Starting phenix.real_space_refine on Thu Jul 2 00:25:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c09_45077/07_2026/9c09_45077_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c09_45077/07_2026/9c09_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_45077/07_2026/9c09_45077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c09_45077/07_2026/9c09_45077.map" model { file = "/net/cci-nas-00/data/ceres_data/9c09_45077/07_2026/9c09_45077_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c09_45077/07_2026/9c09_45077_trim.cif" } resolution = 2.36 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 104 Ad-hoc single atom residues: {' K': 4} Unusual residues: {'D10': 2, 'D12': 1, 'EIC': 1, 'HEX': 2, 'OCT': 5} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain breaks: 4 Time building chain proxies: 1.28, per 1000 atoms: 0.30 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: 0.42 Conformation dependent library (CDL) restraints added in 147.6 milliseconds 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: 0.10 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: 0.61 Time building geometry restraints manager: 0.52 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: 1.650 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.030 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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= 0.226 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 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 ARG 0.022 0.001 ARG U 292 TYR 0.009 0.001 TYR A 229 PHE 0.010 0.001 PHE A 232 TRP 0.017 0.002 TRP U 53 HIS 0.004 0.001 HIS U 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.23 ( 4384) covalent geometry : angle 0.68917 / 0.38 ( 5862) hydrogen bonds : bond 0.10775 / 6.97 ( 333) hydrogen bonds : angle 3.96014 / 3.08 ( 999) *********************** 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 : 0.154 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.6965 time to fit residues: 56.5545 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 : 0.105 ------------------------------------------------------------------------------- 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 24 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 51 GLN U 59 GLN U 90 ASN A 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.093431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.069769 restraints weight = 6726.033| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.46 r_work: 0.2657 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4384 Z= 0.206 Angle : 0.604 5.602 5862 Z= 0.335 Chirality : 0.037 0.139 634 Planarity : 0.004 0.028 714 Dihedral : 10.968 59.858 690 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.30 % Allowed : 12.44 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.33 (0.38), residues: 506 helix: 3.77 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.32 (0.62), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 292 TYR 0.011 0.002 TYR A 251 PHE 0.014 0.002 PHE U 74 TRP 0.012 0.001 TRP U 222 HIS 0.002 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 ( 4384) covalent geometry : angle 0.60436 / 0.34 ( 5862) hydrogen bonds : bond 0.08988 / 6.00 ( 333) hydrogen bonds : angle 3.49546 / 2.66 ( 999) *********************** 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 67 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.203 Fit side-chains REVERT: U 51 GLN cc_start: 0.8528 (tp40) cc_final: 0.8291 (tp-100) REVERT: U 55 GLU cc_start: 0.8871 (tp30) cc_final: 0.8669 (tp30) REVERT: U 191 LYS cc_start: 0.8730 (mppt) cc_final: 0.8335 (mppt) REVERT: A 51 GLN cc_start: 0.8522 (tp40) cc_final: 0.8290 (tp-100) REVERT: A 65 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8324 (mp10) REVERT: A 251 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7753 (t80) outliers start: 10 outliers final: 4 residues processed: 63 average time/residue: 0.7405 time to fit residues: 47.9274 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 : 0.195 ------------------------------------------------------------------------------- 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 91 VAL Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain A residue 280 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.073785 restraints weight = 6685.141| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.49 r_work: 0.2738 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4384 Z= 0.149 Angle : 0.507 4.922 5862 Z= 0.281 Chirality : 0.034 0.134 634 Planarity : 0.003 0.028 714 Dihedral : 9.793 58.293 690 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.07 % Allowed : 13.13 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.73 (0.38), residues: 506 helix: 4.03 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.12 