Starting phenix.real_space_refine on Thu Mar 6 03:22:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c09_45077/03_2025/9c09_45077_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c09_45077/03_2025/9c09_45077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c09_45077/03_2025/9c09_45077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c09_45077/03_2025/9c09_45077.map" model { file = "/net/cci-nas-00/data/ceres_data/9c09_45077/03_2025/9c09_45077_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c09_45077/03_2025/9c09_45077_trim.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 28 5.16 5 C 2880 2.51 5 N 678 2.21 5 O 710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4300 Number of models: 1 Model: "" Number of chains: 4 Chain: "U" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2058 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Chain: "A" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2058 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Chain: "U" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 76 Unusual residues: {'D10': 2, 'D12': 1, 'EIC': 1, 'OCT': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 108 Unusual residues: {' K': 4, 'D10': 2, 'D12': 1, 'EIC': 1, 'HEX': 2, 'OCT': 5} Classifications: {'undetermined': 15} Link IDs: {None: 14} Time building chain proxies: 3.47, per 1000 atoms: 0.81 Number of scatterers: 4300 At special positions: 0 Unit cell: (59.34, 69.66, 94.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 28 16.00 O 710 8.00 N 678 7.00 C 2880 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: 1.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'U' and resid 14 through 65 removed outlier: 5.539A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS U 45 " --> pdb=" O LEU U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 83 Processing helix chain 'U' and resid 97 through 109 Processing helix chain 'U' and resid 122 through 162 Proline residue: U 136 - end of helix Processing helix chain 'U' and resid 193 through 215 removed outlier: 3.912A pdb=" N MET U 215 " --> pdb=" O CYS U 211 " (cutoff:3.500A) Processing helix chain 'U' and resid 223 through 236 Processing helix chain 'U' and resid 255 through 294 removed outlier: 3.760A pdb=" N PHE U 259 " --> pdb=" O GLY U 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 64 removed outlier: 5.554A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 85 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 122 through 162 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 193 through 220 removed outlier: 3.582A pdb=" N MET A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 255 through 294 removed outlier: 3.869A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 689 1.33 - 1.45: 1228 1.45 - 1.57: 2427 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4384 Sorted by residual: bond pdb=" N SER A 67 " pdb=" CA SER A 67 " ideal model delta sigma weight residual 1.454 1.485 -0.032 1.18e-02 7.18e+03 7.16e+00 bond pdb=" N SER U 67 " pdb=" CA SER U 67 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 6.08e+00 bond pdb=" N ARG A 68 " pdb=" CA ARG A 68 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.33e+00 bond pdb=" C1 EIC A 411 " pdb=" O2 EIC A 411 " ideal model delta sigma weight residual 1.250 1.205 0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" C1 EIC U 406 " pdb=" O2 EIC U 406 " ideal model delta sigma weight residual 1.250 1.205 0.045 2.00e-02 2.50e+03 5.12e+00 ... (remaining 4379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 5752 2.20 - 4.41: 85 4.41 - 6.61: 23 6.61 - 8.81: 1 8.81 - 11.02: 1 Bond angle restraints: 5862 Sorted by residual: angle pdb=" C ARG A 83 " pdb=" N ALA A 84 " pdb=" CA ALA A 84 " ideal model delta sigma weight residual 120.28 113.54 6.74 1.34e+00 5.57e-01 2.53e+01 angle pdb=" O THR A 82 " pdb=" C THR A 82 " pdb=" N ARG A 83 " ideal model delta sigma weight residual 122.22 116.70 5.52 1.17e+00 7.31e-01 2.22e+01 angle pdb=" CA GLU U 220 " pdb=" C GLU U 220 " pdb=" O GLU U 220 " ideal model delta sigma weight residual 119.95 114.46 5.49 1.21e+00 6.83e-01 2.06e+01 angle pdb=" CA GLU U 220 " pdb=" C GLU U 220 " pdb=" N GLY U 221 " ideal model delta sigma weight residual 117.76 123.34 -5.58 1.38e+00 5.25e-01 1.64e+01 angle pdb=" N ARG A 83 " pdb=" CA ARG A 83 " pdb=" C ARG A 83 " ideal model delta sigma weight residual 111.82 107.15 4.67 1.16e+00 7.43e-01 1.62e+01 ... (remaining 5857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 2237 17.76 - 35.51: 240 35.51 - 53.27: 47 53.27 - 71.03: 14 71.03 - 88.78: 2 Dihedral angle restraints: 2540 sinusoidal: 1052 harmonic: 1488 Sorted by residual: dihedral pdb=" CA ASP U 96 " pdb=" C ASP U 96 " pdb=" N PHE U 97 " pdb=" CA PHE U 97 " ideal model delta harmonic sigma weight residual 180.00 152.34 27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ASP A 89 " pdb=" C ASP A 89 " pdb=" N ASN A 90 " pdb=" CA ASN A 90 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA TRP A 95 " pdb=" C TRP A 95 " pdb=" N ASP A 96 " pdb=" CA ASP A 96 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 2537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 474 0.034 - 0.067: 111 0.067 - 0.100: 37 0.100 - 0.134: 11 0.134 - 0.167: 1 Chirality restraints: 634 Sorted by residual: chirality pdb=" CA TYR U 216 " pdb=" N TYR U 216 " pdb=" C TYR U 216 " pdb=" CB TYR U 216 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA HIS U 64 " pdb=" N