Starting phenix.real_space_refine on Fri Aug 22 19:47:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c0i_45085/08_2025/9c0i_45085.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c0i_45085/08_2025/9c0i_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_45085/08_2025/9c0i_45085.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c0i_45085/08_2025/9c0i_45085.map" model { file = "/net/cci-nas-00/data/ceres_data/9c0i_45085/08_2025/9c0i_45085.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c0i_45085/08_2025/9c0i_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-2.0-5787/lib/python3.9/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: 1.68, per 1000 atoms: 0.22 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: 0.46 Conformation dependent library (CDL) restraints added in 163.5 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.18 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: 1.41 Time building geometry restraints manager: 0.60 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=" 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 bond pdb=" CA SER A 80 " pdb=" CB SER A 80 " ideal model delta sigma weight residual 1.528 1.475 0.054 1.66e-02 3.63e+03 1.05e+01 ... (remaining 8230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 11683 2.63 - 5.26: 315 5.26 - 7.89: 40 7.89 - 10.51: 4 10.51 - 13.14: 2 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 120.20 107.06 13.14 1.50e+00 4.44e-01 7.68e+01 angle pdb=" C3' U R 23 " pdb=" O3' U R 23 " pdb=" P A R 24 " ideal model delta sigma weight residual 120.20 110.80 9.40 1.50e+00 4.44e-01 3.92e+01 angle pdb=" N ILE A 291 " pdb=" CA ILE A 291 " pdb=" C ILE A 291 " ideal model delta sigma weight residual 112.90 107.57 5.33 9.60e-01 1.09e+00 3.08e+01 angle pdb=" N ILE A 128 " pdb=" CA ILE A 128 " pdb=" C ILE A 128 " ideal model delta sigma weight residual 110.72 105.57 5.15 1.01e+00 9.80e-01 2.60e+01 angle pdb=" O3' A R 210 " pdb=" C3' A R 210 " pdb=" C2' A R 210 " ideal model delta sigma weight residual 113.70 121.17 -7.47 1.50e+00 4.44e-01 2.48e+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 - 0.090: 1355 0.090 - 0.181: 117 0.181 - 0.271: 10 0.271 - 0.362: 5 0.362 - 0.452: 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 2.35 2.80 -0.45 2.00e-01 2.50e+01 5.12e+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 2.35 -2.73 -0.39 2.00e-01 2.50e+01 3.76e+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 2.35 -2.71 -0.37 2.00e-01 2.50e+01 3.34e+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: 0.760 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: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.000 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 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= 0.319 Angle : 1.031 13.142 12044 Z= 0.563 Chirality : 0.057 0.452 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 aren 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 covalent geometry : bond 0.00564 ( 8235) covalent geometry : angle 1.03092 (12044) hydrogen bonds : bond 0.13365 ( 357) hydrogen bonds : angle 5.29712 ( 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 : 0.171 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: 0.7005 time to fit residues: 31.5480 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: 10.0000 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: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.167380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.105437 restraints weight = 8334.771| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.25 r_work: 0.2714 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8235 Z= 0.166 Angle : 0.584 6.187 12044 Z= 0.306 Chirality : 0.037 0.219 1490 Planarity : 0.005 0.047 803 Dihedral : 22.110 177.710 3495 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.61 % Allowed : 9.38 % 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 aren not related in a simple way. whole: 0.95 (0.40), residues: 423 helix: 1.07 (0.35), residues: 212 sheet: 1.26 (0.69), residues: 57 loop : -0.10 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 266 TYR 0.012 0.002 TYR A 245 PHE 0.012 0.002 PHE A 328 TRP 0.003 0.001 TRP A 157 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8235) covalent geometry : angle 0.58425 (12044) hydrogen bonds : bond 0.05725 ( 357) hydrogen bonds : angle 3.41762 ( 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 43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.191 Fit side-chains REVERT: A 250 ASP cc_start: 0.8608 (m-30) cc_final: 0.8327 (m-30) outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 0.7175 time to fit residues: 30.0125 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 : 0.118 ------------------------------------------------------------------------------- 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: 6.9990 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 416 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.167906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.106416 restraints weight = 8329.145| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.39 r_work: 0.2710 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 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 0.030 8235 Z= 0.144 Angle : 0.532 5.743 12044 Z= 0.278 Chirality : 0.035 0.220 1490 Planarity : 0.005 0.046 803 Dihedral : 21.989 177.291 3492 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.61 % Allowed : 11.26 % Favored : 87.13 % 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 aren not related in a simple way. whole: 1.33 (0.41), residues: 423 helix: 1.54 (0.36), residues: 211 sheet: 1.31 (0.68), residues: 57 loop : -0.12 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 266 TYR 0.011 0.002 TYR A 245 PHE 0.011 0.002 PHE A 328 TRP 0.004 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8235) covalent geometry : angle 0.53195 (12044) hydrogen bonds : bond 0.05403 ( 357) hydrogen bonds : angle 3.29668 ( 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: 6 poor density : 35 time to evaluate : 0.115 Fit side-chains REVERT: A 68 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7559 (tttm) outliers start: 6 outliers final: 3 residues processed: 38 average time/residue: 0.6937 time to fit residues: 27.5592 Evaluate side-chains 36 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.186 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 0.0570 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 overall best weight: 2.