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 292 TYR 0.008 0.001 TYR U 229 PHE 0.010 0.001 PHE A 145 TRP 0.009 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 ( 4384) covalent geometry : angle 0.50727 / 0.28 ( 5862) hydrogen bonds : bond 0.07383 / 4.91 ( 333) hydrogen bonds : angle 3.13633 / 2.39 ( 999) *********************** 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 64 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.228 Fit side-chains REVERT: U 51 GLN cc_start: 0.8607 (tp40) cc_final: 0.8406 (tm-30) REVERT: U 70 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7890 (mt-10) REVERT: A 55 GLU cc_start: 0.8780 (tp30) cc_final: 0.8380 (tp30) REVERT: A 292 ARG cc_start: 0.7629 (ttp80) cc_final: 0.7329 (tmm-80) outliers start: 9 outliers final: 5 residues processed: 63 average time/residue: 0.6569 time to fit residues: 42.6848 Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN U 261 ASN A 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.073282 restraints weight = 6599.281| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.44 r_work: 0.2723 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2813 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= 0.152 Angle : 0.513 5.114 5862 Z= 0.283 Chirality : 0.034 0.135 634 Planarity : 0.003 0.029 714 Dihedral : 9.269 58.130 690 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.61 % Allowed : 13.36 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.79 (0.37), residues: 506 helix: 4.06 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.02 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 292 TYR 0.009 0.001 TYR A 229 PHE 0.008 0.001 PHE U 259 TRP 0.008 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 4384) covalent geometry : angle 0.51327 / 0.28 ( 5862) hydrogen bonds : bond 0.07525 / 5.01 ( 333) hydrogen bonds : angle 3.08758 / 2.35 ( 999) *********************** 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 58 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.156 Fit side-chains REVERT: U 51 GLN cc_start: 0.8601 (tp40) cc_final: 0.8355 (tm-30) REVERT: U 59 GLN cc_start: 0.8687 (tp40) cc_final: 0.8447 (tp-100) REVERT: U 70 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7905 (mt-10) REVERT: A 55 GLU cc_start: 0.8799 (tp30) cc_final: 0.8422 (tp30) REVERT: A 59 GLN cc_start: 0.8716 (tp40) cc_final: 0.8515 (tp40) REVERT: A 65 GLN cc_start: 0.8531 (mp10) cc_final: 0.8292 (mp10) outliers start: 7 outliers final: 6 residues processed: 57 average time/residue: 0.7148 time to fit residues: 41.9628 Evaluate side-chains 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 286 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.074088 restraints weight = 6654.074| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.47 r_work: 0.2740 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2920 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= 0.146 Angle : 0.497 5.022 5862 Z= 0.274 Chirality : 0.033 0.131 634 Planarity : 0.003 0.033 714 Dihedral : 8.558 55.914 688 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.61 % Allowed : 13.59 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.90 (0.38), residues: 506 helix: 4.14 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.01 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 292 TYR 0.008 0.001 TYR U 30 PHE 0.007 0.001 PHE U 232 TRP 0.008 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 ( 4384) covalent geometry : angle 0.49735 / 0.27 ( 5862) hydrogen bonds : bond 0.07180 / 4.78 ( 333) hydrogen bonds : angle 3.00290 / 2.29 ( 999) *********************** 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 62 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.159 Fit side-chains REVERT: U 51 GLN cc_start: 0.8584 (tp40) cc_final: 0.8326 (tm-30) REVERT: U 59 GLN cc_start: 0.8654 (tp40) cc_final: 0.8440 (tp-100) REVERT: U 70 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7900 (mt-10) REVERT: U 147 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 55 GLU cc_start: 0.8799 (tp30) cc_final: 0.8445 (tp30) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.6487 time to fit residues: 41.5487 Evaluate side-chains 63 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 286 SER 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 2 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN U 261 ASN A 261 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.074359 restraints weight = 6679.282| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.46 r_work: 0.2748 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2967 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= 0.146 Angle : 0.523 5.374 5862 Z= 0.286 Chirality : 0.034 0.144 634 Planarity : 0.003 0.037 714 Dihedral : 8.432 55.165 688 Min