Starting phenix.real_space_refine on Thu Jul 2 06:58:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0i_45085/07_2026/9c0i_45085.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0i_45085/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9c0i_45085/07_2026/9c0i_45085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0i_45085/07_2026/9c0i_45085.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0i_45085/07_2026/9c0i_45085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0i_45085/07_2026/9c0i_45085.cif" } 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-dev-6108/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, 0 Ad-hoc single atom residues: {' K': 1} Chain breaks: 1 Time building chain proxies: 1.27, per 1000 atoms: 0.17 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: 0.59 Conformation dependent library (CDL) restraints added in 310.9 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: 1.27 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: 1.69 Time building geometry restraints manager: 0.81 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 - 2.63: 11679 2.63 - 5.26: 319 5.26 - 7.89: 40 7.89 - 10.51: 4 10.51 - 13.14: 2 Bond angle restraints: 12044 Sorted by residual: 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=" C3' A R 24 " pdb=" O3' A R 24 " pdb=" P U R 25 " ideal model delta sigma weight residual 120.20 107.06 13.14 1.50e+00 4.44e-01 7.68e+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=" 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 angle pdb=" O2 U R 219 " pdb=" C2 U R 219 " pdb=" N3 U R 219 " ideal model delta sigma weight residual 122.20 117.27 4.93 7.00e-01 2.04e+00 4.95e+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: 1356 0.093 - 0.185: 116 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.120 Find NCS groups from input model: 0.020 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- 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= 0.425 Angle : 1.034 13.142 12044 Z= 0.936 Chirality : 0.058 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 0.00569 / 0.43 ( 8235) covalent geometry : angle 1.03415 / 0.94 (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 : 0.185 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: 0.7193 time to fit residues: 32.4534 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 : 0.156 ------------------------------------------------------------------------------- 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: 20.0000 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 = 0.3884 r_free = 0.3884 target = 0.167529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.105483 restraints weight = 8307.169| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.32 r_work: 0.2725 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8235 Z= 0.162 Angle : 0.545 6.206 12044 Z= 0.332 Chirality : 0.040 0.218 1490 Planarity : 0.005 0.046 803 Dihedral : 22.219 175.873 3495 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.30 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: 0.86 (0.39), residues: 423 helix: 0.94 (0.35), residues: 211 sheet: 1.71 (0.69), residues: 53 loop : -0.22 (0.47), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 336 TYR 0.011 0.002 TYR A 14 PHE 0.012 0.002 PHE A 328 TRP 0.005 0.002 TRP A 157 HIS 0.003 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 8235) covalent geometry : angle 0.54454 / 0.33 (12044) hydrogen bonds : bond 0.06848 / 4.75 ( 357) hydrogen bonds : angle 3.67143 / 2.55 ( 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 : 0.120 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 0.6842 time to fit residues: 25.7884 Evaluate side-chains 33 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.168546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107260 restraints weight = 8313.014| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.60 r_work: 0.2702 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8235 Z= 0.127 Angle : 0.460 6.004 12044 Z= 0.283 Chirality : 0.036 0.225 1490 Planarity : 0.005 0.043 803 Dihedral : 22.161 177.338 3492 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.14 % Allowed : 10.46 % Favored : 87.40 % 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: 1.43 (0.41), residues: 423 helix: 1.55 (0.37), residues: 212 sheet: 1.41 (0.69), residues: 55 loop : 0.04 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 12 TYR 0.013 0.002 TYR A 14 PHE 0.014 0.002 PHE A 328 TRP 0.002 0.001 TRP A 157 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 8235) covalent geometry : angle 0.46046 / 0.28 (12044) hydrogen bonds : bond 0.05790 / 4.03 ( 357) hydrogen bonds : angle 3.32457 / 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 41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.237 Fit side-chains REVERT: A 68 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7544 (tttm) outliers start: 8 outliers final: 5 residues processed: 38 average time/residue: 0.7760 time to fit residues: 30.8461 Evaluate side-chains 35 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 127 THR 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: 6.