Starting phenix.real_space_refine on Tue Aug 4 12:03:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w9l_65781/08_2026/9w9l_65781.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w9l_65781/08_2026/9w9l_65781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w9l_65781/08_2026/9w9l_65781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w9l_65781/08_2026/9w9l_65781.map" model { file = "/net/cci-nas-00/data/ceres_data/9w9l_65781/08_2026/9w9l_65781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w9l_65781/08_2026/9w9l_65781.cif" } resolution = 2.7 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= 0.002 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 6 5.16 5 C 1380 2.51 5 N 351 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 6 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: 2136 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "B" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "C" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Time building chain proxies: 0.50, per 1000 atoms: 0.23 Number of scatterers: 2136 At special positions: 0 Unit cell: (84.63, 68.82, 31.62, 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 6 16.00 O 399 8.00 N 351 7.00 C 1380 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: 0.09 Conformation dependent library (CDL) restraints added in 48.4 milliseconds 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 16 removed outlier: 6.243A pdb=" N VAL A 14 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 34 removed outlier: 6.918A pdb=" N ILE A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ALA C 29 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 28 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N HIS C 31 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET A 30 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE C 33 " --> pdb=" O MET A 30 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 32 " --> pdb=" O PHE C 33 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.246A pdb=" N THR A 60 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 73 removed outlier: 6.264A pdb=" N GLU A 72 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 removed outlier: 6.895A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N LYS A 76 " --> pdb=" O SER C 77 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N TRP C 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TYR A 78 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 91 through 98 removed outlier: 6.357A pdb=" N GLU A 92 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE C 95 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL A 94 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ALA C 97 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N THR A 96 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 110 removed outlier: 6.839A pdb=" N ALA A 109 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 110 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG A 104 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ILE C 107 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR A 106 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ALA C 109 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ALA A 108 " --> pdb=" O ALA C 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 122 removed outlier: 5.724A pdb=" N THR A 118 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL B 121 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA A 120 " --> pdb=" O VAL B 121 " (cutoff:3.500A) 34 hydrogen bonds defined for protein. 102 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: 0.17 Time building geometry restraints manager: 0.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 659 1.34 - 1.46: 326 1.46 - 1.57: 1187 1.57 - 1.69: 0 1.69 - 1.80: 12 Bond restraints: 2184 Sorted by residual: bond pdb=" N THR A 59 " pdb=" CA THR A 59 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.29e+00 bond pdb=" N THR B 59 " pdb=" CA THR B 59 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.28e+00 bond pdb=" N THR C 59 " pdb=" CA THR C 59 " ideal model delta sigma weight residual 1.458 1.488 -0.029 1.19e-02 7.06e+03 6.09e+00 bond pdb=" N LEU B 58 " pdb=" CA LEU B 58 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.84e+00 bond pdb=" N LEU C 58 " pdb=" CA LEU C 58 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.65e+00 ... (remaining 2179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 2684 1.22 - 2.44: 207 2.44 - 3.66: 49 3.66 - 4.87: 20 4.87 - 6.09: 7 Bond angle restraints: 2967 Sorted by residual: angle pdb=" N GLY B 83 " pdb=" CA GLY B 83 " pdb=" C GLY B 83 " ideal model delta sigma weight residual 110.97 115.81 -4.84 1.42e+00 4.96e-01 1.16e+01 angle pdb=" N GLY C 83 " pdb=" CA GLY C 