Starting phenix.real_space_refine on Tue Aug 4 12:04:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9v_65790/08_2026/9w9v_65790.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9v_65790/08_2026/9w9v_65790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w9v_65790/08_2026/9w9v_65790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9v_65790/08_2026/9w9v_65790.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w9v_65790/08_2026/9w9v_65790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9v_65790/08_2026/9w9v_65790.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 3 5.16 5 C 1401 2.51 5 N 357 2.21 5 O 399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2160 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 0.78, per 1000 atoms: 0.36 Number of scatterers: 2160 At special positions: 0 Unit cell: (67.89, 85.56, 32.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 3 16.00 O 399 8.00 N 357 7.00 C 1401 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: 0.12 Conformation dependent library (CDL) restraints added in 69.8 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 522 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 43.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 16 removed outlier: 6.583A pdb=" N MET A 13 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL B 16 " --> pdb=" O MET A 13 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 21 removed outlier: 6.214A pdb=" N ALA A 19 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 27 removed outlier: 6.740A pdb=" N ILE A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 34 removed outlier: 6.464A pdb=" N VAL A 30 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE C 33 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL A 32 " --> pdb=" O PHE C 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.234A pdb=" N LYS A 59 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU B 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLU A 61 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU A 62 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.234A pdb=" N VAL A 65 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 71 through 73 removed outlier: 6.379A pdb=" N VAL A 71 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 80 removed outlier: 6.910A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N LYS A 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N TRP C 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR A 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 92 through 99 removed outlier: 6.786A pdb=" N VAL A 93 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR B 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE A 95 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASN B 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA A 97 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 103 through 110 removed outlier: 9.196A pdb=" N ARG A 104 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N ILE B 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N THR A 106 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N ALA B 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ALA A 108 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ARG C 104 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TYR A 105 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR C 106 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 107 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA C 108 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 118 through 122 removed outlier: 5.729A pdb=" N THR A 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL B 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) 32 hydrogen bonds defined for protein. 96 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: 0.29 Time building geometry restraints manager: 0.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 672 1.34 - 1.45: 301 1.45 - 1.57: 1232 1.57 - 1.68: 0 1.68 - 1.79: 6 Bond restraints: 2211 Sorted by residual: bond pdb=" CA SER B 100 " pdb=" C SER B 100 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.47e-02 4.63e+03 5.13e-01 bond pdb=" CA HIS A 90 " pdb=" CB HIS A 90 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.22e-02 6.72e+03 4.92e-01 bond pdb=" CA HIS B 90 " pdb=" CB HIS B 90 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.22e-02 6.72e+03 4.91e-01 bond pdb=" CA HIS C 90 " pdb=" CB HIS C 90 " ideal model delta sigma weight residual 1.524 1.533 -0.008 1.22e-02 6.72e+03 4.55e-01 bond pdb=" CA SER A 100 " pdb=" C SER A 100 " ideal model delta sigma weight residual 1.531 1.521 0.010 1.47e-02 4.63e+03 4.24e-01 ... (remaining 2206 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 2825 1.27 - 2.53: 133 2.53 - 3.80: 30 3.80 - 5.07: 12 5.07 - 6.33: 3 Bond angle restraints: 3003 Sorted by residual: angle pdb=" N SER B 100 " pdb=" CA SER B 100 " pdb=" C SER B 100 " ideal model delta sigma weight residual 107.67 114.00 -6.33 2.11e+00 2.25e-01 9.01e+00 angle pdb=" N SER A 100 " pdb=" CA SER A 100 " pdb=" C SER A 100 " ideal model delta sigma weight residual 107.67 113.96 -6.29 2.11e+00 2.25e-01 8.89e+00 angle pdb=" N SER C 100 " pdb=" CA SER C 100 " pdb=" C SER C 100 " ideal model delta sigma weight residual 107.67 113.95 -6.28 2.11e+00 2.25e-01 8.86e+00 angle pdb=" C GLY A 67 " pdb=" N ILE A 68 " pdb=" CA ILE A 68 " ideal model delta sigma weight residual 121.97 127.03 -5.06 1.80e+00 3.09e-01 7.90e+00 angle pdb=" C GLY C 67 " pdb=" N ILE C 68 " pdb=" CA ILE C 68 " ideal model delta sigma weight residual 121.97 127.02 -5.05 1.80e+00 3.09e-01 7.88e+00 ... (remaining 2998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 1188 15.53 - 31.06: 87 31.06 - 46.58: 21 46.58 - 62.11: 9 62.11 - 77.64: 3 Dihedral angle restraints: 1308 sinusoidal: 501 harmonic: 807 Sorted by residual: dihedral pdb=" CA ARG A 34 " pdb=" CB ARG A 34 " pdb=" CG ARG A 34 " pdb=" CD ARG A 34 " ideal model delta sinusoidal sigma weight residual 180.00 129.22 50.78 3 1.50e+01 4.44e-03 8.94e+00 dihedral pdb=" CA ARG C 34 " pdb=" CB ARG C 34 " pdb=" CG ARG C 34 " pdb=" CD ARG C 34 " ideal model delta sinusoidal sigma weight residual 180.00 129.23 50.77 3 1.50e+01 4.44e-03 8.94e+00 dihedral pdb=" CA ARG B 34 " pdb=" CB ARG B 34 " pdb=" CG ARG B 34 " pdb=" CD ARG B 34 " ideal model delta sinusoidal sigma weight residual 180.00 129.27 50.73 3 1.50e+01 4.44e-03 8.93e+00 ... (remaining 1305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 177 0.025 - 0.049: 83 0.049 - 0.074: 42 0.074 - 0.098: 15 0.098 - 0.123: 34 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE B 73 " pdb=" N ILE B 73 " pdb=" C ILE B 73 " pdb=" CB ILE B 73 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA VAL B 65 " pdb=" N VAL B 65 " pdb=" C VAL B 65 " pdb=" CB VAL B 65 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 348 not shown) Planarity restraints: 369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 100 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.63e+00 pdb=" C SER B 100 " -0.033 2.00e-02 2.50e+03 pdb=" O SER B 100 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 101 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 100 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C SER A 100 " -0.033 2.00e-02 2.50e+03 pdb=" O SER A 100 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY A 101 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 100 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.57e+00 pdb=" C SER C 100 " -0.033 2.00e-02 2.50e+03 pdb=" O SER C 100 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY C 101 " 0.011 2.00e-02 2.50e+03 ... (remaining 366 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 721 2.87 - 3.37: 1641 3.37 - 3.88: 3847 3.88 - 4.39: 3911 4.39 - 4.90: 7548 Nonbonded interactions: 17668 Sorted by model distance: nonbonded pdb=" OH TYR A 114 " pdb=" OG1 THR C 119 " model vdw 2.356 3.040 nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR B 114 " model vdw 2.359 3.040 nonbonded pdb=" NZ LYS B 35 " pdb=" OE2 GLU B 63 " model vdw 2.412 3.120 nonbonded pdb=" NZ LYS A 35 " pdb=" OE2 GLU A 63 " model vdw 2.412 3.120 nonbonded pdb=" NZ LYS C 35 " pdb=" OE2 GLU C 63 " model vdw 2.412 3.120 ... (remaining 17663 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' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.300 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:8.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 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 : 0.003 0.021 2211 Z= 0.140 Angle : 0.716 6.332 3003 Z= 0.406 Chirality : 0.048 0.123 351 Planarity : 0.005 0.030 369 Dihedral : 13.890 77.641 786 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % 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: -3.29 (0.39), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 21 TYR 0.018 0.002 TYR B 114 PHE 0.010 0.001 PHE A 64 TRP 0.003 0.001 TRP A 79 HIS 0.005 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 ( 2211) covalent geometry : angle 0.71566 / 0.41 ( 3003) hydrogen bonds : bond 0.15083 / 10.54 ( 32) hydrogen bonds : angle 9.75710 / 6.53 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.049 Fit side-chains REVERT: A 59 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7874 (ttmt) REVERT: B 59 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8264 (ttmt) REVERT: B 61 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7681 (mt-10) REVERT: B 92 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7398 (tm-30) REVERT: C 13 MET