HIS U 64 " pdb=" C HIS U 64 " pdb=" CB HIS U 64 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL A 244 " pdb=" N VAL A 244 " pdb=" C VAL A 244 " pdb=" CB VAL A 244 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 631 not shown) Planarity restraints: 714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 210 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C CYS A 210 " 0.041 2.00e-02 2.50e+03 pdb=" O CYS A 210 " -0.015 2.00e-02 2.50e+03 pdb=" N CYS A 211 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 292 " -0.177 9.50e-02 1.11e+02 8.02e-02 5.45e+00 pdb=" NE ARG U 292 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG U 292 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG U 292 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG U 292 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 123 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C GLY A 123 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY A 123 " -0.014 2.00e-02 2.50e+03 pdb=" N LYS A 124 " -0.013 2.00e-02 2.50e+03 ... (remaining 711 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.90: 1636 2.90 - 3.46: 4811 3.46 - 4.02: 7221 4.02 - 4.58: 11060 4.58 - 5.14: 15064 Nonbonded interactions: 39792 Sorted by model distance: nonbonded pdb=" OE2 GLU U 220 " pdb=" OH TYR U 251 " model vdw 2.342 3.040 nonbonded pdb=" O SER A 236 " pdb=" OG1 THR A 237 " model vdw 2.343 3.040 nonbonded pdb=" O SER U 236 " pdb=" OG1 THR U 237 " model vdw 2.385 3.040 nonbonded pdb=" N ASP U 96 " pdb=" OD1 ASP U 96 " model vdw 2.402 3.120 nonbonded pdb=" N ASP A 242 " pdb=" OD1 ASP A 242 " model vdw 2.428 3.120 ... (remaining 39787 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 295 or resid 407)) selection = (chain 'U' and (resid 14 through 295 or resid 407)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.490 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4384 Z= 0.235 Angle : 0.689 11.015 5862 Z= 0.377 Chirality : 0.035 0.167 634 Planarity : 0.005 0.080 714 Dihedral : 15.072 88.783 1588 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.69 % Allowed : 11.29 % Favored : 88.02 % 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: 4.21 (0.39), residues: 506 helix: 4.02 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -2.09 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP U 53 HIS 0.004 0.001 HIS U 77 PHE 0.010 0.001 PHE A 232 TYR 0.009 0.001 TYR A 229 ARG 0.022 0.001 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.435 Fit side-chains REVERT: U 70 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7176 (mt-10) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 1.4760 time to fit residues: 119.9854 Evaluate side-chains 59 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 59 GLN U 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.073562 restraints weight = 6551.876| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.42 r_work: 0.2724 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4384 Z= 0.206 Angle : 0.547 4.915 5862 Z= 0.305 Chirality : 0.035 0.137 634 Planarity : 0.004 0.026 714 Dihedral : 10.322 59.638 690 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.30 % Allowed : 12.21 % Favored : 85.48 % 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: 4.49 (0.38), residues: 506 helix: 3.87 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.20 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 222 HIS 0.002 0.000 HIS U 64 PHE 0.013 0.002 PHE A 145 TYR 0.009 0.001 TYR U 229 ARG 0.007 0.001 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.436 Fit side-chains REVERT: U 51 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8258 (tp-100) REVERT: U 292 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7271 (tmm160) REVERT: A 51 GLN cc_start: 0.8483 (tp-100) cc_final: 0.8206 (tp-100) REVERT: A 59 GLN cc_start: 0.8675 (tp-100) cc_final: 0.8440 (tp40) REVERT: A 65 GLN cc_start: 0.8461 (pm20) cc_final: 0.8217 (mp10) REVERT: A 251 TYR cc_start: 0.8356 (OUTLIER) cc_final: 0.7607 (t80) outliers start: 10 outliers final: 4 residues processed: 72 average time/residue: 1.5079 time to fit residues: 111.8293 Evaluate side-chains 61 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain U residue 286 SER Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 20 optimal weight: 0.0270 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN A 59 GLN A 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.075941 restraints weight = 6521.668| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.44 r_work: 0.2771 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4384 Z= 0.163 Angle : 0.485 4.881 5862 Z= 0.269 Chirality : 0.033 0.135 634 Planarity : 0.003 0.029 714 Dihedral : 9.352 59.471 690 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.30 % Allowed : 13.13 % Favored : 84.56 % 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: 4.76 (0.38), residues: 506 helix: 4.05 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.12 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 PHE 0.008 0.001 PHE A 145 TYR 0.008 0.001 TYR A 30 ARG 0.008 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.418 Fit side-chains REVERT: U 55 GLU cc_start: 0.8720 (tp30) cc_final: 0.8455 (tp30) REVERT: U 70 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7815 (mt-10) REVERT: U 191 LYS cc_start: 0.9033 (mtpt) cc_final: 0.8347 (mppt) REVERT: U 251 TYR cc_start: 0.8385 (OUTLIER) cc_final: 0.8147 (m-80) REVERT: A 59 GLN