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 47 optimal weight: 50.0000 chunk 50 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 0.0270 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.169388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.108614 restraints weight = 8484.215| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.40 r_work: 0.2737 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8235 Z= 0.104 Angle : 0.421 6.252 12044 Z= 0.259 Chirality : 0.034 0.218 1490 Planarity : 0.004 0.038 803 Dihedral : 22.094 178.442 3491 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.41 % Allowed : 11.53 % Favored : 86.06 % 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: 1.69 (0.41), residues: 423 helix: 1.80 (0.36), residues: 212 sheet: 1.47 (0.69), residues: 55 loop : 0.13 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 390 TYR 0.010 0.001 TYR A 86 PHE 0.009 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 0.00204 / 0.10 ( 8235) covalent geometry : angle 0.42146 / 0.26 (12044) hydrogen bonds : bond 0.05273 / 3.69 ( 357) hydrogen bonds : angle 3.22761 / 2.24 ( 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 44 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.204 Fit side-chains REVERT: A 68 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7206 (mttt) outliers start: 9 outliers final: 2 residues processed: 39 average time/residue: 0.7110 time to fit residues: 29.1279 Evaluate side-chains 34 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.167431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.105816 restraints weight = 8402.358| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.38 r_work: 0.2702 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8235 Z= 0.150 Angle : 0.466 5.918 12044 Z= 0.280 Chirality : 0.036 0.222 1490 Planarity : 0.005 0.045 803 Dihedral : 22.074 179.276 3491 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.41 % Allowed : 13.14 % Favored : 84.45 % 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: 1.74 (0.37), residues: 211 sheet: 1.33 (0.68), residues: 55 loop : -0.09 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.012 0.002 TYR A 86 PHE 0.012 0.002 PHE A 328 TRP 0.005 0.001 TRP A 157 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 8235) covalent geometry : angle 0.46590 / 0.28 (12044) hydrogen bonds : bond 0.05896 / 4.10 ( 357) hydrogen bonds : angle 3.28975 / 2.29 ( 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 43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.187 Fit side-chains REVERT: A 68 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7582 (tttm) outliers start: 9 outliers final: 5 residues processed: 39 average time/residue: 0.7381 time to fit residues: 30.1131 Evaluate side-chains 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 130 GLU Chi-restraints excluded: chain A residue 191 ILE 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: 1.9990 chunk 52 optimal weight: 50.0000 chunk 54 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.168753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106936 restraints weight = 8450.680| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.37 r_work: 0.2727 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8235 Z= 0.100 Angle : 0.420 5.744 12044 Z= 0.259 Chirality : 0.034 0.222 1490 Planarity : 0.004 0.044 803 Dihedral : 22.059 178.788 3491 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.14 % Allowed : 13.67 % 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: 1.74 (0.41), residues: 423 helix: 1.95 (0.37), residues: 211 sheet: 1.32 (0.68), residues: 55 loop : 0.06 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 12 TYR 0.011 0.001 TYR A 14 PHE 0.010 0.001 PHE A 328 TRP 0.006 0.001 TRP A 157 HIS 0.002 0.000 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 ( 8235) covalent geometry : angle 0.42034 / 0.26 (12044) hydrogen bonds : bond 0.05286 / 3.69 ( 357) hydrogen bonds : angle 3.22420 / 2.23 ( 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: 8 poor density : 35 time to evaluate : 0.197 Fit side-chains REVERT: A 68 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7463 (tttm) REVERT: A 250 ASP cc_start: 0.8605 (m-30) cc_final: 0.8333 (m-30) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 0.6374 time to fit residues: 26.1230 Evaluate side-chains 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 131 MET Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 60 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 45 optimal weight: 40.0000 chunk 44 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.166471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.104081 restraints weight = 8397.646| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.43 r_work: 0.2678 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8235 Z= 0.195 Angle : 0.508 6.454 12044 Z= 0.299 Chirality : 0.038 0.221 1490 Planarity : 0.005 0.046 803 Dihedral : 22.005 175.633 3491 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.41 % Allowed : 14.48 % 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: 1.37 (0.41), residues: 423 helix: 1.64 (0.36), residues: 211 sheet: 1.15 (0.66), residues: 55 loop : -0.12 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 204 TYR 0.014 0.002 TYR A 245 PHE 0.013 0.002 PHE A 328 TRP 0.007 0.002 TRP A 157 HIS 0.003 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 8235) covalent geometry : angle 0.50796 / 0.30 (12044) hydrogen bonds : bond 0.06451 / 4.48 ( 357) hydrogen bonds : angle 3.35666 / 2.33 ( 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 44 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.209 Fit side-chains REVERT: A 68 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7595 (tttm) outliers start: 9 outliers final: 4 residues processed: 40 average time/residue: 0.6199 time to fit residues: 26.0995 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 : 0.198 ------------------------------------------------------------------------------- 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 191 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 50.0000 chunk 34 optimal weight: 0.9990 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: 1.