Starting phenix.real_space_refine on Thu Jul 2 01:10:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c07_45075/07_2026/9c07_45075_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c07_45075/07_2026/9c07_45075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c07_45075/07_2026/9c07_45075_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c07_45075/07_2026/9c07_45075_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c07_45075/07_2026/9c07_45075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c07_45075/07_2026/9c07_45075.map" } resolution = 2.73 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= 0.003 sd= 0.016 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 3050 2.51 5 N 708 2.21 5 O 722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 4512 Number of models: 1 Model: "" Number of chains: 4 Chain: "U" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2108 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain breaks: 1 Chain: "A" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2108 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain breaks: 1 Chain: "U" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 148 Unusual residues: {'D12': 4, 'EIC': 1, 'HEX': 8, 'OCT': 4} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 144 Ad-hoc single atom residues: {' K': 4} Unusual residues: {'D12': 2, 'EIC': 1, 'HEX': 6, 'OCT': 4, 'R16': 2} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain breaks: 4 Time building chain proxies: 1.03, per 1000 atoms: 0.23 Number of scatterers: 4512 At special positions: 0 Unit cell: (67.635, 85.17, 98.53, 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 722 8.00 N 708 7.00 C 3050 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: 0.27 Conformation dependent library (CDL) restraints added in 89.3 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'U' and resid 14 through 65 removed outlier: 5.455A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N HIS U 45 " --> pdb=" O LEU U 41 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS U 64 " --> pdb=" O PHE U 60 " (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 124 through 166 Proline residue: U 136 - end of helix removed outlier: 3.710A pdb=" N ARG U 166 " --> pdb=" O GLN U 162 " (cutoff:3.500A) Processing helix chain 'U' and resid 193 through 215 removed outlier: 3.781A 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 295 removed outlier: 3.706A pdb=" N PHE U 259 " --> pdb=" O GLY U 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 64 removed outlier: 5.451A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.240A 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 124 through 166 Proline residue: A 136 - end of helix removed outlier: 3.689A pdb=" N ARG A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 220 removed outlier: 3.518A 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: 3.798A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 1005 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: 0.38 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 757 1.33 - 1.45: 1208 1.45 - 1.57: 2577 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4582 Sorted by residual: bond pdb=" N ILE U 219 " pdb=" CA ILE U 219 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.71e+00 bond pdb=" N HIS U 250 " pdb=" CA HIS U 250 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.28e-02 6.10e+03 4.82e+00 bond pdb=" N TRP U 289 " pdb=" CA TRP U 289 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.79e+00 bond pdb=" N TYR U 251 " pdb=" CA TYR U 251 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.44e-02 4.82e+03 4.53e+00 bond pdb=" C1 EIC U 414 " pdb=" O2 EIC U 414 " ideal model delta sigma weight residual 1.250 1.208 0.042 2.00e-02 2.50e+03 4.51e+00 ... (remaining 4577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 5924 1.61 - 3.21: 122 3.21 - 4.82: 23 4.82 - 6.43: 4 6.43 - 8.03: 3 Bond angle restraints: 6076 Sorted by residual: angle pdb=" CA TYR U 216 " pdb=" CB TYR U 216 " pdb=" CG TYR U 216 " ideal model delta sigma weight residual 113.90 121.00 -7.10 1.80e+00 3.09e-01 1.55e+01 angle pdb=" N TYR U 216 " pdb=" CA TYR U 216 " pdb=" C TYR U 216 " ideal model delta sigma weight residual 113.28 107.13 6.15 1.57e+00 4.06e-01 1.53e+01 angle pdb=" C MET U 215 " pdb=" N TYR U 216 " pdb=" CA TYR U 216 " ideal model delta sigma weight residual 126.45 119.68 6.77 1.77e+00 3.19e-01 1.46e+01 angle pdb=" N GLU A 252 " pdb=" CA GLU A 252 " pdb=" C GLU A 252 " ideal model delta sigma weight residual 110.80 102.77 8.03 2.13e+00 2.20e-01 