Starting phenix.real_space_refine on Fri Dec 27 23:32:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b0l_44046/12_2024/9b0l_44046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b0l_44046/12_2024/9b0l_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_44046/12_2024/9b0l_44046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b0l_44046/12_2024/9b0l_44046.map" model { file = "/net/cci-nas-00/data/ceres_data/9b0l_44046/12_2024/9b0l_44046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b0l_44046/12_2024/9b0l_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-5532/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: 5.33, 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: 2.26 Conformation dependent library (CDL) restraints added in 499.4 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: 2.95 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: 3.48 Time building geometry restraints manager: 2.49 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.010 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.540 ------------------------------------------------------------------------------- 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 7501 Z= 0.225 Angle : 0.583 9.541 10829 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 *********************** 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 : 0.577 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: 1.3728 time to fit residues: 109.7504 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 : 0.575 ------------------------------------------------------------------------------- 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: 0.6980 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7501 Z= 0.295 Angle : 0.598 6.616 10829 Z= 0.317 Chirality : 0.038 0.216 1323 Planarity : 0.005 0.043 799 Dihedral : 23.443 160.354 2683 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.81 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: 1.07 (0.39), residues: 464 helix: 1.94 (0.34), residues: 218 sheet: -0.09 (0.81), residues: 58 loop : -0.45 (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 0.002 PHE P 304 TYR 0.020 0.002 TYR P 387 ARG 0.003 0.001 ARG P 299 *********************** 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 67 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.557 Fit side-chains REVERT: P 67 LYS cc_start: 0.7888 (pttp) cc_final: 0.7520 (ptmt) REVERT: P 97 PRO cc_start: 0.7560 (Cg_exo) cc_final: 0.7350 (Cg_endo) REVERT: P 276 LYS cc_start: 0.8165 (ttpp) cc_final: 0.7573 (tttm) REVERT: P 328 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.5810 (mtm110) REVERT: P 346 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: P 382 ARG cc_start: 0.6854 (ttp80) cc_final: 0.6417 (ttt-90) outliers start: 14 outliers final: 4 residues processed: 63 average time/residue: 1.3093 time to fit residues: 87.1757 Evaluate side-chains 50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.0870 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7501 Z= 0.229 Angle : 0.545 5.602 10829 Z= 0.291 Chirality : 0.036 0.187 1323 Planarity : 0.004 0.034 799 Dihedral : 23.229 163.272 2683 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.97 % Allowed : 14.84 % Favored : 82.19 % 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: 1.13 (0.39), residues: 464 helix: 2.02 (0.34), residues: 218 sheet: -0.13 (0.76), residues: 58 loop : -0.46 (0.42), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 *********************** 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 66 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.614 Fit side-chains REVERT: P 67 LYS cc_start: 0.7811 (pttp) cc_final: 0.7452 (ptmt) REVERT: P 97 PRO cc_start: 0.7499 (Cg_exo) cc_final: 0.7290 (Cg_endo) REVERT: P 276 LYS cc_start: 0.8097 (ttpp) cc_final: 0.7548 (tttm) REVERT: P 328 ARG cc_start: 0.6326 (OUTLIER) cc_final: 0.5634 (mtm110) REVERT: P 382 ARG cc_start: 0.6894 (ttp80) cc_final: 0.6460 (ttt-90) outliers start: 13 outliers final: 2 residues processed: 64 average time/residue: 1.2365 time to fit residues: 83.7993 Evaluate side-chains 48 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 328 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 0.0670 chunk 36 optimal weight: 0.2980 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7501 Z= 0.232 Angle : 0.551 7.346 10829 Z= 0.292 Chirality : 0.036 0.168 1323 Planarity : 0.004 0.035 799 Dihedral : 23.187 162.241 2683 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.51 % Allowed : 17.81 % Favored : 79.68 % 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: 1.09 (0.39), residues: 464 helix: 2.00 (0.34), residues: 218 sheet: -0.13 (0.74), residues: 58 loop : -0.50 (0.43), 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 388 PHE 0.012 0.002 PHE P 156 TYR 0.015 0.001 TYR P 387 ARG 0.003 0.000 ARG P 390 *********************** 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 60 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.601 Fit side-chains REVERT: P 67 LYS cc_start: 0.7801 (pttp) cc_final: 0.7442 (ptmt) REVERT: P 97 PRO cc_start: 0.7481 (Cg_exo) cc_final: 