83 " pdb=" C GLY C 83 " ideal model delta sigma weight residual 110.97 115.80 -4.83 1.42e+00 4.96e-01 1.16e+01 angle pdb=" N GLY A 83 " pdb=" CA GLY A 83 " pdb=" C GLY A 83 " ideal model delta sigma weight residual 110.97 115.78 -4.81 1.42e+00 4.96e-01 1.15e+01 angle pdb=" CA TYR B 114 " pdb=" CB TYR B 114 " pdb=" CG TYR B 114 " ideal model delta sigma weight residual 113.90 118.79 -4.89 1.80e+00 3.09e-01 7.38e+00 angle pdb=" CA TYR A 114 " pdb=" CB TYR A 114 " pdb=" CG TYR A 114 " ideal model delta sigma weight residual 113.90 118.76 -4.86 1.80e+00 3.09e-01 7.28e+00 ... (remaining 2962 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.33: 1056 12.33 - 24.66: 155 24.66 - 36.98: 49 36.98 - 49.31: 15 49.31 - 61.64: 12 Dihedral angle restraints: 1287 sinusoidal: 489 harmonic: 798 Sorted by residual: dihedral pdb=" CA GLU C 66 " pdb=" C GLU C 66 " pdb=" N GLY C 67 " pdb=" CA GLY C 67 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU B 66 " pdb=" C GLU B 66 " pdb=" N GLY B 67 " pdb=" CA GLY B 67 " ideal model delta harmonic sigma weight residual 180.00 -160.23 -19.77 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLU A 66 " pdb=" C GLU A 66 " pdb=" N GLY A 67 " pdb=" CA GLY A 67 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 1284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 198 0.035 - 0.069: 74 0.069 - 0.103: 44 0.103 - 0.138: 29 0.138 - 0.172: 3 Chirality restraints: 348 Sorted by residual: chirality pdb=" CA SER A 85 " pdb=" N SER A 85 " pdb=" C SER A 85 " pdb=" CB SER A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA SER C 85 " pdb=" N SER C 85 " pdb=" C SER C 85 " pdb=" CB SER C 85 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" CA SER B 85 " pdb=" N SER B 85 " pdb=" C SER B 85 " pdb=" CB SER B 85 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 345 not shown) Planarity restraints: 366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 114 " 0.011 2.00e-02 2.50e+03 8.78e-03 1.54e+00 pdb=" CG TYR C 114 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 114 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR C 114 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 114 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 114 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 114 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 114 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 31 " 0.012 2.00e-02 2.50e+03 1.01e-02 1.52e+00 pdb=" CG HIS C 31 " -0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS C 31 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS C 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS C 31 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 31 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 31 " 0.012 2.00e-02 2.50e+03 1.01e-02 1.52e+00 pdb=" CG HIS B 31 " -0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS B 31 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS B 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS B 31 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS B 31 " 0.006 2.00e-02 2.50e+03 ... (remaining 363 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 288 2.77 - 3.30: 1899 3.30 - 3.83: 3747 3.83 - 4.37: 4220 4.37 - 4.90: 7997 Nonbonded interactions: 18151 Sorted by model distance: nonbonded pdb=" OH TYR A 69 " pdb=" O ASN C 27 " model vdw 2.237 3.040 nonbonded pdb=" O ASN A 27 " pdb=" OH TYR B 69 " model vdw 2.242 3.040 nonbonded pdb=" NZ LYS B 35 " pdb=" OE1 GLU B 63 " model vdw 2.332 3.120 nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR B 114 " model vdw 2.346 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" OG1 THR C 119 " model vdw 2.347 3.040 ... (remaining 18146 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 2.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 2.640 Find NCS groups from input model: 0.010 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:4.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 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 0.032 2184 Z= 0.234 Angle : 0.843 6.093 2967 Z= 0.489 Chirality : 0.055 0.172 348 Planarity : 0.004 0.020 366 Dihedral : 14.990 61.636 771 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 23.38 % Favored : 76.62 % 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: -3.63 (0.41), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.31), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 34 TYR 0.021 0.002 TYR C 114 PHE 0.016 0.002 PHE A 64 TRP 0.003 0.001 TRP B 79 HIS 0.007 0.002 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.23 ( 2184) covalent geometry : angle 0.84314 / 0.49 ( 2967) hydrogen bonds : bond 0.14608 / 9.05 ( 34) hydrogen bonds : angle 9.62834 / 6.40 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.4763 time