Starting phenix.real_space_refine on Tue Aug 4 23:14:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0i_45085/08_2026/9c0i_45085.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0i_45085/08_2026/9c0i_45085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c0i_45085/08_2026/9c0i_45085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0i_45085/08_2026/9c0i_45085.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c0i_45085/08_2026/9c0i_45085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0i_45085/08_2026/9c0i_45085.map" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 K 1 8.98 5 P 197 5.49 5 Mg 1 5.21 5 S 13 5.16 5 C 4108 2.51 5 N 1355 2.21 5 O 2001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7676 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3481 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 13, 'TRANS': 411} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} Chain: "R" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 4089 Classifications: {'RNA': 192} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 12, 'rna3p_pur': 81, 'rna3p_pyr': 81} Link IDs: {'rna2p': 30, 'rna3p': 161} Chain breaks: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.88, per 1000 atoms: 0.24 Number of scatterers: 7676 At special positions: 0 Unit cell: (130.832, 125.528, 83.096, 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) K 1 19.00 S 13 16.00 P 197 15.00 Mg 1 11.99 O 2001 8.00 N 1355 7.00 C 4108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 249.3 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 814 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 4 sheets defined 54.4% alpha, 17.6% beta 71 base pairs and 116 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 removed outlier: 3.521A pdb=" N ASP A 5 " --> pdb=" O ASN A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.598A pdb=" N SER A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 76 through 101 removed outlier: 3.986A pdb=" N GLY A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 97 " --> pdb=" O HIS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 149 through 162 Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 185 through 193 Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 237 through 246 removed outlier: 3.744A pdb=" N MET A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 260 removed outlier: 3.746A pdb=" N ARG A 260 " --> pdb=" O TYR A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 282 through 291 Processing helix chain 'A' and resid 300 through 303 removed outlier: 3.855A pdb=" N THR A 303 " --> pdb=" O THR A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 303' Processing helix chain 'A' and resid 336 through 368 removed outlier: 3.765A pdb=" N LEU A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 364 " --> pdb=" O SER A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 385 Processing helix chain 'A' and resid 391 through 404 removed outlier: 3.522A pdb=" N TYR A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 3.850A pdb=" N LYS A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 74 removed outlier: 6.259A pdb=" N PHE A 44 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 267 removed outlier: 4.837A pdb=" N GLU A 297 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 263 through 267 removed outlier: 3.569A pdb=" N CYS A 134 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 323 197 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 172 hydrogen bonds 304 hydrogen bond angles 0 basepair planarities 71 basepair parallelities 116 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 853 1.31 - 1.44: 3375 1.44 - 1.56: 3600 1.56 - 1.68: 385 1.68 - 1.81: 22 Bond restraints: 8235 Sorted by residual: bond pdb=" CA SER A 22 " pdb=" CB SER A 22 " ideal model delta sigma weight residual 1.532 1.465 0.067 1.59e-02 3.96e+03 1.77e+01 bond pdb=" CA ALA A 26 " pdb=" CB ALA A 26 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.55e-02 4.16e+03 1.51e+01 bond pdb=" C PRO A 20 " pdb=" O PRO A 20 " ideal model delta sigma weight residual 1.233 1.186 0.047 1.24e-02 6.50e+03 1.45e+01 bond pdb=" N9 A R 123 " pdb=" C4 A R 123 " ideal model delta sigma weight residual 1.374 1.397 -0.023 6.00e-03 2.78e+04 1.44e+01 bond pdb=" C PRO A 199 " pdb=" O PRO A 199 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.30e-02 5.92e+03 1.40e+01 ... (remaining 8230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 11408 2.53 - 5.06: 588 5.06 - 7.59: 41 7.59 - 10.11: 4 10.11 - 12.64: 3 Bond angle restraints: 12044 Sorted by residual: angle pdb=" C3' A R 24 " pdb=" O3' A R 24 " pdb=" P U R 25 " ideal model delta sigma weight residual 119.70 107.06 12.64 1.20e+00 6.94e-01 1.11e+02 angle pdb=" C1' C R 185 " pdb=" N1 C R 185 " pdb=" C2 C R 185 " ideal model