0.7278 (Cg_endo) REVERT: P 276 LYS cc_start: 0.8127 (ttpp) cc_final: 0.7565 (tttm) REVERT: P 328 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5652 (mtm110) REVERT: P 382 ARG cc_start: 0.6907 (ttp80) cc_final: 0.6471 (ttt-90) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 1.3480 time to fit residues: 81.0990 Evaluate side-chains 50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 430 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7501 Z= 0.211 Angle : 0.536 6.013 10829 Z= 0.285 Chirality : 0.035 0.161 1323 Planarity : 0.004 0.035 799 Dihedral : 23.158 163.048 2683 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.28 % Allowed : 19.41 % 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: 1.12 (0.39), residues: 464 helix: 2.02 (0.34), residues: 218 sheet: -0.17 (0.74), residues: 58 loop : -0.46 (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 0.013 0.001 TYR P 387 ARG 0.003 0.000 ARG P 299 *********************** 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 62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.621 Fit side-chains REVERT: P 67 LYS cc_start: 0.7793 (pttp) cc_final: 0.7427 (ptmt) REVERT: P 97 PRO cc_start: 0.7458 (Cg_exo) cc_final: 0.7256 (Cg_endo) REVERT: P 276 LYS cc_start: 0.7999 (ttpp) cc_final: 0.7504 (tttm) REVERT: P 328 ARG cc_start: 0.6416 (OUTLIER) cc_final: 0.5685 (mtm110) REVERT: P 382 ARG cc_start: 0.6894 (ttp80) cc_final: 0.6461 (ttt-90) outliers start: 10 outliers final: 5 residues processed: 60 average time/residue: 1.4221 time to fit residues: 90.0594 Evaluate side-chains 50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 430 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7501 Z= 0.251 Angle : 0.553 5.563 10829 Z= 0.293 Chirality : 0.036 0.160 1323 Planarity : 0.004 0.036 799 Dihedral : 23.147 160.716 2683 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.97 % Allowed : 20.32 % 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: 0.98 (0.39), residues: 464 helix: 1.92 (0.34), residues: 218 sheet: -0.20 (0.73), residues: 58 loop : -0.56 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 68 HIS 0.002 0.001 HIS P 215 PHE 0.013 0.002 PHE P 444 TYR 0.016 0.001 TYR P 387 ARG 0.004 0.000 ARG P 299 *********************** 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: 13 poor density : 50 time to evaluate : 0.557 Fit side-chains REVERT: P 67 LYS cc_start: 0.7822 (pttp) cc_final: 0.7461 (ptmt) REVERT: P 276 LYS cc_start: 0.8007 (ttpp) cc_final: 0.7414 (mttt) REVERT: P 278 GLU cc_start: 0.6144 (mp0) cc_final: 0.5824 (mp0) REVERT: P 328 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5488 (mtm110) REVERT: P 382 ARG cc_start: 0.6882 (ttp80) cc_final: 0.6388 (ttt-90) outliers start: 13 outliers final: 6 residues processed: 61 average time/residue: 1.2098 time to fit residues: 78.1405 Evaluate side-chains 55 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 430 VAL Chi-restraints excluded: chain P residue 454 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 39 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7501 Z= 0.239 Angle : 0.548 5.973 10829 Z= 0.290 Chirality : 0.036 0.212 1323 Planarity : 0.005 0.079 799 Dihedral : 23.138 161.170 2683 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.28 % Allowed : 21.23 % Favored : 76.48 % 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: 0.95 (0.39), residues: 464 helix: 1.92 (0.34), residues: 218 sheet: -0.18 (0.73), residues: 58 loop : -0.62 (0.44), 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 215 PHE 0.013 0.002 PHE P 156 TYR 0.015 0.001 TYR P 387 ARG 0.007 0.001 ARG P 390 *********************** 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 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.524 Fit side-chains REVERT: P 61 LYS cc_start: 0.7965 (mmmt) cc_final: 0.7213 (ttmm) REVERT: P 67 LYS cc_start: 0.7791 (pttp) cc_final: 0.7400 (ptmt) REVERT: P 276 LYS cc_start: 0.7962 (ttpp) cc_final: 0.7421 (mttt) REVERT: P 278 GLU cc_start: 0.6296 (mp0) cc_final: 0.6035 (mp0) REVERT: P 328 ARG cc_start: 0.6306 (OUTLIER) cc_final: 0.5608 (mtm110) REVERT: P 382 ARG cc_start: 0.6871 (ttp80) cc_final: 0.6445 (ttt-90) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 1.3088 time to fit residues: 85.7767 Evaluate side-chains 57 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 430 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.0270 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7501 Z= 0.236 Angle : 0.551 5.808 10829 Z= 0.291 Chirality : 0.035 0.168 1323 Planarity : 0.004 0.039 799 Dihedral : 23.131 161.351 2683 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.51 % Allowed : 21.69 % Favored : 75.80 % 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: 0.93 (0.39), residues: 464 helix: 1.89 (0.34), residues: 218 sheet: -0.16 (0.73), residues: 58 loop : -0.63 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 68 HIS 0.002 0.001 HIS P 215 PHE 0.012 0.002 PHE P 156 TYR 0.015 0.001 TYR P 387 ARG 0.003 0.000 ARG P 299 *********************** 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: 11 poor density : 50 time to evaluate : 