Nonbonded Distance : 2.539 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.93 (0.38), residues: 506 helix: 4.17 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.01 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG U 292 TYR 0.008 0.001 TYR U 30 PHE 0.007 0.001 PHE U 232 TRP 0.008 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 ( 4384) covalent geometry : angle 0.52253 / 0.29 ( 5862) hydrogen bonds : bond 0.07066 / 4.70 ( 333) hydrogen bonds : angle 2.98873 / 2.29 ( 999) *********************** 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 64 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.176 Fit side-chains REVERT: U 51 GLN cc_start: 0.8598 (tp40) cc_final: 0.8336 (tm-30) REVERT: U 59 GLN cc_start: 0.8643 (tp40) cc_final: 0.8432 (tp-100) REVERT: U 70 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7899 (mt-10) REVERT: U 147 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 54 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 55 GLU cc_start: 0.8805 (tp30) cc_final: 0.8523 (tp30) REVERT: A 59 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8599 (tp40) REVERT: A 251 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8278 (m-80) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.7497 time to fit residues: 49.2804 Evaluate side-chains 59 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 286 SER 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 47 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN A 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.071217 restraints weight = 6719.304| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.48 r_work: 0.2691 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4384 Z= 0.173 Angle : 0.566 6.296 5862 Z= 0.310 Chirality : 0.035 0.155 634 Planarity : 0.004 0.045 714 Dihedral : 8.558 56.166 688 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.38 % Allowed : 15.44 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.75 (0.38), residues: 506 helix: 4.05 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.10 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 292 TYR 0.009 0.001 TYR U 229 PHE 0.008 0.001 PHE A 97 TRP 0.007 0.001 TRP U 53 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 ( 4384) covalent geometry : angle 0.56572 / 0.31 ( 5862) hydrogen bonds : bond 0.08044 / 5.36 ( 333) hydrogen bonds : angle 3.18188 / 2.42 ( 999) *********************** 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 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.160 Fit side-chains REVERT: U 51 GLN cc_start: 0.8610 (tp40) cc_final: 0.8342 (tm-30) REVERT: U 59 GLN cc_start: 0.8658 (tp40) cc_final: 0.8440 (tp-100) REVERT: U 70 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7979 (mt-10) REVERT: U 147 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7903 (tm-30) REVERT: A 55 GLU cc_start: 0.8800 (tp30) cc_final: 0.8449 (tp30) REVERT: A 59 GLN cc_start: 0.8843 (tp40) cc_final: 0.8518 (tp40) outliers start: 6 outliers final: 5 residues processed: 54 average time/residue: 0.7173 time to fit residues: 39.8878 Evaluate side-chains 54 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 247 GLN 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 17 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.097763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.073969 restraints weight = 6626.013| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.47 r_work: 0.2744 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4384 Z= 0.151 Angle : 0.550 7.337 5862 Z= 0.300 Chirality : 0.034 0.135 634 Planarity : 0.004 0.047 714 Dihedral : 7.645 51.183 686 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.61 % Allowed : 15.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.87 (0.38), residues: 506 helix: 4.13 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.05 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 292 TYR 0.008 0.001 TYR U 30 PHE 0.007 0.001 PHE U 232 TRP 0.008 0.001 TRP U 53 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 ( 4384) covalent geometry : angle 0.54978 / 0.30 ( 5862) hydrogen bonds : bond 0.07164 / 4.76 ( 333) hydrogen bonds : angle 3.01162 / 2.30 ( 999) *********************** 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 62 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.160 Fit side-chains REVERT: U 51 GLN cc_start: 0.8589 (tp40) cc_final: 0.8325 (tm-30) REVERT: U 70 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7976 (mt-10) REVERT: U 147 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7896 (tm-30) REVERT: U 292 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7568 (ttp80) REVERT: A 55 GLU cc_start: 0.8811 (tp30) cc_final: 0.8487 (tp30) REVERT: A 59 GLN cc_start: 0.8766 (tp40) cc_final: 0.8489 (tp40) outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.6325 time to fit residues: 39.8329 Evaluate side-chains 65 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 60 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 247 GLN 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 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.073851 restraints weight = 6728.727| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.50 r_work: 0.2739 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4384 Z= 0.156 Angle : 0.587 7.890 5862 Z= 0.319 Chirality : 0.034 0.141 634 Planarity : 0.004 0.050 714 Dihedral : 7.442 51.595 686 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.15 % Allowed : 15.67 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.85 (0.38), residues: 506 helix: 4.12 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.06 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 292 TYR 0.008 0.001 TYR U 30 PHE 0.007 0.001 PHE U 232 TRP 0.008 0.001 TRP A 53 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 ( 4384) covalent geometry : angle 0.58672 / 0.32 ( 5862) hydrogen bonds : bond 0.07158 / 4.76 ( 333) hydrogen bonds : angle 3.00254 / 2.30 ( 999) *********************** 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 : 0.169 Fit side-chains REVERT: U 51 GLN cc_start: 0.8592 (tp40) cc_final: 0.8323 (tm-30) REVERT: U 70 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7958 (mt-10) REVERT: U 147 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7879 (tm-30) REVERT: A 54 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8444 (tm-30) REVERT: A 55 GLU cc_start: 0.8809 (tp30) cc_final: 0.8548 (tp30) REVERT: A 59 GLN cc_start: 0.8732 (tp40) cc_final: 0.8494 (tp40) outliers start: 5 outliers final: 6 residues processed: 63 average time/residue: 0.7482 time to fit residues: 48.4060 Evaluate side-chains 58 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 247 GLN 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: 0.9980 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.073650 restraints weight = 6666.663| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.48 r_work: 0.2738 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3100 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= 0.158 Angle : 0.587 8.211 5862 Z= 0.318 Chirality : 0.034 0.158 634 Planarity : 0.004 0.056 714 Dihedral : 7.405 51.950 686 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.90 (0.38), residues: 506 helix: 4.15 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.05 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG U 292 TYR 0.008 0.001 TYR U 229 PHE 0.007 0.001 PHE U 232 TRP 0.008 0.001 TRP U 53 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 ( 4384) covalent geometry : angle 0.58685 / 0.32 ( 5862) hydrogen bonds : bond 0.07186 / 4.78 ( 333) hydrogen bonds : angle 3.00913 / 2.30 ( 999) ********************** 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 55 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.176 Fit side-chains REVERT: U 51 GLN cc_start: 0.8583 (tp40) cc_final: 0.8329 (tm-30) REVERT: U 70 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7982 (mt-10) REVERT: U 147 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7875 (tm-30) REVERT: U 292 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7462 (tmm-80) REVERT: A 55 GLU cc_start: 0.8814 (tp30) cc_final: 0.8507 (tp30) REVERT: A 59 GLN cc_start: 0.8708 (tp40) cc_final: 0.8486 (tp40) outliers start: 5 outliers final: 5 residues processed: 55 average time/residue: 0.6400 time to fit residues: 36.3090 Evaluate side-chains 60 residues out of total 434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 247 GLN 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 4 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.072053 restraints weight = 6629.724| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.45 r_work: 0.2703 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4384 Z= 0.169 Angle : 0.603 8.096 5862 Z= 0.327 Chirality : 0.035 0.175 634 Planarity : 0.003 0.049 714 Dihedral : 7.641 51.763 686 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.15 % Allowed : 15.67 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.82 (0.38), residues: 506 helix: 4.10 (0.24), residues: 404 sheet: None (None), residues: 0 loop : -1.11 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG U 292 TYR 0.009 0.001 TYR U 229 PHE 0.008 0.001 PHE A 97 TRP 0.007 0.001 TRP A 53 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 ( 4384) covalent geometry : angle 0.60255 / 0.33 ( 5862) hydrogen bonds : bond 0.07696 / 5.13 ( 333) hydrogen bonds : angle 3.10277 / 2.37 ( 999) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1873.31 seconds wall clock time: 32 minutes 38.01 seconds (1958.01 seconds total)