delta sigma weight residual 118.80 128.89 -10.09 1.10e+00 8.26e-01 8.42e+01 angle pdb=" N1 C R 185 " pdb=" C2 C R 185 " pdb=" O2 C R 185 " ideal model delta sigma weight residual 118.90 123.35 -4.45 6.00e-01 2.78e+00 5.50e+01 angle pdb=" C3' U R 23 " pdb=" O3' U R 23 " pdb=" P A R 24 " ideal model delta sigma weight residual 119.70 110.80 8.90 1.20e+00 6.94e-01 5.50e+01 angle pdb=" N1 C R 185 " pdb=" C6 C R 185 " pdb=" C5 C R 185 " ideal model delta sigma weight residual 121.00 124.60 -3.60 5.00e-01 4.00e+00 5.19e+01 ... (remaining 12039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.22: 4669 33.22 - 66.44: 471 66.44 - 99.66: 49 99.66 - 132.87: 2 132.87 - 166.09: 1 Dihedral angle restraints: 5192 sinusoidal: 3929 harmonic: 1263 Sorted by residual: dihedral pdb=" O4' A R 123 " pdb=" C1' A R 123 " pdb=" N9 A R 123 " pdb=" C4 A R 123 " ideal model delta sinusoidal sigma weight residual 68.00 151.57 -83.57 1 1.70e+01 3.46e-03 2.95e+01 dihedral pdb=" O4' U R 205 " pdb=" C1' U R 205 " pdb=" N1 U R 205 " pdb=" C2 U R 205 " ideal model delta sinusoidal sigma weight residual -160.00 -88.78 -71.22 1 1.50e+01 4.44e-03 2.89e+01 dihedral pdb=" CA THR A 282 " pdb=" C THR A 282 " pdb=" N LEU A 283 " pdb=" CA LEU A 283 " ideal model delta harmonic sigma weight residual -180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 5189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1174 0.093 - 0.185: 298 0.185 - 0.278: 10 0.278 - 0.370: 5 0.370 - 0.463: 3 Chirality restraints: 1490 Sorted by residual: chirality pdb=" P DG P 1 " pdb=" OP1 DG P 1 " pdb=" OP2 DG P 1 " pdb=" O5' DG P 1 " both_signs ideal model delta sigma weight residual True 2.34 2.80 -0.46 2.00e-01 2.50e+01 5.35e+00 chirality pdb=" P DT P 5 " pdb=" OP1 DT P 5 " pdb=" OP2 DT P 5 " pdb=" O5' DT P 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.73 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" P DA P 2 " pdb=" OP1 DA P 2 " pdb=" OP2 DA P 2 " pdb=" O5' DA P 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.71 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1487 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G R 33 " -0.030 2.00e-02 2.50e+03 1.41e-02 5.97e+00 pdb=" N9 G R 33 " 0.035 2.00e-02 2.50e+03 pdb=" C8 G R 33 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G R 33 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G R 33 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G R 33 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G R 33 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G R 33 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G R 33 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G R 33 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G R 33 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G R 33 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 404 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ASN A 404 " 0.040 2.00e-02 2.50e+03 pdb=" O ASN A 404 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 405 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 383 " 0.186 9.50e-02 1.11e+02 8.38e-02 5.06e+00 pdb=" NE ARG A 383 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 383 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 383 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 383 " 0.002 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.70: 412 2.70 - 3.31: 6858 3.31 - 3.92: 17454 3.92 - 4.53: 22336 4.53 - 5.14: 29347 Nonbonded interactions: 76407 Sorted by model distance: nonbonded pdb=" OD2 ASP A 140 " pdb="MG MG A 501 " model vdw 2.090 2.170 nonbonded pdb=" O LYS A 55 " pdb=" OG SER A 64 " model vdw 2.334 3.040 nonbonded pdb=" OG1 THR A 208 " pdb=" OD2 ASP A 211 " model vdw 2.393 3.040 nonbonded pdb=" OG SER A 195 " pdb=" OP2 C R 218 " model vdw 2.404 3.040 nonbonded pdb=" NH2 ARG A 217 " pdb=" O6 G R 22 " model vdw 2.407 3.120 ... (remaining 76402 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: 0.900 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.330 Find NCS groups from input model: 0.030 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: 0.000 Load rotamer database and sin/cos tables:9.