0.572 Fit side-chains REVERT: P 61 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7196 (ttmm) REVERT: P 67 LYS cc_start: 0.7795 (pttp) cc_final: 0.7410 (ptmt) REVERT: P 276 LYS cc_start: 0.7947 (ttpp) cc_final: 0.7366 (mttm) REVERT: P 278 GLU cc_start: 0.6376 (mp0) cc_final: 0.6151 (mp0) REVERT: P 328 ARG cc_start: 0.6349 (OUTLIER) cc_final: 0.5431 (mtm110) REVERT: P 346 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: P 382 ARG cc_start: 0.6887 (ttp80) cc_final: 0.6453 (ttt-90) REVERT: P 496 MET cc_start: 0.7472 (ttp) cc_final: 0.7007 (ptt) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 1.3421 time to fit residues: 84.3201 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 : 0.571 ------------------------------------------------------------------------------- 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 346 GLU 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 48 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 P 404 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7501 Z= 0.353 Angle : 0.619 7.014 10829 Z= 0.326 Chirality : 0.039 0.170 1323 Planarity : 0.004 0.037 799 Dihedral : 23.297 154.197 2683 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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 (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: 0.54 (0.38), residues: 464 helix: 1.54 (0.34), residues: 218 sheet: -0.39 (0.72), residues: 56 loop : -0.78 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 68 HIS 0.004 0.001 HIS P 215 PHE 0.015 0.003 PHE P 264 TYR 0.020 0.002 TYR P 387 ARG 0.004 0.001 ARG P 299 *********************** 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 61 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.504 Fit side-chains REVERT: P 61 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7297 (ttmm) REVERT: P 67 LYS cc_start: 0.7798 (pttp) cc_final: 0.7431 (ptmt) REVERT: P 276 LYS cc_start: 0.7921 (ttpp) cc_final: 0.7299 (mttt) REVERT: P 278 GLU cc_start: 0.6481 (mp0) cc_final: 0.6194 (mp0) REVERT: P 328 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5631 (mtm110) REVERT: P 346 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: P 382 ARG cc_start: 0.6819 (ttp80) cc_final: 0.6407 (ttt-90) REVERT: P 496 MET cc_start: 0.7558 (ttp) cc_final: 0.7122 (ptt) outliers start: 13 outliers final: 8 residues processed: 57 average time/residue: 1.2226 time to fit residues: 74.0046 Evaluate side-chains 57 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 430 VAL Chi-restraints excluded: chain P residue 454 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7501 Z= 0.236 Angle : 0.562 7.222 10829 Z= 0.296 Chirality : 0.036 0.170 1323 Planarity : 0.004 0.035 799 Dihedral : 23.201 158.221 2683 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.51 % Allowed : 22.37 % 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 (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: 0.74 (0.39), residues: 464 helix: 1.74 (0.34), residues: 218 sheet: -0.27 (0.73), residues: 56 loop : -0.73 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 PHE 0.013 0.002 PHE P 156 TYR 0.015 0.001 TYR P 387 ARG 0.003 0.000 ARG P 299 ********************** 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 63 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.506 Fit side-chains REVERT: P 61 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7254 (ttmm) REVERT: P 67 LYS cc_start: 0.7785 (pttp) cc_final: 0.7409 (ptmt) REVERT: P 276 LYS cc_start: 0.7798 (ttpp) cc_final: 0.7203 (mttm) REVERT: P 278 GLU cc_start: 0.6562 (mp0) cc_final: 0.6305 (mp0) REVERT: P 328 ARG cc_start: 0.6088 (OUTLIER) cc_final: 0.5334 (mtm110) REVERT: P 382 ARG cc_start: 0.6815 (ttp80) cc_final: 0.6400 (ttt-90) REVERT: P 421 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5484 (mptm) REVERT: P 496 MET cc_start: 0.7498 (ttp) cc_final: 0.7088 (ptt) outliers start: 11 outliers final: 6 residues processed: 59 average time/residue: 1.2177 time to fit residues: 76.2485 Evaluate side-chains 59 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 54 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 1 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 = 0.4119 r_free = 0.4119 target = 0.175562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130202 restraints weight = 8192.696| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.20 r_work: 0.3378 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7501 Z= 0.210 Angle : 0.553 6.917 10829 Z= 0.292 Chirality : 0.035 0.168 1323 Planarity : 0.004 0.035 799 Dihedral : 23.179 159.802 2683 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.28 % Allowed : 22.83 % Favored : 74.89 % 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: 0.85 (0.39), residues: 464 helix: 1.87 (0.34), residues: 218 sheet: -0.21 (0.73), residues: 56 loop : -0.72 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP P 516 HIS 0.002 0.001 HIS P 215 PHE 0.013 0.002 PHE P 156 TYR 0.013 0.001 TYR P 387 ARG 0.003 0.000 ARG P 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2313.56 seconds wall clock time: 43 minutes 13.19 seconds (2593.19 seconds total)