cc_start: 0.8746 (tp40) cc_final: 0.8520 (tp40) REVERT: A 65 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8046 (mp10) outliers start: 10 outliers final: 4 residues processed: 65 average time/residue: 1.3337 time to fit residues: 89.5955 Evaluate side-chains 61 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain U residue 286 SER Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.0020 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.076212 restraints weight = 6629.021| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.45 r_work: 0.2773 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4384 Z= 0.161 Angle : 0.490 5.316 5862 Z= 0.269 Chirality : 0.033 0.134 634 Planarity : 0.003 0.024 714 Dihedral : 8.781 57.529 690 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.61 % Allowed : 14.75 % Favored : 83.64 % 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: 4.87 (0.38), residues: 506 helix: 4.16 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.22 (0.62), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE A 145 TYR 0.008 0.001 TYR U 30 ARG 0.006 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.482 Fit side-chains REVERT: U 55 GLU cc_start: 0.8756 (tp30) cc_final: 0.8501 (tp30) REVERT: U 59 GLN cc_start: 0.8611 (tp40) cc_final: 0.8345 (tp-100) REVERT: U 70 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7868 (mt-10) REVERT: A 65 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7980 (mp10) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 1.3306 time to fit residues: 89.4540 Evaluate side-chains 61 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 286 SER Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.072208 restraints weight = 6656.079| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.46 r_work: 0.2713 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4384 Z= 0.215 Angle : 0.534 5.271 5862 Z= 0.296 Chirality : 0.034 0.136 634 Planarity : 0.003 0.025 714 Dihedral : 8.837 54.846 688 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.07 % Allowed : 14.29 % Favored : 83.64 % 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: 4.64 (0.37), residues: 506 helix: 4.03 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.44 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 PHE 0.009 0.001 PHE A 74 TYR 0.009 0.001 TYR U 229 ARG 0.004 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.426 Fit side-chains REVERT: U 55 GLU cc_start: 0.8792 (tp30) cc_final: 0.8490 (tp30) REVERT: U 59 GLN cc_start: 0.8661 (tp40) cc_final: 0.8391 (tp-100) REVERT: U 70 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7964 (mt-10) REVERT: U 191 LYS cc_start: 0.9104 (mtpt) cc_final: 0.8390 (mppt) REVERT: A 87 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8760 (mmt-90) outliers start: 9 outliers final: 5 residues processed: 65 average time/residue: 1.5145 time to fit residues: 101.3095 Evaluate side-chains 61 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 286 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 49 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.074037 restraints weight = 6616.419| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.45 r_work: 0.2733 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4384 Z= 0.191 Angle : 0.523 5.109 5862 Z= 0.288 Chirality : 0.034 0.135 634 Planarity : 0.003 0.035 714 Dihedral : 8.652 59.239 688 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.84 % Allowed : 14.52 % Favored : 83.64 % 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: 4.79 (0.37), residues: 506 helix: 4.14 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.42 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE A 232 TYR 0.008 0.001 TYR U 229 ARG 0.010 0.001 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.518 Fit side-chains REVERT: U 55 GLU cc_start: 0.8790 (tp30) cc_final: 0.8478 (tp30) REVERT: U 59 GLN cc_start: 0.8609 (tp40) cc_final: 0.8352 (tp-100) REVERT: U 70 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7935 (mt-10) REVERT: U 147 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 87 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8575 (mpt180) outliers start: 8 outliers final: 5 residues processed: 67 average time/residue: 1.5494 time to fit residues: 106.9213 Evaluate side-chains 62 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 286 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.075103 restraints weight = 6612.299| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.45 r_work: 0.2759 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4384 Z= 0.175 Angle : 0.520 6.453 5862 Z= 0.285 Chirality : 0.033 0.147 634 Planarity : 0.003 0.042 714 Dihedral : 8.313 52.747 688 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.61 % Allowed : 14.98 % Favored : 83.41 % 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: 4.80 (0.38), residues: 506 helix: 4.15 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.44 (0.60), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE U 259 TYR 0.008 0.001 TYR U 229 ARG 0.014 0.001 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.451 Fit side-chains REVERT: U 55 GLU cc_start: 0.8779 (tp30) cc_final: 0.8483 (tp30) REVERT: U 59 GLN cc_start: 0.8601 (tp40) cc_final: 0.8380 (tp-100) REVERT: U 70 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7929 (mt-10) REVERT: U 147 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7825 (tm-30) REVERT: A 147 