Starting phenix.real_space_refine on Mon Apr 28 04:59:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b0l_44046/04_2025/9b0l_44046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b0l_44046/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b0l_44046/04_2025/9b0l_44046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b0l_44046/04_2025/9b0l_44046.map" model { file = "/net/cci-nas-00/data/ceres_data/9b0l_44046/04_2025/9b0l_44046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b0l_44046/04_2025/9b0l_44046.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {' C%rna3p_pyr:plan2': 1, ' C%rna3p_pyr:plan': 1, ' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1, ' U%rna3p_pyr:plan': 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: 5.38, per 1000 atoms: 0.76 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: 2.48 Conformation dependent library (CDL) restraints added in 482.2 milliseconds 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: 2.89 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: 3.02 Time building geometry restraints manager: 2.55 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.640 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.580 ------------------------------------------------------------------------------- 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 : 7.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.003 0.001 TRP P 84 HIS 0.003 0.001 HIS P 215 PHE 0.011 0.001 PHE P 444 TYR 0.013 0.001 TYR P 387 ARG 0.002 0.000 ARG P 446 Details of bonding type rmsd hydrogen bonds : bond 0.12816 ( 372) hydrogen bonds : angle 5.83987 ( 896) metal coordination : bond 0.00571 ( 4) metal coordination : angle 2.77286 ( 6) covalent geometry : bond 0.00367 ( 7501) covalent geometry : angle 0.58303 (10829) *********************** 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 : 0.603 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: 1.3047 time to fit residues: 104.6689 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 : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.172011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128161 restraints weight = 8309.055| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.20 r_work: 0.3320 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7505 Z= 0.220 Angle : 0.611 7.002 10835 Z= 0.323 Chirality : 0.038 0.196 1323 Planarity : 0.005 0.044 799 Dihedral : 23.479 161.009 2683 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.39), residues: 464 helix: 1.87 (0.34), residues: 218 sheet: -0.16 (0.81), residues: 58 loop : -0.51 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 68 HIS 0.002 0.001 HIS P 399 PHE 0.014 0.003 PHE P 304 TYR 0.020 0.002 TYR P 387 ARG 0.003 0.001 ARG P 299 Details of bonding type rmsd hydrogen bonds : bond 0.05206 ( 372) hydrogen bonds : angle 4.33176 ( 896) metal coordination : bond 0.00803 ( 4) metal coordination : angle 2.62364 ( 6) covalent geometry : bond 0.00491 ( 7501) covalent geometry : angle 0.60774 (10829) *********************** 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 68 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 1.878 Fit side-chains REVERT: P 276 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8405 (tttm) REVERT: P 328 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6325 (mtm110) REVERT: P 346 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: P 382 ARG cc_start: 0.8468 (ttp80) cc_final: 0.7985 (ttt-90) outliers start: 14 outliers final: 4 residues processed: 64 average time/residue: 2.2514 time to fit residues: 152.9504 Evaluate side-chains 48 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 3 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.0030 chunk 14 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.176264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.132666 restraints weight = 8448.231| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.14 r_work: 0.3381 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7505 Z= 0.155 Angle : 0.547 5.969 10835 Z= 0.290 Chirality : 0.035 0.185 1323 Planarity : 0.004 0.036 799 Dihedral : 23.230 163.884 2683 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.51 % Allowed : 15.53 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.39), residues: 464 helix: 2.02 (0.34), residues: 218 sheet: -0.16 (0.76), residues: 58 loop : -0.48 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 PHE 0.013 0.002 PHE P 156 TYR 0.016 0.001 TYR P 387 ARG 0.003 0.000 ARG P 88 Details of bonding type rmsd hydrogen bonds : bond 0.04721 ( 372) hydrogen bonds : angle 3.94013 ( 896) metal coordination : bond 0.00428 ( 4) metal coordination : angle 3.01108 ( 6) covalent geometry : bond 0.00343 ( 7501) covalent geometry : angle 0.54303 (10829) *********************** 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 60 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.525 Fit side-chains REVERT: P 328 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6492 (mtm110) REVERT: P 382 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8103 (ttt-90) REVERT: P 421 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7401 (tppt) outliers start: 11 outliers final: 1 residues processed: 58 average time/residue: 1.1946 time to fit residues: 73.3853 Evaluate side-chains 43 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 328 ARG Chi-restraints excluded: chain P residue 421 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.174873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131072 restraints weight = 8428.032| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.14 r_work: 0.3372 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 0.036 7505 Z= 0.181 Angle : 0.561 7.099 10835 Z= 0.296 Chirality : 0.036 0.165 1323 Planarity : 0.004 0.035 799 Dihedral : 23.184 161.316 2683 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.74 % Allowed : 17.81 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.39), residues: 464 helix: 1.93 (0.34), residues: 218 sheet: -0.18 (0.74), residues: 58 loop : -0.54 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 68 HIS 0.002 0.001 HIS P 388 PHE 0.012 0.002 PHE P 156 TYR 0.015 0.001 TYR P 387 ARG 0.003 0.000 ARG P 299 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 372) hydrogen bonds : angle 3.88294 ( 896) metal coordination : bond 0.00669 ( 4) metal coordination : angle 2.54691 ( 6) covalent geometry : bond 0.00401 ( 7501) covalent geometry : angle 0.55837 (10829) *********************** 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 57 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.561 Fit side-chains REVERT: P 328 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6329 (mtm110) REVERT: P 382 ARG cc_start: 0.8518 (ttp80) cc_final: 0.8083 (ttt-90) REVERT: P 421 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7410 (mmtp) outliers start: 12 outliers final: 6 residues processed: 55 average time/residue: 1.2359 time to fit residues: 71.9841 Evaluate side-chains 49 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 421 LYS Chi-restraints excluded: chain P residue 430 VAL Chi-restraints excluded: chain P residue 454 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 35 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 18 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.176683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.133370 restraints weight = 8342.167| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.16 r_work: 0.3387 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2211 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= 0.149 Angle : 0.540 6.796 10835 Z= 0.285 Chirality : 0.035 0.158 1323 Planarity : 0.004 0.035 799 Dihedral : 23.165 162.935 2683 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.20 % Allowed : 18.49 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.39), residues: 464 helix: 2.02 (0.34), residues: 218 sheet: -0.23 (0.72), residues: 58 loop : -0.47 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 516 HIS 0.002 0.001 HIS P 399 PHE 0.014 0.002 PHE P 156 TYR 0.013 0.001 TYR P 387 ARG 0.005 0.000 ARG P 390 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 372) hydrogen bonds : angle 3.78279 ( 896) metal coordination : bond 0.00483 ( 4) metal coordination : angle 2.42265 ( 6) covalent geometry : bond 0.00327 ( 7501) covalent geometry : angle 0.53730 (10829) *********************** 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: 14 poor density : 45 time to evaluate : 0.621 Fit side-chains REVERT: P 328 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6477 (mtm110) REVERT: P 382 ARG cc_start: 0.8530 (ttp80) cc_final: 0.8111 (ttt180) REVERT: P 421 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7351 (tppt) outliers start: 14 outliers final: 5 residues processed: 57 average time/residue: 1.2802 time to fit residues: 77.1900 Evaluate side-chains 48 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.513 ------------------------------------------------------------------------------- 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 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 53 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.0980 chunk 45 optimal weight: 0.0370 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 57 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.3058 ------------------------------------------------------------------------------- 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 = 0.4130 r_free = 0.4130 target = 0.176800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131421 restraints weight = 8309.534| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.20 r_work: 0.3398 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2362 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= 0.141 Angle : 0.523 5.570 10835 Z= 0.276 Chirality : 0.034 0.161 1323 Planarity : 0.004 0.035 799 Dihedral : 23.119 164.682 2683 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.51 % Allowed : 20.78 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.39), residues: 464 helix: 2.15 (0.34), residues: 218 sheet: -0.16 (0.72), residues: 58 loop : -0.47 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 PHE 0.013 0.002 PHE P 156 TYR 0.012 0.001 