1.42e+01 angle pdb=" N ASN A 288 " pdb=" CA ASN A 288 " pdb=" C ASN A 288 " ideal model delta sigma weight residual 111.07 107.44 3.63 1.07e+00 8.73e-01 1.15e+01 ... (remaining 6071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.96: 2340 11.96 - 23.91: 216 23.91 - 35.87: 67 35.87 - 47.82: 36 47.82 - 59.78: 21 Dihedral angle restraints: 2680 sinusoidal: 1162 harmonic: 1518 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 180.00 153.68 26.32 0 5.00e+00 4.00e-02 2.77e+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 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+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 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 2677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 476 0.033 - 0.066: 117 0.066 - 0.099: 33 0.099 - 0.132: 13 0.132 - 0.164: 7 Chirality restraints: 646 Sorted by residual: chirality pdb=" CA THR U 110 " pdb=" N THR U 110 " pdb=" C THR U 110 " pdb=" CB THR U 110 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CA ALA U 249 " pdb=" N ALA U 249 " pdb=" C ALA U 249 " pdb=" CB ALA U 249 " both_signs ideal model delta sigma weight residual False 2.48 2.65 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CB THR U 110 " pdb=" CA THR U 110 " pdb=" OG1 THR U 110 " pdb=" CG2 THR U 110 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 643 not shown) Planarity restraints: 732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG U 68 " 0.274 9.50e-02 1.11e+02 1.23e-01 9.24e+00 pdb=" NE ARG U 68 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG U 68 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG U 68 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG U 68 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR U 110 " -0.009 2.00e-02 2.50e+03 1.94e-02 3.74e+00 pdb=" C THR U 110 " 0.033 2.00e-02 2.50e+03 pdb=" O THR U 110 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE U 111 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 110 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C THR A 110 " 0.026 2.00e-02 2.50e+03 pdb=" O THR A 110 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE A 111 " -0.009 2.00e-02 2.50e+03 ... (remaining 729 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 1490 2.84 - 3.42: 4985 3.42 - 3.99: 7754 3.99 - 4.57: 11582 4.57 - 5.14: 16725 Nonbonded interactions: 42536 Sorted by model distance: nonbonded pdb=" OE2 GLU U 220 " pdb=" OH TYR U 257 " model vdw 2.267 3.040 nonbonded pdb=" O SER U 109 " pdb=" OG1 THR U 110 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR U 78 " pdb=" OE2 GLU A 79 " model vdw 2.373 3.040 nonbonded pdb=" O ASN A 277 " pdb=" OG SER A 280 " model vdw 2.384 3.040 nonbonded pdb=" NH1 ARG A 19 " pdb=" OD1 ASN A 288 " model vdw 2.392 3.120 ... (remaining 42531 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 295 or resid 408 or resid 410 through 414)) selection = (chain 'U' and (resid 14 through 295 or resid 408 or resid 410 through 414)) } 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: 1.480 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.260 Find NCS groups from input model: 0.050 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 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 0.042 4582 Z= 0.227 Angle : 0.583 8.031 6076 Z= 0.353 Chirality : 0.038 0.164 646 Planarity : 0.005 0.123 732 Dihedral : 12.727 59.778 1708 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.23 % Allowed : 3.60 % Favored : 96.17 % 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: 4.88 (0.39), residues: 516 helix: 4.11 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -1.19 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 19 TYR 0.010 0.001 TYR A 30 PHE 0.011 0.001 PHE A 232 TRP 0.010 0.001 TRP A 53 HIS 0.002 0.001 HIS U 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.23 ( 4582) covalent geometry : angle 0.58309 / 0.35 ( 6076) hydrogen bonds : bond 0.10002 / 5.93 ( 335) hydrogen bonds : angle 3.54219 / 2.56 ( 1005) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: U 59 GLN cc_start: 0.8808 (tp40) cc_final: 0.8494 (tm-30) REVERT: A 162 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8502 (tm130) outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.8700 time to fit residues: 57.8552 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.087790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.068653 restraints weight = 8686.426| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.49 r_work: 0.2704 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4582 Z= 0.134 Angle : 0.516 5.320 6076 Z= 0.277 Chirality : 0.034 0.146 646 Planarity : 0.003 0.024 732 Dihedral : 11.983 59.244 772 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.90 % Allowed : 8.56 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 5.01 (0.38), residues: 516 helix: 4.12 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.71 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG U 292 TYR 0.018 0.001 TYR A 155 PHE 0.008 0.001 PHE U 262 TRP 0.009 0.001 TRP U 95 HIS 0.003 0.001 HIS U 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4582) covalent geometry : angle 0.51571 / 0.28 ( 6076) hydrogen bonds : bond 0.05412 / 3.63 ( 335) hydrogen bonds : angle 2.90223 / 2.14 ( 1005) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.177 Fit side-chains REVERT: U 51 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7905 (tm-30) REVERT: U 65 GLN cc_start: 0.7794 (mp10) cc_final: 0.7540 (mp10) REVERT: U 155 TYR cc_start: 0.7875 (t80) cc_final: 0.7477 (m-80) REVERT: A 155 TYR cc_start: 0.7932 (t80) cc_final: 0.7503 (t80) REVERT: A 162 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8688 (tm-30) outliers start: 4 outliers final: 0 residues processed: 41 average time/residue: 0.7789 time to fit residues: 32.8652 Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.089579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.070635 restraints weight = 8637.553| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.44 r_work: 0.2760 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4582 Z= 0.113 Angle : 0.453 4.842 6076 Z= 0.245 Chirality : 0.033 0.131 646 Planarity : 0.003 0.022 732 Dihedral : 10.252 59.539 772 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 5.05 (0.38), residues: 516 helix: 4.15 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.69 (0.69), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 292 TYR 0.013 0.001 TYR A 155 PHE 0.008 0.001 PHE A 262 TRP 0.010 0.001 TRP U 95 HIS 0.004 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 4582) covalent geometry : angle 0.45323 / 0.24 ( 6076) hydrogen bonds : bond 0.04710 / 3.17 ( 335) hydrogen bonds : angle 2.73560 / 2.01 ( 1005) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.161 Fit side-chains REVERT: U 51 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7956 (tm-30) REVERT: U 65 GLN cc_start: 0.7696 (mp10) cc_final: 0.7346 (mp-120) REVERT: U 155 TYR cc_start: 0.7788 (t80) cc_final: 0.7460 (t80) REVERT: A 65 GLN cc_start: 0.7708 (pm20) cc_final: 0.7495 (pm20) REVERT: A 155 TYR cc_start: 0.7793 (t80) cc_final: 0.7337 (t80) REVERT: A 162 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8691 (tm-30) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.7852 time to fit residues: 33.1588 Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.0040 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.071840 restraints weight = 8514.692| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.46 r_work: 0.2758 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4582 Z= 0.109 Angle : 0.436 4.879 6076 Z= 0.237 Chirality : 0.032 0.126 646 Planarity : 0.002 0.021 732 Dihedral : 9.126 58.506 772 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % 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: 5.07 (0.38), residues: 516 helix: 4.21 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -0.80 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG U 292 TYR 0.011 0.001 TYR A 155 PHE 0.007 0.001 PHE U 232 TRP 0.008 0.001 TRP U 95 HIS 0.002 0.000 HIS U 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 4582) covalent geometry : angle 0.43630 / 0.24 ( 6076) hydrogen bonds : bond 0.04565 / 3.09 ( 335) hydrogen bonds : angle 2.68498 / 1.98 ( 1005) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.200 Fit side-chains REVERT: U 51 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7900 (tm-30) REVERT: U 65 GLN cc_start: 0.7682 (mp10) cc_final: 0.7430 (mp10) REVERT: U 155 TYR cc_start: 0.7820 (t80) cc_final: 0.7436 (t80) REVERT: A 155 TYR cc_start: 0.7775 (t80) cc_final: 0.7352 (t80) outliers start: 0 outliers final: 1 residues processed: 40 average time/residue: 0.8537 time to fit residues: 35.1646 Evaluate side-chains 40 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.069003 restraints weight = 8719.080| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.50 r_work: 0.2696 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4582 Z= 0.128 Angle : 0.455 4.959 6076 Z= 0.249 Chirality : 0.033 0.129 646 Planarity : 0.002 0.020 732 Dihedral : 8.957 59.444 772 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.13 % Allowed : 10.36 % Favored : 88.51 % 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: 5.07 (0.38), residues: 516 helix: 4.22 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -0.82 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 292 TYR 0.010 0.001 TYR A 155 PHE 0.008 0.001 PHE A 262 TRP 0.007 0.001 TRP U 95 HIS 0.002 0.000 HIS U 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4582) covalent geometry : angle 0.45538 / 0.25 ( 6076) hydrogen bonds : bond 0.05017 / 3.39 ( 335) hydrogen bonds : angle 2.75389 / 2.04 ( 1005) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.199 Fit side-chains REVERT: U 51 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7906 (tm-30) REVERT: U 65 GLN cc_start: 0.7728 (mp10) cc_final: 0.7366 (mp-120) REVERT: U 155 TYR cc_start: 0.7839 (t80) cc_final: 0.7455 (t80) REVERT: A 155 TYR cc_start: 0.7813 (t80) cc_final: 0.7375 (t80) outliers start: 5 outliers final: 0 residues processed: 44 average time/residue: 0.7857 time to fit residues: 35.6347 Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 4.9990 chunk 7 optimal weight: 0.0050 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.089293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.070431 restraints weight = 8743.217| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.45 r_work: 0.2733 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4582 Z= 0.118 Angle : 0.476 5.465 6076 Z= 0.262 Chirality : 0.032 0.126 646 Planarity : 0.002 0.020 732 Dihedral : 8.428 59.052 772 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.45 % Allowed : 11.49 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.10 (0.38), residues: 516 helix: 4.18 (0.24), residues: 416 sheet: None (None), residues: 0 loop : -0.65 (0.70), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 292 TYR 0.008 0.001 TYR A 155 PHE 0.007 0.001 PHE U 232 TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 4582) covalent geometry : angle 0.47600 / 0.26 ( 6076) hydrogen bonds : bond 0.04745 / 3.20 ( 335) hydrogen bonds : angle 2.69843 / 1.99 ( 1005) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.165 Fit side-chains REVERT: U 51 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7892 (tm-30) REVERT: U 65 GLN cc_start: 0.7728 (mp10) cc_final: 0.7439 (mp10) REVERT: U 155 TYR cc_start: 0.7872 (t80) cc_final: 0.7465 (t80) REVERT: A 155 TYR cc_start: 0.7779 (t80) cc_final: 0.7325 (t80) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.7714 time to fit residues: 33.3438 Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.088699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.069498 restraints weight = 8829.249| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.51 r_work: 0.2739 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4582 Z= 0.124 Angle : 0.494 7.623 6076 Z= 0.267 Chirality : 0.033 0.126 646 Planarity : 0.002 0.019 732 Dihedral : 8.302 58.606 772 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.10 (0.38), residues: 516 helix: 4.24 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -0.84 (0.70), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 292 TYR 0.008 0.001 TYR A 155 PHE 0.008 0.001 PHE U 232 TRP 0.008 0.001 TRP U 95 HIS 0.002 0.000 HIS U 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 4582) covalent geometry : angle 0.49384 / 0.27 ( 6076) hydrogen bonds : bond 0.04845 / 3.27 ( 335) hydrogen bonds : angle 2.71357 / 2.01 ( 1005) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.165 Fit side-chains REVERT: U 51 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7924 (tm-30) REVERT: U 65 GLN cc_start: 0.7751 (mp10) cc_final: 0.7442 (mp10) REVERT: U 155 TYR cc_start: 0.7897 (t80) cc_final: 0.7486 (t80) REVERT: A 155 TYR cc_start: 0.7797 (t80) cc_final: 0.7325 (t80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.7315 time to fit residues: 29.3904 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.069637 restraints weight = 8675.919| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.41 r_work: 0.2734 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4582 Z= 0.126 Angle : 0.498 7.431 6076 Z= 0.269 Chirality : 0.033 0.128 646 Planarity : 0.002 0.019 732 Dihedral : 8.180 57.557 772 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.45 % Allowed : 12.16 % Favored : 87.39 % 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: 5.10 (0.38), residues: 516 helix: 4.24 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -0.83 (0.70), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 292 TYR 0.008 0.001 TYR A 30 PHE 0.008 