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 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 : 0.006 0.069 8235 Z= 0.439 Angle : 1.159 12.642 12044 Z= 1.051 Chirality : 0.074 0.463 1490 Planarity : 0.008 0.084 803 Dihedral : 21.515 166.093 4378 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.80 % Allowed : 8.31 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.37), residues: 423 helix: -0.44 (0.31), residues: 205 sheet: 1.13 (0.68), residues: 57 loop : -0.29 (0.48), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG A 383 TYR 0.023 0.003 TYR A 83 PHE 0.021 0.004 PHE A 328 TRP 0.006 0.001 TRP A 8 HIS 0.008 0.002 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.44 ( 8235) covalent geometry : angle 1.15860 / 1.05 (12044) hydrogen bonds : bond 0.13365 / 8.76 ( 357) hydrogen bonds : angle 5.29712 / 3.69 ( 862) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.201 Fit side-chains REVERT: A 390 ARG cc_start: 0.8246 (mtm180) cc_final: 0.8028 (mtp180) outliers start: 3 outliers final: 3 residues processed: 43 average time/residue: 0.7750 time to fit residues: 35.0015 Evaluate side-chains 35 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 294 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.167702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.105484 restraints weight = 8289.146| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.30 r_work: 0.2724 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8995 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8235 Z= 0.161 Angle : 0.570 6.700 12044 Z= 0.339 Chirality : 0.041 0.257 1490 Planarity : 0.005 0.046 803 Dihedral : 22.172 171.821 3495 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.34 % Allowed : 9.65 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.39), residues: 423 helix: 0.96 (0.35), residues: 211 sheet: 1.72 (0.69), residues: 53 loop : -0.23 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 187 TYR 0.011 0.002 TYR A 245 PHE 0.012 0.002 PHE A 328 TRP 0.003 0.001 TRP A 157 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 ( 8235) covalent geometry : angle 0.57037 / 0.34 (12044) hydrogen bonds : bond 0.07106 / 4.92 ( 357) hydrogen bonds : angle 3.66201 / 2.54 ( 862) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.194 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.6991 time to fit residues: 26.4431 Evaluate side-chains 32 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 130 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.0980 chunk 30 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.169882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.108991 restraints weight = 8251.475| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.34 r_work: 0.2733 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8235 Z= 0.118 Angle : 0.461 6.456 12044 Z= 0.278 Chirality : 0.035 0.261 1490 Planarity : 0.004 0.041 803 Dihedral : 22.091 170.020 3492 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.88 % Allowed : 10.19 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.41), residues: 423 helix: 1.59 (0.36), residues: 212 sheet: 1.72 (0.68), residues: 53 loop : 0.08 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 290 TYR 0.011 0.001 TYR A 86 PHE 0.012 0.001 PHE A 328 TRP 0.002 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 ( 8235) covalent geometry : angle 0.46140 / 0.28 (12044) hydrogen bonds : bond 0.05842 / 4.05 ( 357) hydrogen bonds : angle 3.32064 / 2.30 ( 862) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.195 Fit side-chains REVERT: A 68 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7512 (tttm) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.7538 time to fit residues: 30.7339 Evaluate side-chains 36 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 292 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 50.0000 chunk 50 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 overall best weight: 1.8684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.167846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.107743 restraints weight = 8414.777| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.36 r_work: 0.2708 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8235 Z= 0.128 Angle : 0.471 6.617 12044 Z= 0.276 Chirality : 0.036 0.255 1490 Planarity : 0.005 0.044 803 Dihedral : 22.020 171.497 3491 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.95 % Allowed : 10.46 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.41), residues: 423 helix: 1.75 (0.36), residues: 211 sheet: 1.15 (0.68), residues: 57 loop : -0.02 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 204 TYR 0.012 0.002 TYR A 14 PHE 0.011 0.002 PHE A 328 TRP 0.005 0.001 TRP A 157 HIS 0.004 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 8235) covalent geometry : angle 0.47100 / 0.28 (12044) hydrogen bonds : bond 0.05910 / 4.07 ( 357) hydrogen bonds : angle 3.29108 / 2.29 ( 862) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.142 Fit side-chains REVERT: A 68 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7566 (tttm) outliers start: 11 outliers final: 5 residues processed: 42 average time/residue: 0.6874 time to fit residues: 30.2620 Evaluate side-chains 38 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 191 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 40.0000 chunk 14 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.166259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.104237 