.7929 (ttt-90) REVERT: P 390 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7425 (mmt90) REVERT: P 421 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7490 (mttm) outliers start: 10 outliers final: 5 residues processed: 56 average time/residue: 0.6101 time to fit residues: 36.0550 Evaluate side-chains 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 328 ARG Chi-restraints excluded: chain P residue 390 ARG Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 34 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 203 ASN P 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.175660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130166 restraints weight = 8380.852| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.21 r_work: 0.3379 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7505 Z= 0.151 Angle : 0.545 7.113 10835 Z= 0.286 Chirality : 0.035 0.185 1323 Planarity : 0.004 0.035 799 Dihedral : 23.162 162.193 2683 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.28 % Allowed : 23.29 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.93 (0.39), residues: 464 helix: 1.90 (0.34), residues: 218 sheet: -0.18 (0.73), residues: 56 loop : -0.63 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 299 TYR 0.013 0.001 TYR P 387 PHE 0.013 0.002 PHE P 156 TRP 0.003 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 7501) covalent geometry : angle 0.54039 (10829) hydrogen bonds : bond 0.04598 ( 372) hydrogen bonds : angle 3.76531 ( 896) metal coordination : bond 0.00541 ( 4) metal coordination : angle 2.96735 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.212 Fit side-chains REVERT: P 61 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7710 (ttmm) REVERT: P 328 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6383 (mtm110) REVERT: P 382 ARG cc_start: 0.8394 (ttp80) cc_final: 0.7832 (ttt-90) REVERT: P 390 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7446 (mmt90) REVERT: P 421 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7380 (mttp) outliers start: 10 outliers final: 6 residues processed: 58 average time/residue: 0.6407 time to fit residues: 39.1327 Evaluate side-chains 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 272 THR Chi-restraints excluded: chain P residue 273 VAL Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 328 ARG Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 390 ARG Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 0.0370 chunk 18 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 11 optimal weight: 0.1980 chunk 36 optimal weight: 0.3980 overall best weight: 0.2258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.177474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132452 restraints weight = 8377.756| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.20 r_work: 0.3410 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7505 Z= 0.131 Angle : 0.538 6.523 10835 Z= 0.283 Chirality : 0.034 0.178 1323 Planarity : 0.004 0.035 799 Dihedral : 23.140 163.945 2683 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.28 % Allowed : 23.29 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.04 (0.39), residues: 464 helix: 1.99 (0.34), residues: 218 sheet: -0.03 (0.74), residues: 56 loop : -0.61 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 299 TYR 0.009 0.001 TYR P 387 PHE 0.014 0.002 PHE P 156 TRP 0.004 0.001 TRP P 516 HIS 0.002 0.000 HIS P 399 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 7501) covalent geometry : angle 0.53431 (10829) hydrogen bonds : bond 0.04461 ( 372) hydrogen bonds : angle 3.71715 ( 896) metal coordination : bond 0.00429 ( 4) metal coordination : angle 2.59690 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.208 Fit side-chains REVERT: P 199 THR cc_start: 0.8549 (m) cc_final: 0.8343 (p) REVERT: P 382 ARG cc_start: 0.8359 (ttp80) cc_final: 0.7791 (ttt-90) REVERT: P 390 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7406 (mmt90) REVERT: P 421 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7377 (mttp) outliers start: 10 outliers final: 3 residues processed: 55 average time/residue: 0.6160 time to fit residues: 35.8762 Evaluate side-chains 50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 390 ARG Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 21 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.173297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127047 restraints weight = 8276.453| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.23 r_work: 0.3334 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7505 Z= 0.206 Angle : 0.585 7.212 10835 Z= 0.307 Chirality : 0.037 0.177 1323 Planarity : 0.004 0.036 799 Dihedral : 23.182 158.407 2683 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.83 % Allowed : 23.97 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.76 (0.39), residues: 464 helix: 1.77 (0.34), residues: 218 sheet: -0.25 (0.73), residues: 56 loop : -0.73 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 328 TYR 0.016 0.001 TYR P 387 PHE 0.014 0.002 PHE P 264 TRP 0.005 0.001 TRP P 68 HIS 0.003 0.001 HIS P 215 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 7501) covalent geometry : angle 0.58153 (10829) hydrogen bonds : bond 0.04871 ( 372) hydrogen bonds : angle 3.88997 ( 896) metal coordination : bond 0.00803 ( 4) metal coordination : angle 2.89650 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 928 Ramachandran restraints generated. 464 Oldfield, 0 Emsley, 464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.199 Fit side-chains REVERT: P 61 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7766 (ttmm) REVERT: P 382 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7968 (ttt-90) REVERT: P 390 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7598 (mmt90) REVERT: P 421 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7360 (mttp) REVERT: P 460 THR cc_start: 0.8697 (m) cc_final: 0.8497 (p) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 0.6895 time to fit residues: 39.1104 Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 291 THR Chi-restraints excluded: chain P residue 339 THR Chi-restraints excluded: chain P residue 390 ARG Chi-restraints excluded: chain P residue 421 LYS Chi-restraints excluded: chain P residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.172478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126414 restraints weight = 8271.897| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.21 r_work: 0.3332 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7505 Z= 0.214 Angle : 0.597 7.155 10835 Z= 0.312 Chirality : 0.038 0.180 1323 Planarity : 0.004 0.036 799 Dihedral : 23.250 156.196 2683 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.28 % Allowed : 23.06 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.61 (0.39), residues: 464 helix: 1.64 (0.34), residues: 218 sheet: -0.33 (0.73), residues: 56 loop : -0.80 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 299 TYR 0.017 0.001 TYR P 387 PHE 0.013 0.002 PHE P 264 TRP 0.005 0.001 TRP P 68 HIS 0.003 0.001 HIS P 215 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 7501) covalent geometry : angle 0.59266 (10829) hydrogen bonds : bond 0.04913 ( 372) hydrogen bonds : angle 3.96760 ( 896) metal coordination : bond 0.00845 ( 4) metal coordination : angle 3.11363 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.85 seconds wall clock time: 46 minutes 55.47 seconds (2815.47 seconds total)