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.167171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.105272 restraints weight = 8458.466| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.38 r_work: 0.2699 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8235 Z= 0.148 Angle : 0.463 5.255 12044 Z= 0.279 Chirality : 0.036 0.222 1490 Planarity : 0.005 0.043 803 Dihedral : 21.987 174.602 3491 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.34 % Allowed : 15.55 % 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: 1.45 (0.41), residues: 423 helix: 1.73 (0.37), residues: 211 sheet: 1.16 (0.66), residues: 55 loop : -0.08 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 204 TYR 0.012 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 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 ( 8235) covalent geometry : angle 0.46323 / 0.28 (12044) hydrogen bonds : bond 0.05944 / 4.13 ( 357) hydrogen bonds : angle 3.30764 / 2.30 ( 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 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.140 Fit side-chains REVERT: A 68 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7510 (tttm) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.5635 time to fit residues: 22.5716 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 : 0.120 ------------------------------------------------------------------------------- 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 191 ILE 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: 40.0000 chunk 48 optimal weight: 30.0000 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.167097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.105177 restraints weight = 8386.994| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.38 r_work: 0.2700 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8235 Z= 0.154 Angle : 0.462 5.662 12044 Z= 0.277 Chirality : 0.036 0.223 1490 Planarity : 0.005 0.045 803 Dihedral : 21.804 167.692 3491 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.34 % Allowed : 15.82 % Favored : 82.84 % 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: 1.44 (0.41), residues: 423 helix: 1.72 (0.36), residues: 211 sheet: 1.17 (0.66), residues: 55 loop : -0.11 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 204 TYR 0.011 0.002 TYR A 86 PHE 0.011 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 0.00338 / 0.15 ( 8235) covalent geometry : angle 0.46195 / 0.28 (12044) hydrogen bonds : bond 0.05940 / 4.11 ( 357) hydrogen bonds : angle 3.29837 / 2.29 ( 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 41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.118 Fit side-chains REVERT: A 68 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7572 (tttm) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 0.6620 time to fit residues: 27.1938 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 : 0.187 ------------------------------------------------------------------------------- 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 191 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 10.0000 chunk 32 optimal weight: 0.4980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 40.0000 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.167806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.106264 restraints weight = 8363.443| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.32 r_work: 0.2710 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8235 Z= 0.110 Angle : 0.430 4.700 12044 Z= 0.263 Chirality : 0.034 0.219 1490 Planarity : 0.004 0.041 803 Dihedral : 21.788 167.449 3491 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.34 % Allowed : 15.82 % Favored : 82.84 % 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: 1.62 (0.41), residues: 423 helix: 1.90 (0.36), residues: 211 sheet: 1.22 (0.66), residues: 55 loop : -0.06 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 390 TYR 0.011 0.001 TYR A 86 PHE 0.008 0.001 PHE A 44 TRP 0.005 0.001 TRP A 157 HIS 0.008 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 8235) covalent geometry : angle 0.42998 / 0.26 (12044) hydrogen bonds : bond 0.05561 / 3.86 ( 357) hydrogen bonds : angle 3.27189 / 2.27 ( 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 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.203 Fit side-chains REVERT: A 68 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7518 (tttm) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.6652 time to fit residues: 26.6873 Evaluate side-chains 41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 191 ILE 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: 0.3980 chunk 30 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- 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 = 0.3870 r_free = 0.3870 target = 0.166411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.104735 restraints weight = 8346.444| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.57 r_work: 0.2663 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8235 Z= 0.185 Angle : 0.496 6.148 12044 Z= 0.293 Chirality : 0.037 0.221 1490 Planarity : 0.005 0.045 803 Dihedral : 21.747 163.553 3491 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.34 % Allowed : 15.82 % Favored : 82.84 % 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: 1.34 (0.41), residues: 423 helix: 1.68 (0.36), residues: 211 sheet: 1.19 (0.65), residues: 55 loop : -0.25 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 390 TYR 0.013 0.002 TYR A 245 PHE 0.013 0.002 PHE A 328 TRP 0.006 0.002 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 ( 8235) covalent geometry : angle 0.49615 / 0.29 (12044) hydrogen bonds : bond 0.06378 / 4.42 ( 357) hydrogen bonds : angle 3.35677 / 2.34 ( 862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2289.72 seconds wall clock time: 39 minutes 45.35 seconds (2385.35 seconds total)