restraints weight = 8381.857| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.29 r_work: 0.2686 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9011 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8235 Z= 0.189 Angle : 0.546 6.686 12044 Z= 0.311 Chirality : 0.039 0.263 1490 Planarity : 0.006 0.048 803 Dihedral : 22.007 174.076 3491 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.41 % Allowed : 12.87 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.41), residues: 423 helix: 1.52 (0.36), residues: 211 sheet: 0.90 (0.65), residues: 57 loop : -0.23 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 204 TYR 0.014 0.002 TYR A 86 PHE 0.015 0.002 PHE A 328 TRP 0.006 0.002 TRP A 157 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 8235) covalent geometry : angle 0.54647 / 0.31 (12044) hydrogen bonds : bond 0.06860 / 4.76 ( 357) hydrogen bonds : angle 3.41731 / 2.38 ( 862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.207 Fit side-chains REVERT: A 68 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7611 (tttm) outliers start: 9 outliers final: 5 residues processed: 38 average time/residue: 0.7558 time to fit residues: 30.1193 Evaluate side-chains 39 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 292 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 9 optimal weight: 3.9990 chunk 52 optimal weight: 50.0000 chunk 54 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.168716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.107230 restraints weight = 8458.223| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.36 r_work: 0.2726 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8235 Z= 0.108 Angle : 0.434 6.126 12044 Z= 0.259 Chirality : 0.033 0.253 1490 Planarity : 0.004 0.041 803 Dihedral : 21.841 175.633 3491 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.41 % Allowed : 13.40 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.41), residues: 423 helix: 1.82 (0.36), residues: 212 sheet: 1.21 (0.66), residues: 55 loop : 0.00 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 346 TYR 0.010 0.001 TYR A 86 PHE 0.010 0.001 PHE A 44 TRP 0.006 0.001 TRP A 157 HIS 0.002 0.000 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 ( 8235) covalent geometry : angle 0.43447 / 0.26 (12044) hydrogen bonds : bond 0.05401 / 3.72 ( 357) hydrogen bonds : angle 3.27034 / 2.27 ( 862) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.196 Fit side-chains REVERT: A 68 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7215 (mtpt) outliers start: 9 outliers final: 4 residues processed: 39 average time/residue: 0.7782 time to fit residues: 31.8523 Evaluate side-chains 39 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 292 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 45 optimal weight: 50.0000 chunk 44 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 48 optimal weight: 30.0000 chunk 7 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.165497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.103423 restraints weight = 8381.894| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.28 r_work: 0.2665 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8235 Z= 0.238 Angle : 0.584 7.617 12044 Z= 0.324 Chirality : 0.042 0.264 1490 Planarity : 0.006 0.048 803 Dihedral : 21.863 178.482 3491 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.34 % Allowed : 15.01 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.41), residues: 423 helix: 1.50 (0.37), residues: 211 sheet: 0.90 (0.65), residues: 57 loop : -0.35 (0.48), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 336 TYR 0.015 0.003 TYR A 245 PHE 0.015 0.002 PHE A 328 TRP 0.007 0.002 TRP A 157 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 ( 8235) covalent geometry : angle 0.58374 / 0.32 (12044) hydrogen bonds : bond 0.07244 / 4.98 ( 357) hydrogen bonds : angle 3.44439 / 2.40 ( 862) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.197 Fit side-chains REVERT: A 68 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7573 (tttm) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.7598 time to fit residues: 30.3208 Evaluate side-chains 38 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 127 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 50.0000 chunk 34 optimal weight: 0.7980 chunk 58 optimal weight: 20.0000 chunk 47 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.168793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.107155 restraints weight = 8474.552| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.36 r_work: 0.2727 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8235 Z= 0.099 Angle : 0.421 5.561 12044 Z= 0.255 Chirality : 0.033 0.253 1490 Planarity : 0.004 0.039 803 Dihedral : 21.738 179.035 3491 