Starting phenix.real_space_refine on Thu Nov 14 21:10:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0i_45085/11_2024/9c0i_45085.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0i_45085/11_2024/9c0i_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0i_45085/11_2024/9c0i_45085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0i_45085/11_2024/9c0i_45085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0i_45085/11_2024/9c0i_45085.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c0i_45085/11_2024/9c0i_45085.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 1, 'ASP:plan': 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: 4.77, per 1000 atoms: 0.62 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: 2.19 Conformation dependent library (CDL) restraints added in 478.6 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: 3.78 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: 3.16 Time building geometry restraints manager: 2.51 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: 0.570 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 23.550 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- 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= 0.344 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (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 TRP 0.006 0.001 TRP A 8 HIS 0.008 0.002 HIS A 263 PHE 0.021 0.004 PHE A 328 TYR 0.023 0.003 TYR A 83 ARG 0.015 0.002 ARG A 383 *********************** 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 : 0.560 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: 1.5876 time to fit residues: 71.8312 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 : 0.583 ------------------------------------------------------------------------------- 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 51 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8235 Z= 0.153 Angle : 0.531 6.070 12044 Z= 0.279 Chirality : 0.035 0.219 1490 Planarity : 0.004 0.045 803 Dihedral : 22.038 178.165 3495 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.07 % Allowed : 9.38 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.40), residues: 423 helix: 1.17 (0.35), residues: 212 sheet: 1.27 (0.69), residues: 57 loop : 0.02 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 157 HIS 0.002 0.001 HIS A 263 PHE 0.011 0.001 PHE A 328 TYR 0.010 0.001 TYR A 245 ARG 0.003 0.000 ARG A 290 *********************** 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: 4 poor density : 39 time to evaluate : 0.612 Fit side-chains REVERT: A 250 ASP cc_start: 0.8752 (m-30) cc_final: 0.8524 (m-30) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 1.6722 time to fit residues: 72.0803 Evaluate side-chains 33 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 31 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 30 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 30.0000 chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8235 Z= 0.273 Angle : 0.596 6.819 12044 Z= 0.309 Chirality : 0.038 0.224 1490 Planarity : 0.005 0.047 803 Dihedral : 22.032 173.276 3491 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.61 % Allowed : 10.19 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.41), residues: 423 helix: 1.43 (0.36), residues: 211 sheet: 1.23 (0.68), residues: 57 loop : -0.21 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 157 HIS 0.003 0.001 HIS A 263 PHE 0.014 0.002 PHE A 328 TYR 0.011 0.002 TYR A 245 ARG 0.005 0.001 ARG A 336 *********************** 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 40 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.582 Fit side-chains REVERT: A 68 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7655 (tttm) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 1.6735 time to fit residues: 63.4344 Evaluate side-chains 36 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 130 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 40.0000 chunk 15 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8235 Z= 0.144 Angle : 0.476 5.065 12044 Z= 0.250 Chirality : 0.032 0.218 1490 Planarity : 0.004 0.044 803 Dihedral : 21.736 166.330 3491 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.88 % Allowed : 10.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.41), residues: 423 helix: 1.86 (0.37), residues: 212 sheet: 1.46 (0.67), residues: 55 loop : -0.05 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 157 HIS 0.002 0.001 HIS A 170 PHE 0.009 0.001 PHE A 44 TYR 0.010 0.001 TYR A 245 ARG 0.003 0.001 ARG A 204 *********************** 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 42 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.566 Fit side-chains REVERT: A 68 LYS cc_start: 0.7925 (tttm) cc_final: 0.7511 (mtpt) outliers start: 7 outliers final: 2 residues processed: 38 average time/residue: 1.6159 time to fit residues: 64.6939 Evaluate side-chains 34 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 38 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 52 optimal weight: 40.0000 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8235 Z= 0.312 Angle : 0.603 6.601 12044 Z= 0.312 Chirality : 0.038 0.224 1490 Planarity : 0.005 0.045 803 Dihedral : 21.717 160.386 3491 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.88 % Allowed : 12.33 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.41), residues: 423 helix: 1.56 (0.37), residues: 211 sheet: 1.02 (0.65), residues: 57 loop : -0.30 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 157 HIS 0.003 0.001 HIS A 263 PHE 0.014 0.002 PHE A 328 TYR 0.012 0.002 TYR A 245 ARG 0.003 0.001 ARG A 336 *********************** 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 44 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.573 Fit side-chains REVERT: A 68 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7647 (tttm) REVERT: A 123 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8711 (ttm170) outliers start: 7 outliers final: 3 residues processed: 40 average time/residue: 1.5657 time to fit residues: 65.8006 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 : 0.606 ------------------------------------------------------------------------------- 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 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8235 Z= 0.144 Angle : 0.469 5.241 12044 Z= 0.247 Chirality : 0.032 0.216 1490 Planarity : 0.004 0.044 803 Dihedral : 21.439 161.489 3491 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.34 % Allowed : 14.