TYR P 387 ARG 0.003 0.000 ARG P 299 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 372) hydrogen bonds : angle 3.68533 ( 896) metal coordination : bond 0.00453 ( 4) metal coordination : angle 2.13686 ( 6) covalent geometry : bond 0.00309 ( 7501) covalent geometry : angle 0.52035 (10829) *********************** 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 63 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.582 Fit side-chains REVERT: P 328 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6513 (mtm110) REVERT: P 382 ARG cc_start: 0.8394 (ttp80) cc_final: 0.7854 (ttt-90) REVERT: P 421 LYS cc_start: 0.7499 (OUTLIER) cc_final: 0.7268 (tppt) outliers start: 11 outliers final: 6 residues processed: 61 average time/residue: 1.1434 time to fit residues: 74.0902 Evaluate side-chains 53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 55 SER 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 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 59 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.170613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123874 restraints weight = 8248.333| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.28 r_work: 0.3297 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7505 Z= 0.273 Angle : 0.635 6.269 10835 Z= 0.333 Chirality : 0.040 0.181 1323 Planarity : 0.005 0.036 799 Dihedral : 23.316 153.294 2683 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.20 % Allowed : 20.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.38), residues: 464 helix: 1.57 (0.34), residues: 218 sheet: -0.35 (0.73), residues: 56 loop : -0.75 (0.42), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 68 HIS 0.004 0.001 HIS P 215 PHE 0.015 0.003 PHE P 264 TYR 0.022 0.002 TYR P 387 ARG 0.004 0.001 ARG P 299 Details of bonding type rmsd hydrogen bonds : bond 0.05277 ( 372) hydrogen bonds : angle 4.06734 ( 896) metal coordination : bond 0.00972 ( 4) metal coordination : angle 2.80843 ( 6) covalent geometry : bond 0.00609 ( 7501) covalent geometry : angle 0.63209 (10829) *********************** 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 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.606 Fit side-chains REVERT: P 61 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7790 (ttmm) REVERT: P 328 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6522 (mtm110) REVERT: P 346 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7957 (mp0) REVERT: P 382 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7920 (ttt-90) REVERT: P 390 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7432 (mmt90) outliers start: 14 outliers final: 8 residues processed: 55 average time/residue: 1.1940 time to fit residues: 69.7477 Evaluate side-chains 53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 55 SER 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 430 VAL Chi-restraints excluded: chain P residue 454 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.0970 chunk 18 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.173619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127814 restraints weight = 8242.975| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.20 r_work: 0.3348 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7505 Z= 0.182 Angle : 0.568 6.186 10835 Z= 0.299 Chirality : 0.036 0.214 1323 Planarity : 0.004 0.036 799 Dihedral : 23.237 157.278 2683 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.97 % Allowed : 22.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.38), residues: 464 helix: 1.67 (0.34), residues: 218 sheet: -0.34 (0.72), residues: 56 loop : -0.67 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 68 HIS 0.003 0.001 HIS P 215 PHE 0.013 0.002 PHE P 156 TYR 0.016 0.001 TYR P 387 ARG 0.004 0.000 ARG P 299 Details of bonding type rmsd hydrogen bonds : bond 0.04787 ( 372) hydrogen bonds : angle 3.90571 ( 896) metal coordination : bond 0.00757 ( 4) metal coordination : angle 2.85678 ( 6) covalent geometry : bond 0.00405 ( 7501) covalent geometry : angle 0.56459 (10829) *********************** 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 60 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.500 Fit side-chains REVERT: P 61 LYS cc_start: 0.8271 (mmmt) cc_final: 0.7765 (ttmm) REVERT: P 328 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6310 (mtm110) REVERT: P 346 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: P 381 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7868 (t0) REVERT: P 382 ARG cc_start: 0.8360 (ttp80) cc_final: 0.7924 (ttt-90) REVERT: P 390 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7449 (mmt90) outliers start: 13 outliers final: 7 residues processed: 57 average time/residue: 1.2300 time to fit residues: 74.1518 Evaluate side-chains 55 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 77 THR 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 346 GLU Chi-restraints excluded: chain P residue 381 ASN Chi-restraints excluded: chain P residue 390 ARG 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 22 optimal weight: 0.6980 chunk 29 optimal weight: 0.0070 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 overall best weight: 0.3198 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.176652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.131383 restraints weight = 8389.212| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.18 r_work: 0.3397 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2628 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= 0.144 Angle : 0.539 6.476 10835 Z= 0.284 Chirality : 0.034 0.182 1323 Planarity : 0.004 0.035 799 Dihedral : 23.152 162.665 2683 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.97 % Allowed : 22.