to fit residues: 16.9379 Evaluate side-chains 30 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.048 ------------------------------------------------------------------------------- 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: 3.9990 chunk 24 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.119196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.099835 restraints weight = 2633.285| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.02 r_work: 0.3362 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2184 Z= 0.227 Angle : 0.573 3.740 2967 Z= 0.316 Chirality : 0.050 0.134 348 Planarity : 0.004 0.035 366 Dihedral : 5.632 20.270 294 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.87 % Allowed : 21.65 % Favored : 77.49 % 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: -3.50 (0.43), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.016 0.002 TYR A 114 PHE 0.010 0.002 PHE A 64 TRP 0.004 0.001 TRP A 79 HIS 0.004 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 ( 2184) covalent geometry : angle 0.57348 / 0.32 ( 2967) hydrogen bonds : bond 0.02971 / 1.72 ( 34) hydrogen bonds : angle 6.49726 / 4.40 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.056 Fit side-chains REVERT: C 62 GLU cc_start: 0.7473 (pt0) cc_final: 0.7075 (tt0) REVERT: C 104 ARG cc_start: 0.8580 (mtt90) cc_final: 0.8376 (mtt-85) outliers start: 2 outliers final: 1 residues processed: 40 average time/residue: 0.5926 time to fit residues: 24.0442 Evaluate side-chains 39 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.127134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.108905 restraints weight = 2470.943| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.96 r_work: 0.3473 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2184 Z= 0.107 Angle : 0.484 3.862 2967 Z= 0.264 Chirality : 0.048 0.136 348 Planarity : 0.002 0.015 366 Dihedral : 4.849 17.734 294 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.30 % Allowed : 20.78 % Favored : 77.92 % 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: -3.35 (0.43), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.012 0.001 TYR A 114 PHE 0.010 0.002 PHE A 64 TRP 0.001 0.000 TRP B 79 HIS 0.002 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 2184) covalent geometry : angle 0.48367 / 0.26 ( 2967) hydrogen bonds : bond 0.02391 / 1.42 ( 34) hydrogen bonds : angle 6.02270 / 4.08 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.049 Fit side-chains REVERT: A 21 ARG cc_start: 0.8366 (mtp85) cc_final: 0.8100 (mtp85) REVERT: C 62 GLU cc_start: 0.7414 (pt0) cc_final: 0.6994 (tt0) REVERT: C 63 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8486 (mt-10) REVERT: C 104 ARG cc_start: 0.8545 (mtt90) cc_final: 0.8338 (mtt-85) outliers start: 3 outliers final: 3 residues processed: 42 average time/residue: 0.5458 time to fit residues: 23.2531 Evaluate side-chains 41 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain C residue 28 VAL 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 3 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 overall best weight: 2.4144 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.120190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101121 restraints weight = 2518.162| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.91 r_work: 0.3391 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 2184 Z= 0.223 Angle : 0.561 5.001 2967 Z= 0.305 Chirality : 0.050 0.136 348 Planarity : 0.003 0.017 366 Dihedral : 5.416 19.099 294 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.60 % Allowed : 20.35 % Favored : 77.06 % 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: -3.43 (0.42), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.32), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.018 0.002 TYR A 114 PHE 0.011 0.002 PHE A 64 TRP 0.004 0.001 TRP B 79 HIS 0.003 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 ( 2184) covalent geometry : angle 0.56066 / 0.30 ( 2967) hydrogen bonds : bond 0.02576 / 1.54 ( 34) hydrogen bonds : angle 5.88988 / 3.96 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.084 Fit side-chains REVERT: A 21 ARG cc_start: 0.8440 (mtp85) cc_final: 0.8175 (mtp85) REVERT: C 62 GLU cc_start: 0.7478 (pt0) cc_final: 0.7022 (tt0) REVERT: C 104 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8371 (mtt-85) outliers start: 6 outliers final: 6 residues processed: 45 average time/residue: 0.8405 time to fit residues: 38.3746 Evaluate side-chains 47 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 35 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.123543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.105049 restraints weight = 2531.577| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.88 r_work: 0.3442 