0.001 PHE U 232 TRP 0.008 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 4582) covalent geometry : angle 0.49784 / 0.27 ( 6076) hydrogen bonds : bond 0.04942 / 3.34 ( 335) hydrogen bonds : angle 2.73043 / 2.02 ( 1005) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.115 Fit side-chains REVERT: U 51 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7913 (tm-30) REVERT: U 65 GLN cc_start: 0.7758 (mp10) cc_final: 0.7448 (mp10) REVERT: A 48 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7697 (mm-40) outliers start: 2 outliers final: 0 residues processed: 40 average time/residue: 0.7350 time to fit residues: 30.2944 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 21 optimal weight: 0.4980 chunk 26 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.071615 restraints weight = 8596.546| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.46 r_work: 0.2771 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 4582 Z= 0.117 Angle : 0.491 7.126 6076 Z= 0.265 Chirality : 0.032 0.125 646 Planarity : 0.002 0.019 732 Dihedral : 7.754 56.196 772 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.23 % Allowed : 12.16 % Favored : 87.61 % 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: 5.15 (0.38), residues: 516 helix: 4.27 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -0.78 (0.71), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 292 TYR 0.007 0.001 TYR A 30 PHE 0.008 0.001 PHE U 232 TRP 0.009 0.001 TRP U 95 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 4582) covalent geometry : angle 0.49073 / 0.26 ( 6076) hydrogen bonds : bond 0.04511 / 3.04 ( 335) hydrogen bonds : angle 2.65305 / 1.96 ( 1005) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.176 Fit side-chains REVERT: U 51 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7864 (tm-30) REVERT: U 65 GLN cc_start: 0.7664 (mp10) cc_final: 0.7375 (mp10) REVERT: A 48 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7650 (mm-40) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.7652 time to fit residues: 29.9761 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.069534 restraints weight = 8679.657| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.46 r_work: 0.2715 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4582 Z= 0.132 Angle : 0.517 7.532 6076 Z= 0.280 Chirality : 0.033 0.131 646 Planarity : 0.002 0.019 732 Dihedral : 7.979 56.000 772 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.23 % Allowed : 12.61 % Favored : 87.16 % 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: 5.15 (0.38), residues: 516 helix: 4.28 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -0.82 (0.70), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 83 TYR 0.008 0.001 TYR A 30 PHE 0.008 0.001 PHE A 262 TRP 0.007 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 4582) covalent geometry : angle 0.51715 / 0.28 ( 6076) hydrogen bonds : bond 0.05009 / 3.38 ( 335) hydrogen bonds : angle 2.74329 / 2.04 ( 1005) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.177 Fit side-chains REVERT: U 51 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7873 (tm-30) REVERT: U 65 GLN cc_start: 0.7710 (mp10) cc_final: 0.7435 (mp10) REVERT: U 155 TYR cc_start: 0.7590 (t80) cc_final: 0.7386 (t80) REVERT: A 48 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7658 (mm-40) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.7584 time to fit residues: 29.7345 Evaluate side-chains 38 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.088054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.069230 restraints weight = 8679.077| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.48 r_work: 0.2707 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4582 Z= 0.133 Angle : 0.516 8.083 6076 Z= 0.279 Chirality : 0.033 0.131 646 Planarity : 0.002 0.019 732 Dihedral : 8.022 55.513 772 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.23 % Allowed : 12.39 % Favored : 87.39 % 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: 5.13 (0.38), residues: 516 helix: 4.26 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -0.82 (0.70), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG U 83 TYR 0.007 0.001 TYR A 30 PHE 0.008 0.001 PHE U 232 TRP 0.007 0.001 TRP U 95 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4582) covalent geometry : angle 0.51583 / 0.28 ( 6076) hydrogen bonds : bond 0.05054 / 3.41 ( 335) hydrogen bonds : angle 2.75076 / 2.04 ( 1005) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1396.93 seconds wall clock time: 24 minutes 37.31 seconds (1477.31 seconds total)