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.167877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.105493 restraints weight = 8470.225| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.36 r_work: 0.2704 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1942 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= 0.143 Angle : 0.513 5.143 12044 Z= 0.268 Chirality : 0.034 0.221 1490 Planarity : 0.004 0.044 803 Dihedral : 21.709 164.968 3492 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.68 % Allowed : 11.26 % 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 aren not related in a simple way. whole: 1.47 (0.41), residues: 423 helix: 1.72 (0.37), residues: 211 sheet: 1.42 (0.67), residues: 55 loop : -0.16 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 204 TYR 0.011 0.002 TYR A 86 PHE 0.011 0.001 PHE A 328 TRP 0.005 0.001 TRP A 157 HIS 0.003 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8235) covalent geometry : angle 0.51264 (12044) hydrogen bonds : bond 0.05075 ( 357) hydrogen bonds : angle 3.24584 ( 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 45 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.121 Fit side-chains REVERT: A 68 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7552 (tttm) outliers start: 10 outliers final: 4 residues processed: 40 average time/residue: 0.6831 time to fit residues: 28.6453 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 : 0.119 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.165799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.103066 restraints weight = 8363.574| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.35 r_work: 0.2672 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8235 Z= 0.227 Angle : 0.607 6.967 12044 Z= 0.314 Chirality : 0.038 0.224 1490 Planarity : 0.005 0.045 803 Dihedral : 21.700 160.691 3492 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.41 % Allowed : 13.94 % 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 aren not related in a simple way. whole: 1.15 (0.40), residues: 423 helix: 1.49 (0.37), residues: 211 sheet: 1.22 (0.64), residues: 55 loop : -0.35 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 336 TYR 0.013 0.002 TYR A 245 PHE 0.013 0.002 PHE A 44 TRP 0.006 0.002 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 8235) covalent geometry : angle 0.60680 (12044) hydrogen bonds : bond 0.06495 ( 357) hydrogen bonds : angle 3.41891 ( 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 : 0.141 Fit side-chains REVERT: A 68 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7591 (tttm) outliers start: 9 outliers final: 3 residues processed: 39 average time/residue: 0.6712 time to fit residues: 27.4734 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 : 0.184 ------------------------------------------------------------------------------- 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 191 ILE 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: 40.0000 chunk 54 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.170202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109569 restraints weight = 8300.222| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.31 r_work: 0.2683 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8235 Z= 0.128 Angle : 0.488 5.251 12044 Z= 0.256 Chirality : 0.033 0.218 1490 Planarity : 0.004 0.045 803 Dihedral : 21.438 162.095 3492 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.95 % Allowed : 13.67 % 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 aren not related in a simple way. whole: 1.46 (0.41), residues: 423 helix: 1.77 (0.37), residues: 212 sheet: 1.30 (0.66), residues: 55 loop : -0.21 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.011 0.001 TYR A 245 PHE 0.010 0.001 PHE A 44 TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8235) covalent geometry : angle 0.48768 (12044) hydrogen bonds : bond 0.04794 ( 357) hydrogen bonds : angle 3.21483 ( 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 47 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.176 Fit side-chains REVERT: A 68 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7027 (mttt) outliers start: 11 outliers final: 2 residues processed: 40 average time/residue: 0.6670 time to fit residues: 27.9550 Evaluate side-chains 39 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.126 ------------------------------------------------------------------------------- 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 191 ILE 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: 5.9990 chunk 9 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3877 r_free = 0.3877 target = 0.166826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.104783 restraints weight = 8294.470| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.38 r_work: 0.2682 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8235 Z= 0.254 Angle : 0.623 6.883 12044 Z= 0.321 Chirality : 0.039 0.224 1490 Planarity : 0.005 0.046 803 Dihedral : 21.619 162.313 3491 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.88 % Allowed : 15.82 % Favored : 82.31 % 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 aren not related in a simple way. whole: 1.07 (0.40), residues: 423 helix: 1.47 (0.36), residues: 211 sheet: 1.07 (0.66), residues: 55 loop : -0.41 (0.48), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 336 TYR 0.013 0.002 TYR A 245 PHE 0.014 0.002 PHE A 44 TRP 0.006 0.002 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 8235) covalent geometry : angle 0.62345 (12044) hydrogen bonds : bond 0.06712 ( 357) hydrogen bonds : angle 3.44034 ( 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 43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.144 Fit side-chains REVERT: A 68 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7554 (tttm) outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 