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.41), residues: 423 helix: 1.91 (0.37), residues: 212 sheet: 1.40 (0.66), residues: 55 loop : -0.06 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 77 PHE 0.009 0.001 PHE A 44 TYR 0.011 0.001 TYR A 86 ARG 0.002 0.000 ARG A 336 *********************** 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 41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.632 Fit side-chains REVERT: A 68 LYS cc_start: 0.7947 (tttm) cc_final: 0.7490 (mtpt) outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 1.5729 time to fit residues: 64.5862 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 : 0.512 ------------------------------------------------------------------------------- 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 191 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8235 Z= 0.150 Angle : 0.471 5.213 12044 Z= 0.247 Chirality : 0.032 0.219 1490 Planarity : 0.004 0.041 803 Dihedral : 21.392 161.612 3491 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.88 % Allowed : 14.21 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.42), residues: 423 helix: 1.98 (0.37), residues: 212 sheet: 1.46 (0.66), residues: 55 loop : -0.02 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS A 263 PHE 0.010 0.001 PHE A 44 TYR 0.011 0.001 TYR A 14 ARG 0.002 0.000 ARG A 336 *********************** 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: 7 poor density : 37 time to evaluate : 0.600 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 43 average time/residue: 1.7351 time to fit residues: 78.1909 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 : 0.562 ------------------------------------------------------------------------------- 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 191 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 0.0050 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 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 : 0.004 0.037 8235 Z= 0.218 Angle : 0.510 5.255 12044 Z= 0.266 Chirality : 0.034 0.219 1490 Planarity : 0.004 0.043 803 Dihedral : 21.394 161.492 3491 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.88 % Allowed : 14.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.41), residues: 423 helix: 1.89 (0.37), residues: 211 sheet: 1.40 (0.66), residues: 55 loop : -0.16 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS A 263 PHE 0.011 0.001 PHE A 328 TYR 0.012 0.002 TYR A 245 ARG 0.002 0.000 ARG A 204 *********************** 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 43 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.600 Fit side-chains REVERT: A 68 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7443 (mtpt) outliers start: 7 outliers final: 5 residues processed: 39 average time/residue: 1.6432 time to fit residues: 67.3206 Evaluate side-chains 42 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 164 GLU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 366 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 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 : 0.003 0.033 8235 Z= 0.207 Angle : 0.505 5.246 12044 Z= 0.264 Chirality : 0.033 0.221 1490 Planarity : 0.004 0.044 803 Dihedral : 21.392 161.534 3491 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.61 % Allowed : 14.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.41), residues: 423 helix: 1.88 (0.37), residues: 211 sheet: 1.37 (0.66), residues: 55 loop : -0.15 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 157 HIS 0.002 0.001 HIS A 263 PHE 0.010 0.001 PHE A 44 TYR 0.012 0.002 TYR A 245 ARG 0.003 0.000 ARG A 336 *********************** 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 42 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.539 Fit side-chains REVERT: A 68 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7443 (mtpt) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 1.6649 time to fit residues: 68.1243 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 : 0.564 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 366 GLU 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 48 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8235 Z= 0.291 Angle : 0.575 6.056 12044 Z= 0.299 Chirality : 0.037 0.222 1490 Planarity : 0.005 0.045 803 Dihedral : 21.521 161.442 3491 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.34 % Allowed : 15.01 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.41), residues: 423 helix: 1.69 (0.37), residues: 211 sheet: 0.98 (0.65), residues: 57 loop : -0.22 (0.50), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 157 HIS 0.003 0.001 HIS A 263 PHE 0.012 0.002 PHE A 328 TYR 0.013 0.002 TYR A 245 ARG 0.003 0.000 ARG A 266 ********************** 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 41 residues out of total 381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.648 Fit side-chains REVERT: A 66 THR cc_start: 0.7618 (m) cc_final: 0.6901 (p) REVERT: A 68 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7665 (tttm) outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 1.4223 time to fit residues: 57.2817 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 : 0.574 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.167324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.107651 restraints weight = 8147.577| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.17 r_work: 0.2708 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8235 Z= 0.210 Angle : 0.537 5.281 12044 Z= 0.281 Chirality : 0.035 0.222 1490 Planarity : 0.005 0.046 803 Dihedral : 21.507 161.525 3491 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.07 % Allowed : 14.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.41), residues: 423 helix: 1.77 (0.37), residues: 211 sheet: 1.23 (0.66), residues: 55 loop : -0.22 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 157 HIS 0.002 0.001 HIS A 81 PHE 0.011 0.001 PHE A 44 TYR 0.011 0.002 TYR A 14 ARG 0.002 0.000 ARG A 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2003.69 seconds wall clock time: 36 minutes 59.70 seconds (2219.70 seconds total)