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 2184 Z= 0.160 Angle : 0.520 4.750 2967 Z= 0.282 Chirality : 0.049 0.136 348 Planarity : 0.002 0.014 366 Dihedral : 5.127 18.416 294 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.60 % Allowed : 20.35 % Favored : 77.06 % 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: -3.41 (0.43), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 34 TYR 0.015 0.002 TYR A 114 PHE 0.010 0.002 PHE A 64 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 2184) covalent geometry : angle 0.52013 / 0.28 ( 2967) hydrogen bonds : bond 0.02344 / 1.40 ( 34) hydrogen bonds : angle 5.74040 / 3.88 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.083 Fit side-chains REVERT: A 21 ARG cc_start: 0.8452 (mtp85) cc_final: 0.8177 (mtp85) REVERT: B 80 LYS cc_start: 0.8656 (tttt) cc_final: 0.8248 (tttt) REVERT: C 62 GLU cc_start: 0.7517 (pt0) cc_final: 0.7036 (tt0) REVERT: C 104 ARG cc_start: 0.8662 (mtt90) cc_final: 0.8393 (mtt-85) outliers start: 6 outliers final: 6 residues processed: 45 average time/residue: 0.7828 time to fit residues: 35.7458 Evaluate side-chains 47 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 35 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.118930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099247 restraints weight = 2499.605| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.00 r_work: 0.3348 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 2184 Z= 0.283 Angle : 0.592 4.308 2967 Z= 0.324 Chirality : 0.051 0.138 348 Planarity : 0.003 0.015 366 Dihedral : 5.742 20.079 294 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.03 % Allowed : 19.05 % Favored : 77.92 % 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: -3.51 (0.42), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.32), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 34 TYR 0.020 0.002 TYR C 114 PHE 0.010 0.003 PHE A 64 TRP 0.005 0.002 TRP B 79 HIS 0.003 0.001 HIS B 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.28 ( 2184) covalent geometry : angle 0.59185 / 0.32 ( 2967) hydrogen bonds : bond 0.02586 / 1.58 ( 34) hydrogen bonds : angle 5.82334 / 3.92 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.086 Fit side-chains REVERT: A 21 ARG cc_start: 0.8476 (mtp85) cc_final: 0.8203 (mtp85) REVERT: C 21 ARG cc_start: 0.6211 (mmt-90) cc_final: 0.5251 (mmt-90) REVERT: C 62 GLU cc_start: 0.7540 (pt0) cc_final: 0.7037 (tt0) REVERT: C 104 ARG cc_start: 0.8682 (mtt90) cc_final: 0.8415 (mtt-85) outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 0.7597 time to fit residues: 36.2571 Evaluate side-chains 48 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 35 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.123332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104858 restraints weight = 2482.323| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.88 r_work: 0.3439 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2184 Z= 0.150 Angle : 0.514 4.100 2967 Z= 0.280 Chirality : 0.049 0.135 348 Planarity : 0.002 0.014 366 Dihedral : 5.159 18.099 294 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.03 % Allowed : 19.91 % Favored : 77.06 % 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: -3.34 (0.43), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 34 TYR 0.014 0.001 TYR A 114 PHE 0.009 0.002 PHE A 64 TRP 0.002 0.001 TRP B 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 2184) covalent geometry : angle 0.51431 / 0.28 ( 2967) hydrogen bonds : bond 0.02290 / 1.39 ( 34) hydrogen bonds : angle 5.70122 / 3.85 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.090 Fit side-chains REVERT: A 21 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8189 (mtp85) REVERT: A 30 MET cc_start: 0.8544 (mtp) cc_final: 0.8315 (mtp) REVERT: B 80 LYS cc_start: 0.8662 (tttt) cc_final: 0.8258 (tttt) REVERT: C 104 ARG cc_start: 0.8620 (mtt90) cc_final: 0.8371 (mtt-85) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.8051 time to fit residues: 36.7876 Evaluate side-chains 46 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 35 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 9 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.128656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.110885 restraints weight = 2433.103| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.92 r_work: 0.3530 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2184 Z= 0.096 Angle : 0.480 4.129 2967 Z= 0.259 Chirality : 0.048 0.135 348 Planarity : 0.002 0.014 366 Dihedral : 4.765 16.584 294 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.16 % Allowed : 20.35 % Favored : 77.49 % 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: -3.20 (0.44), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.010 