0.6652 time to fit residues: 27.8825 Evaluate side-chains 41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 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 50 LYS Chi-restraints excluded: chain A residue 68 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 7 optimal weight: 0.6980 chunk 52 optimal weight: 30.0000 chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 0.4980 chunk 28 optimal weight: 0.0970 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3924 r_free = 0.3924 target = 0.171129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.113438 restraints weight = 8391.257| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.32 r_work: 0.2793 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 8235 Z= 0.088 Angle : 0.439 5.329 12044 Z= 0.232 Chirality : 0.030 0.215 1490 Planarity : 0.004 0.040 803 Dihedral : 21.317 160.782 3491 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 3.68 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 aren not related in a simple way. whole: 1.77 (0.42), residues: 423 helix: 2.01 (0.37), residues: 212 sheet: 1.38 (0.66), residues: 55 loop : -0.01 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 204 TYR 0.009 0.001 TYR A 86 PHE 0.007 0.001 PHE A 328 TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00173 ( 8235) covalent geometry : angle 0.43870 (12044) hydrogen bonds : bond 0.04027 ( 357) hydrogen bonds : angle 3.09056 ( 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: 4 poor density : 36 time to evaluate : 0.197 Fit side-chains REVERT: A 68 LYS cc_start: 0.7802 (tttm) cc_final: 0.7251 (mttt) REVERT: A 250 ASP cc_start: 0.8593 (m-30) cc_final: 0.8300 (m-30) REVERT: A 305 ILE cc_start: 0.9117 (mt) cc_final: 0.8869 (mm) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.7969 time to fit residues: 30.9978 Evaluate side-chains 37 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS 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: 4.9990 chunk 57 optimal weight: 20.0000 chunk 48 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3883 r_free = 0.3883 target = 0.167585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.107526 restraints weight = 8230.565| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.10 r_work: 0.2721 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2368 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= 0.157 Angle : 0.506 5.366 12044 Z= 0.264 Chirality : 0.033 0.220 1490 Planarity : 0.004 0.042 803 Dihedral : 21.353 161.543 3491 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.80 % Allowed : 16.62 % Favored : 82.57 % 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 aren not related in a simple way. whole: 1.58 (0.41), residues: 423 helix: 1.90 (0.37), residues: 211 sheet: 1.32 (0.66), residues: 55 loop : -0.18 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 336 TYR 0.011 0.002 TYR A 245 PHE 0.011 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 covalent geometry : bond 0.00349 ( 8235) covalent geometry : angle 0.50552 (12044) hydrogen bonds : bond 0.05280 ( 357) hydrogen bonds : angle 3.21269 ( 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 39 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.123 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 38 average time/residue: 0.7229 time to fit residues: 28.7863 Evaluate side-chains 39 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 164 GLU 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: 0.7980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 57 optimal weight: 20.0000 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3890 r_free = 0.3890 target = 0.168198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109134 restraints weight = 8209.048| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.25 r_work: 0.2729 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2373 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= 0.112 Angle : 0.480 5.308 12044 Z= 0.253 Chirality : 0.032 0.220 1490 Planarity : 0.004 0.042 803 Dihedral : 21.349 161.584 3491 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.07 % Allowed : 16.09 % 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 aren not related in a simple way. whole: 1.65 (0.41), residues: 423 helix: 1.95 (0.37), residues: 211 sheet: 1.35 (0.66), residues: 55 loop : -0.13 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 390 TYR 0.010 0.001 TYR A 14 PHE 0.009 0.001 PHE A 44 TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8235) covalent geometry : angle 0.48030 (12044) hydrogen bonds : bond 0.05014 ( 357) hydrogen bonds : angle 3.19130 ( 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: 4 poor density : 36 time to evaluate : 0.203 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 39 average time/residue: 0.7520 time to fit residues: 30.8192 Evaluate side-chains 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 164 GLU 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: 0.1980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3892 r_free = 0.3892 target = 0.168333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.107375 restraints weight = 8215.119| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.10 r_work: 0.2741 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8235 Z= 0.122 Angle : 0.479 5.342 12044 Z= 0.251 Chirality : 0.032 0.217 1490 Planarity : 0.004 0.041 803 Dihedral : 21.328 161.742 3491 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.80 % Allowed : 16.62 % Favored : 82.57 % 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 aren not related in a simple way. whole: 1.67 (0.41), residues: 423 helix: 1.95 (0.37), residues: 211 sheet: 1.41 (0.66), residues: 55 loop : -0.11 (0.50), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.011 0.001 TYR A 86 PHE 0.010 0.001 PHE A 44 TRP 0.007 0.001 TRP A 157 HIS 0.003 0.001 HIS A 263 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8235) covalent geometry : angle 0.47904 (12044) hydrogen bonds : bond 0.04944 ( 357) hydrogen bonds : angle 3.16168 ( 862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2633.16 seconds wall clock time: 45 minutes 28.79 seconds (2728.79 seconds total)