cc_start: 0.7952 (tpt) cc_final: 0.7424 (tpt) REVERT: C 59 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7989 (ttmt) REVERT: C 63 GLU cc_start: 0.8194 (tt0) cc_final: 0.7937 (tt0) REVERT: C 104 ARG cc_start: 0.8070 (mtt180) cc_final: 0.7858 (mtp85) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.6788 time to fit residues: 26.1094 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 0.0050 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.129203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113839 restraints weight = 2497.554| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.77 r_work: 0.3488 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2211 Z= 0.099 Angle : 0.485 3.866 3003 Z= 0.268 Chirality : 0.046 0.119 351 Planarity : 0.004 0.023 369 Dihedral : 4.514 17.447 297 Min Nonbonded Distance : 2.676 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.82 % Favored : 92.80 % Rotamer: Outliers : 1.28 % Allowed : 15.38 % Favored : 83.33 % 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: -3.08 (0.41), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.31), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 34 TYR 0.015 0.001 TYR A 114 PHE 0.007 0.001 PHE A 95 TRP 0.002 0.001 TRP B 79 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 2211) covalent geometry : angle 0.48468 / 0.27 ( 3003) hydrogen bonds : bond 0.02221 / 1.56 ( 32) hydrogen bonds : angle 5.72941 / 3.82 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.053 Fit side-chains REVERT: A 59 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7894 (ttpt) REVERT: B 61 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7662 (mt-10) REVERT: B 74 ASP cc_start: 0.8792 (t0) cc_final: 0.8531 (t0) REVERT: B 92 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7444 (tm-30) REVERT: C 59 LYS cc_start: 0.8350 (ttmt) cc_final: 0.7950 (ttmt) REVERT: C 63 GLU cc_start: 0.8416 (tt0) cc_final: 0.8160 (tt0) REVERT: C 92 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7816 (tm-30) outliers start: 3 outliers final: 0 residues processed: 42 average time/residue: 0.7195 time to fit residues: 30.6328 Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 0.0770 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 overall best weight: 3.0944 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.119739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.103430 restraints weight = 2620.129| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.80 r_work: 0.3346 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2211 Z= 0.180 Angle : 0.589 4.114 3003 Z= 0.327 Chirality : 0.048 0.126 351 Planarity : 0.004 0.026 369 Dihedral : 5.016 20.104 297 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.28 % Allowed : 15.81 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.14 (0.40), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 34 TYR 0.019 0.002 TYR A 114 PHE 0.010 0.002 PHE A 95 TRP 0.004 0.001 TRP B 79 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 ( 2211) covalent geometry : angle 0.58854 / 0.33 ( 3003) hydrogen bonds : bond 0.02564 / 1.80 ( 32) hydrogen bonds : angle 5.36405 / 3.65 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.050 Fit side-chains REVERT: A 59 LYS cc_start: 0.8444 (ttmt) cc_final: 0.7979 (tttt) REVERT: A 62 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8133 (tt0) REVERT: B 61 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7717 (mt-10) REVERT: C 59 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8278 (tttt) REVERT: C 63 GLU cc_start: 0.8404 (tt0) cc_final: 0.8133 (tt0) outliers start: 3 outliers final: 0 residues processed: 43 average time/residue: 0.7887 time to fit residues: 34.3865 Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.113571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.097205 restraints weight = 2644.042| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.78 r_work: 0.3273 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 2211 Z= 0.317 Angle : 0.732 4.378 3003 Z= 0.406 Chirality : 0.053 0.128 351 Planarity : 0.004 0.030 369 Dihedral : 5.630 21.280 297 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.43 % Allowed : 17.95 % Favored : 81.62 % 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: -3.30 (0.38), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.29), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 103 TYR 0.026 0.003 TYR C 114 PHE 0.014 0.003 PHE B 87 TRP 0.006 0.002 TRP C 79 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.32 ( 2211) covalent geometry : angle 0.73247 / 0.41 ( 3003) hydrogen bonds : bond 0.02765 / 1.91 ( 32) hydrogen bonds : angle 5.48667 / 3.74 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.091 Fit side-chains REVERT: A 59 