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.34 % Allowed : 14.75 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.41), residues: 423 helix: 1.89 (0.37), residues: 211 sheet: 1.21 (0.66), residues: 55 loop : -0.10 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 389 TYR 0.009 0.001 TYR A 86 PHE 0.008 0.001 PHE A 44 TRP 0.007 0.001 TRP A 157 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.10 ( 8235) covalent geometry : angle 0.42076 / 0.26 (12044) hydrogen bonds : bond 0.05372 / 3.68 ( 357) hydrogen bonds : angle 3.27261 / 2.27 ( 862) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.201 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 37 average time/residue: 0.7263 time to fit residues: 28.3207 Evaluate side-chains 39 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 282 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 50.0000 chunk 48 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.166812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.104510 restraints weight = 8367.669| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.22 r_work: 0.2702 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8235 Z= 0.166 Angle : 0.492 5.633 12044 Z= 0.282 Chirality : 0.037 0.258 1490 Planarity : 0.005 0.044 803 Dihedral : 21.722 178.499 3491 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.80 % Allowed : 15.82 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.41), residues: 423 helix: 1.75 (0.36), residues: 211 sheet: 0.99 (0.65), residues: 57 loop : -0.20 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 336 TYR 0.013 0.002 TYR A 245 PHE 0.012 0.002 PHE A 328 TRP 0.007 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 ( 8235) covalent geometry : angle 0.49208 / 0.28 (12044) hydrogen bonds : bond 0.06171 / 4.23 ( 357) hydrogen bonds : angle 3.32187 / 2.31 ( 862) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.194 Fit side-chains REVERT: A 68 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7509 (tttm) outliers start: 3 outliers final: 2 residues processed: 35 average time/residue: 0.7201 time to fit residues: 26.5211 Evaluate side-chains 37 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 57 optimal weight: 50.0000 chunk 30 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.105206 restraints weight = 8356.490| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.27 r_work: 0.2713 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8235 Z= 0.120 Angle : 0.450 5.513 12044 Z= 0.266 Chirality : 0.034 0.256 1490 Planarity : 0.004 0.044 803 Dihedral : 21.706 178.245 3491 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.07 % Allowed : 15.55 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.41), residues: 423 helix: 1.83 (0.36), residues: 211 sheet: 1.24 (0.65), residues: 55 loop : -0.19 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.011 0.002 TYR A 86 PHE 0.008 0.001 PHE A 44 TRP 0.005 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 8235) covalent geometry : angle 0.45020 / 0.27 (12044) hydrogen bonds : bond 0.05806 / 3.98 ( 357) hydrogen bonds : angle 3.29656 / 2.29 ( 862) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.202 Fit side-chains REVERT: A 68 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7520 (tttm) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.7446 time to fit residues: 28.9747 Evaluate side-chains 38 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 42 optimal weight: 10.0000 chunk 40 optimal weight: 0.0980 chunk 30 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 51 optimal weight: 30.0000 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 40.0000 chunk 54 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS A 293 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.166774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.104273 restraints weight = 8349.562| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.29 r_work: 0.2687 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8235 Z= 0.158 Angle : 0.499 5.656 12044 Z= 0.285 Chirality : 0.037 0.258 1490 Planarity : 0.005 0.045 803 Dihedral : 21.658 172.725 3491 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.07 % Allowed : 15.82 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.41), residues: 423 helix: 1.72 (0.36), residues: 211 sheet: 0.93 (0.64), residues: 57 loop : -0.28 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 204 TYR 0.013 0.002 TYR A 86 PHE 0.012 0.002 PHE A 328 TRP 0.006 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 8235) covalent geometry : angle 0.49883 / 0.29 (12044) hydrogen bonds : bond 0.06275 / 4.32 ( 357) hydrogen bonds : angle 3.33913 / 2.32 ( 862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.12 seconds wall clock time: 44 minutes 7.36 seconds (2647.36 seconds total)