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.39), residues: 464 helix: 1.89 (0.34), residues: 218 sheet: -0.23 (0.73), residues: 56 loop : -0.60 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 PHE 0.013 0.002 PHE P 156 TYR 0.012 0.001 TYR P 387 ARG 0.004 0.000 ARG P 299 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 372) hydrogen bonds : angle 3.73966 ( 896) metal coordination : bond 0.00558 ( 4) metal coordination : angle 2.82202 ( 6) covalent geometry : bond 0.00316 ( 7501) covalent geometry : angle 0.53479 (10829) *********************** 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 63 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.556 Fit side-chains REVERT: P 61 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7707 (ttmm) REVERT: P 382 ARG cc_start: 0.8372 (ttp80) cc_final: 0.7854 (ttt-90) REVERT: P 390 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7381 (mmt90) outliers start: 13 outliers final: 7 residues processed: 60 average time/residue: 1.0891 time to fit residues: 69.6902 Evaluate side-chains 53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 55 SER Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 203 ASN Chi-restraints excluded: chain P residue 272 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 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 5 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.4103 r_free = 0.4103 target = 0.173957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.127590 restraints weight = 8415.572| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.23 r_work: 0.3343 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7505 Z= 0.192 Angle : 0.583 7.603 10835 Z= 0.306 Chirality : 0.037 0.181 1323 Planarity : 0.004 0.035 799 Dihedral : 23.157 159.707 2683 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.05 % Allowed : 23.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.39), residues: 464 helix: 1.76 (0.34), residues: 218 sheet: -0.28 (0.73), residues: 56 loop : -0.69 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 PHE 0.014 0.002 PHE P 156 TYR 0.016 0.001 TYR P 387 ARG 0.004 0.000 ARG P 299 Details of bonding type rmsd hydrogen bonds : bond 0.04778 ( 372) hydrogen bonds : angle 3.85519 ( 896) metal coordination : bond 0.00738 ( 4) metal coordination : angle 2.73590 ( 6) covalent geometry : bond 0.00427 ( 7501) covalent geometry : angle 0.57915 (10829) ********************** 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: 9 poor density : 46 time to evaluate : 0.557 Fit side-chains REVERT: P 61 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7750 (ttmm) REVERT: P 346 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7923 (mp0) REVERT: P 382 ARG cc_start: 0.8404 (ttp80) cc_final: 0.7963 (ttt-90) REVERT: P 390 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7497 (mmt90) outliers start: 9 outliers final: 6 residues processed: 53 average time/residue: 1.1002 time to fit residues: 62.1201 Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 77 THR 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 339 THR Chi-restraints excluded: chain P residue 346 GLU Chi-restraints excluded: chain P residue 390 ARG 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 46 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 34 optimal weight: 0.2980 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 31 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.174669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.128810 restraints weight = 8243.538| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 1.21 r_work: 0.3362 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2688 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= 0.174 Angle : 0.569 7.331 10835 Z= 0.299 Chirality : 0.036 0.182 1323 Planarity : 0.004 0.036 799 Dihedral : 23.140 160.249 2683 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.39), residues: 464 helix: 1.78 (0.34), residues: 218 sheet: -0.27 (0.74), residues: 56 loop : -0.70 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 PHE 0.014 0.002 PHE P 156 TYR 0.014 0.001 TYR P 387 ARG 0.003 0.000 ARG P 299 Details of bonding type rmsd hydrogen bonds : bond 0.04665 ( 372) hydrogen bonds : angle 3.83714 ( 896) metal coordination : bond 0.00640 ( 4) metal coordination : angle 2.72093 ( 6) covalent geometry : bond 0.00387 ( 7501) covalent geometry : angle 0.56574 (10829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5519.45 seconds wall clock time: 96 minutes 25.44 seconds (5785.44 seconds total)