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8224 (tttt) REVERT: B 35 LYS cc_start: 0.8558 (tttt) cc_final: 0.8325 (tttp) REVERT: B 59 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8291 (ttpt) REVERT: B 61 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7690 (mt-10) REVERT: C 59 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8274 (ttmt) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.8546 time to fit residues: 36.4033 Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.118181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.102169 restraints weight = 2617.937| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.78 r_work: 0.3351 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2211 Z= 0.164 Angle : 0.571 4.143 3003 Z= 0.314 Chirality : 0.048 0.125 351 Planarity : 0.003 0.032 369 Dihedral : 5.205 20.589 297 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.43 % Allowed : 17.52 % Favored : 82.05 % 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: -3.26 (0.39), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 34 TYR 0.020 0.002 TYR A 114 PHE 0.009 0.002 PHE A 95 TRP 0.002 0.001 TRP C 79 HIS 0.003 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 2211) covalent geometry : angle 0.57074 / 0.31 ( 3003) hydrogen bonds : bond 0.02106 / 1.46 ( 32) hydrogen bonds : angle 5.16637 / 3.55 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.086 Fit side-chains REVERT: A 59 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8189 (tttt) REVERT: B 35 LYS cc_start: 0.8539 (tttt) cc_final: 0.8289 (tttp) REVERT: B 59 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8155 (ttpt) REVERT: B 62 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8186 (tt0) REVERT: C 59 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8155 (ttmt) REVERT: C 66 GLU cc_start: 0.8516 (tt0) cc_final: 0.8281 (tm-30) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.7850 time to fit residues: 34.2400 Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 0.0070 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.123303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107722 restraints weight = 2566.381| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.75 r_work: 0.3409 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2211 Z= 0.105 Angle : 0.498 4.040 3003 Z= 0.273 Chirality : 0.046 0.123 351 Planarity : 0.003 0.025 369 Dihedral : 4.684 18.895 297 Min Nonbonded Distance : 2.671 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.33 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 18.38 % Favored : 81.62 % 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: -3.18 (0.39), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 34 TYR 0.016 0.001 TYR A 114 PHE 0.007 0.001 PHE A 95 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 2211) covalent geometry : angle 0.49758 / 0.27 ( 3003) hydrogen bonds : bond 0.01721 / 1.21 ( 32) hydrogen bonds : angle 4.89506 / 3.38 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.053 Fit side-chains REVERT: A 59 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8093 (tttt) REVERT: C 59 LYS cc_start: 0.8404 (ttmt) cc_final: 0.8009 (tttt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.8235 time to fit residues: 32.5744 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 3 optimal weight: 0.0010 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.117703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.101931 restraints weight = 2450.614| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.73 r_work: 0.3367 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2211 Z= 0.167 Angle : 0.572 4.073 3003 Z= 0.316 Chirality : 0.047 0.124 351 Planarity : 0.003 0.033 369 Dihedral : 4.964 20.620 297 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 18.38 % Favored : 81.62 % 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: -3.18 (0.39), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 34 TYR 0.020 0.002 TYR A 114 PHE 0.009 0.002 PHE A 95 TRP 0.002 0.001 TRP A 79 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 2211) covalent geometry : angle 0.57183 / 0.32 ( 3003) hydrogen bonds : bond 0.01974 / 1.39 ( 32) hydrogen bonds : angle 4.96406 / 3.41 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.089 Fit side-chains REVERT: A 59 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8098 (tttt) REVERT: B 61 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7752 (mt-10) REVERT: B 76 LYS cc_start: 0.8850 (mttp) cc_final: 0.8634 (mttt) REVERT: C 59 LYS cc_start: 0.8480 (ttmt) cc_final: 0.8107 (tttt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.7613 time to fit residues: 30.9209 Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.115272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100347 