0.001 TYR A 114 PHE 0.008 0.001 PHE A 64 TRP 0.001 0.000 TRP A 79 HIS 0.002 0.001 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 ( 2184) covalent geometry : angle 0.48003 / 0.26 ( 2967) hydrogen bonds : bond 0.02061 / 1.24 ( 34) hydrogen bonds : angle 5.42946 / 3.63 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.086 Fit side-chains REVERT: A 21 ARG cc_start: 0.8462 (mtp85) cc_final: 0.8186 (mtp85) REVERT: B 80 LYS cc_start: 0.8619 (tttt) cc_final: 0.8208 (ttmt) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.8205 time to fit residues: 36.6101 Evaluate side-chains 45 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain C residue 28 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3809 r_free = 0.3809 target = 0.127256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.109290 restraints weight = 2474.445| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.87 r_work: 0.3518 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2184 Z= 0.109 Angle : 0.486 4.120 2967 Z= 0.263 Chirality : 0.048 0.134 348 Planarity : 0.002 0.015 366 Dihedral : 4.757 16.691 294 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.60 % Allowed : 19.48 % Favored : 77.92 % 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 (0.44), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 34 TYR 0.012 0.001 TYR A 114 PHE 0.008 0.001 PHE A 64 TRP 0.001 0.001 TRP B 79 HIS 0.002 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 2184) covalent geometry : angle 0.48602 / 0.26 ( 2967) hydrogen bonds : bond 0.02104 / 1.26 ( 34) hydrogen bonds : angle 5.29013 / 3.53 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.051 Fit side-chains REVERT: A 21 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8204 (mtp85) REVERT: B 80 LYS cc_start: 0.8611 (tttt) cc_final: 0.8223 (tttt) outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 0.6309 time to fit residues: 29.4642 Evaluate side-chains 46 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 7.9990 chunk 14 optimal weight: 0.0010 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.0470 chunk 13 optimal weight: 0.0010 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 0.0770 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.2048 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.140768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.125036 restraints weight = 2499.005| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.89 r_work: 0.3719 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2184 Z= 0.071 Angle : 0.452 4.201 2967 Z= 0.241 Chirality : 0.047 0.136 348 Planarity : 0.002 0.015 366 Dihedral : 4.210 14.638 294 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.87 % Allowed : 21.21 % Favored : 77.92 % 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 (0.43), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 103 TYR 0.006 0.001 TYR B 78 PHE 0.007 0.001 PHE A 64 TRP 0.003 0.000 TRP C 79 HIS 0.001 0.000 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00154 / 0.07 ( 2184) covalent geometry : angle 0.45245 / 0.24 ( 2967) hydrogen bonds : bond 0.01842 / 1.14 ( 34) hydrogen bonds : angle 5.03256 / 3.33 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 522 Ramachandran restraints generated. 261 Oldfield, 0 Emsley, 261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.106 Fit side-chains REVERT: A 21 ARG cc_start: 0.8520 (mtp85) cc_final: 0.8233 (mtp85) REVERT: B 80 LYS cc_start: 0.8552 (tttt) cc_final: 0.8157 (ttmt) outliers start: 2 outliers final: 2 residues processed: 47 average time/residue: 0.5588 time to fit residues: 26.7040 Evaluate side-chains 41 residues out of total 231 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 28 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.122506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.103068 restraints weight = 2523.818| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.00 r_work: 0.3423 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2184 Z= 0.192 Angle : 0.545 4.024 2967 Z= 0.298 Chirality : 0.050 0.142 348 Planarity : 0.003 0.022 366 Dihedral : 5.044 17.841 294 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 1.30 % Allowed : 22.51 % Favored : 76.19 % 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: -3.14 (0.44), residues: 261 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 104 TYR 0.017 0.002 TYR A 114 PHE 0.010 0.002 PHE A 64 TRP 0.003 0.001 TRP A 79 HIS 0.003 0.001 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 2184) covalent geometry : angle 0.54520 / 0.30 ( 2967) hydrogen bonds : bond 0.02369 / 1.41 ( 34) hydrogen bonds : angle 5.22543 / 3.45 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1050.14 seconds wall clock time: 18 minutes 33.37 seconds (1113.37 seconds total)