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7796 (tm-30) outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 1.4007 time to fit residues: 94.0444 Evaluate side-chains 60 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 286 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.073054 restraints weight = 6528.758| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.44 r_work: 0.2723 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4384 Z= 0.209 Angle : 0.556 6.935 5862 Z= 0.307 Chirality : 0.034 0.159 634 Planarity : 0.003 0.031 714 Dihedral : 8.076 59.627 686 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.15 % Allowed : 15.90 % Favored : 82.95 % 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: 4.68 (0.38), residues: 506 helix: 4.08 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.51 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 53 HIS 0.003 0.000 HIS A 64 PHE 0.008 0.001 PHE A 74 TYR 0.009 0.001 TYR A 229 ARG 0.010 0.001 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.434 Fit side-chains REVERT: U 51 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8293 (tm-30) REVERT: U 55 GLU cc_start: 0.8790 (tp30) cc_final: 0.8463 (tp30) REVERT: U 59 GLN cc_start: 0.8598 (tp40) cc_final: 0.8372 (tp-100) REVERT: U 70 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7969 (mt-10) REVERT: U 147 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 147 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7852 (tm-30) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 1.4807 time to fit residues: 93.0567 Evaluate side-chains 59 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 286 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.073702 restraints weight = 6601.566| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.46 r_work: 0.2731 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4384 Z= 0.200 Angle : 0.562 7.892 5862 Z= 0.307 Chirality : 0.034 0.163 634 Planarity : 0.004 0.053 714 Dihedral : 7.772 52.896 686 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.15 % Allowed : 15.90 % Favored : 82.95 % 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: 4.73 (0.38), residues: 506 helix: 4.12 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.55 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.003 0.000 HIS A 64 PHE 0.007 0.001 PHE A 97 TYR 0.008 0.001 TYR U 229 ARG 0.017 0.001 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.484 Fit side-chains REVERT: U 51 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8295 (tm-30) REVERT: U 55 GLU cc_start: 0.8772 (tp30) cc_final: 0.8464 (tp30) REVERT: U 59 GLN cc_start: 0.8653 (tp40) cc_final: 0.8435 (tp-100) REVERT: U 70 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7971 (mt-10) REVERT: U 147 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7849 (tm-30) REVERT: A 147 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7827 (tm-30) outliers start: 5 outliers final: 5 residues processed: 63 average time/residue: 1.6331 time to fit residues: 105.8477 Evaluate side-chains 61 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 286 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.073459 restraints weight = 6556.267| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.44 r_work: 0.2728 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4384 Z= 0.211 Angle : 0.597 8.472 5862 Z= 0.325 Chirality : 0.034 0.168 634 Planarity : 0.003 0.052 714 Dihedral : 7.636 53.098 686 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.92 % Allowed : 16.13 % Favored : 82.95 % 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: 4.72 (0.38), residues: 506 helix: 4.11 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.56 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.003 0.000 HIS A 64 PHE 0.007 0.001 PHE U 232 TYR 0.008 0.001 TYR U 229 ARG 0.020 0.001 ARG U 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.453 Fit side-chains REVERT: U 51 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8313 (tm-30) REVERT: U 55 GLU cc_start: 0.8776 (tp30) cc_final: 0.8417 (tp30) REVERT: U 59 GLN cc_start: 0.8641 (tp40) cc_final: 0.8419 (tp-100) REVERT: U 70 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8006 (mt-10) REVERT: U 147 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 147 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7835 (tm-30) outliers start: 4 outliers final: 4 residues processed: 59 average time/residue: 1.4832 time to fit residues: 90.2390 Evaluate side-chains 60 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 286 SER Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.0470 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.076354 restraints weight = 6615.459| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.47 r_work: 0.2779 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4384 Z= 0.177 Angle : 0.556 8.500 5862 Z= 0.301 Chirality : 0.034 0.164 634 Planarity : 0.003 0.054 714 Dihedral : 7.280 53.929 686 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.15 % Allowed : 16.13 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 4.88 (0.38), residues: 506 helix: 4.23 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.51 (0.59), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.006 0.001 PHE U 259 TYR 0.008 0.001 TYR A 30 ARG 0.020 0.001 ARG U 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3723.63 seconds wall clock time: 64 minutes 12.98 seconds (3852.98 seconds total)