restraints weight = 2518.719| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.64 r_work: 0.3320 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2211 Z= 0.231 Angle : 0.635 4.173 3003 Z= 0.351 Chirality : 0.049 0.126 351 Planarity : 0.004 0.036 369 Dihedral : 5.296 21.076 297 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 19.23 % Favored : 80.77 % 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: -3.16 (0.39), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 34 TYR 0.023 0.002 TYR A 114 PHE 0.011 0.002 PHE B 95 TRP 0.004 0.001 TRP C 79 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.23 ( 2211) covalent geometry : angle 0.63530 / 0.35 ( 3003) hydrogen bonds : bond 0.02219 / 1.54 ( 32) hydrogen bonds : angle 5.13902 / 3.52 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.088 Fit side-chains REVERT: A 59 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8188 (tttt) REVERT: B 62 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8241 (tt0) REVERT: C 66 GLU cc_start: 0.8523 (tt0) cc_final: 0.8283 (tm-30) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.5479 time to fit residues: 22.2703 Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 0.0000 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.119649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104249 restraints weight = 2420.250| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.73 r_work: 0.3391 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2211 Z= 0.122 Angle : 0.529 4.052 3003 Z= 0.291 Chirality : 0.047 0.124 351 Planarity : 0.003 0.035 369 Dihedral : 4.897 19.751 297 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.43 % Allowed : 20.09 % Favored : 79.49 % 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: -3.11 (0.40), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.018 0.002 TYR A 114 PHE 0.008 0.001 PHE A 95 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 ( 2211) covalent geometry : angle 0.52930 / 0.29 ( 3003) hydrogen bonds : bond 0.01862 / 1.30 ( 32) hydrogen bonds : angle 4.93402 / 3.37 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.083 Fit side-chains REVERT: A 59 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8145 (tttt) REVERT: B 62 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8267 (tt0) REVERT: C 59 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8183 (tttt) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.8666 time to fit residues: 33.3904 Evaluate side-chains 37 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.114943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.099445 restraints weight = 2589.994| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.74 r_work: 0.3319 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2211 Z= 0.216 Angle : 0.673 11.807 3003 Z= 0.359 Chirality : 0.049 0.125 351 Planarity : 0.004 0.038 369 Dihedral : 5.290 21.128 297 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.43 % Allowed : 20.09 % Favored : 79.49 % 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: -3.15 (0.39), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.022 0.002 TYR A 114 PHE 0.010 0.002 PHE B 95 TRP 0.003 0.001 TRP C 79 HIS 0.004 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 ( 2211) covalent geometry : angle 0.67295 / 0.36 ( 3003) hydrogen bonds : bond 0.02251 / 1.56 ( 32) hydrogen bonds : angle 5.08578 / 3.48 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.087 Fit side-chains REVERT: A 59 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8185 (tttt) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.6493 time to fit residues: 25.0567 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.3701 r_free = 0.3701 target = 0.118683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.103492 restraints weight = 2565.217| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.69 r_work: 0.3399 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2211 Z= 0.122 Angle : 0.576 10.228 3003 Z= 0.305 Chirality : 0.047 0.124 351 Planarity : 0.003 0.035 369 Dihedral : 4.981 19.661 297 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.95 % Favored : 91.67 % Rotamer: Outliers : 0.43 % Allowed : 18.80 % Favored : 80.77 % 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: -3.14 (0.39), residues: 264 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.30), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.017 0.002 TYR A 114 PHE 0.008 0.001 PHE A 95 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 2211) covalent geometry : angle 0.57638 / 0.31 ( 3003) hydrogen bonds : bond 0.01871 / 1.31 ( 32) hydrogen bonds : angle 4.91871 / 3.36 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1089.29 seconds wall clock time: 19 minutes 16.57 seconds (1156.57 seconds total)