Starting phenix.real_space_refine on Tue Aug 4 12:44:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/13br_76947/08_2026/13br_76947.cif Found real_map, /net/cci-nas-00/data/ceres_data/13br_76947/08_2026/13br_76947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/13br_76947/08_2026/13br_76947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/13br_76947/08_2026/13br_76947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/13br_76947/08_2026/13br_76947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/13br_76947/08_2026/13br_76947.map" } resolution = 3.1 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= 0.004 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 14 5.16 5 C 1869 2.51 5 N 479 2.21 5 O 573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 2935 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 749 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 39 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "H" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 899 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 118} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 1287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1287 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain breaks: 3 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 3, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 0.83, per 1000 atoms: 0.28 Number of scatterers: 2935 At special positions: 0 Unit cell: (55.92, 78.288, 89.472, 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 14 16.00 O 573 8.00 N 479 7.00 C 1869 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 166 " distance=2.03 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: 0.13 Conformation dependent library (CDL) restraints added in 64.0 milliseconds 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 698 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 20.1% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'A' and resid 51 through 55 removed outlier: 4.119A pdb=" N ARG A 55 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 88 removed outlier: 4.588A pdb=" N GLN A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 removed outlier: 3.687A pdb=" N GLN A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 164 removed outlier: 4.004A pdb=" N VAL A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.579A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'L' and resid 47 through 49 removed outlier: 6.626A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP L 35 " --> pdb=" O MET L 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 65 through 67 Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 60 removed outlier: 4.861A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 60 removed outlier: 4.861A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL H 93 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.718A pdb=" N GLY A 31 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARG A 40 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A 29 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 15 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 112 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 125 through 126 118 hydrogen bonds defined for protein. 315 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: 0.25 Time building geometry restraints manager: 0.19 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: 934 1.34 - 1.46: 798 1.46 - 1.58: 1249 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3003 Sorted by residual: bond pdb=" N ASP A 90 " pdb=" CA ASP A 90 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.22e-02 6.72e+03 8.09e+00 bond pdb=" N ASN A 89 " pdb=" CA ASN A 89 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.31e+00 bond pdb=" N ASN A 92 " pdb=" CA ASN A 92 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.68e+00 bond pdb=" N SER A 94 " pdb=" CA SER A 94 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 5.84e+00 bond pdb=" N SER A 91 " pdb=" CA SER A 91 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.32e-02 5.74e+03 5.13e+00 ... (remaining 2998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 3997 1.96 - 3.92: 64 3.92 - 5.87: 9 5.87 - 7.83: 3 7.83 - 9.79: 2 Bond angle restraints: 4075 Sorted by residual: angle pdb=" N SER A 91 " pdb=" CA SER A 91 " pdb=" C SER A 91 " ideal model delta sigma weight residual 113.16 108.40 4.76 1.24e+00 6.50e-01 1.48e+01 angle pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" O GLY A 93 " ideal model delta sigma weight residual 121.41 118.19 3.22 8.80e-01 1.29e+00 1.33e+01 angle pdb=" CB MET A 78 " pdb=" CG MET A 78 " pdb=" SD MET A 78 " ideal model delta sigma weight residual 112.70 122.49 -9.79 3.00e+00 1.11e-01 1.06e+01 angle pdb=" N GLY L 85 " pdb=" CA GLY L 85 " pdb=" C GLY L 85 " ideal model delta sigma weight residual 113.18 120.83 -7.65 2.37e+00 1.78e-01 1.04e+01 angle pdb=" N PRO L 96 " pdb=" CA PRO L 96 " pdb=" C PRO L 96 " ideal model delta sigma weight residual 112.47 105.97 6.50 2.06e+00 2.36e-01 9.95e+00 ... (remaining 4070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 1450 17.21 - 34.41: 217 34.41 - 51.62: 66 51.62 - 68.82: 8 68.82 - 86.03: 4 Dihedral angle restraints: 1745 sinusoidal: 643 harmonic: 1102 Sorted by residual: dihedral pdb=" CA THR L 95 " pdb=" C THR L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual 180.00 129.55 50.45 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA PRO L 96 " pdb=" C PRO L 96 " pdb=" N LEU L 97 " pdb=" CA LEU L 97 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA VAL L 84 " pdb=" C VAL L 84 " pdb=" N GLY L 85 " pdb=" CA GLY L 85 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 1742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 285 0.032 - 0.063: 103 0.063 - 0.094: 38 0.094 - 0.126: 12 0.126 - 0.157: 1 Chirality restraints: 439 Sorted by residual: chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA ILE A 13 " pdb=" N ILE A 13 " pdb=" C ILE A 13 " pdb=" CB ILE A 13 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.12e-01 ... (remaining 436 not shown) Planarity restraints: 520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 95 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO L 96 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 89 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C ASN A 89 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN A 89 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP A 90 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR L 70 " -0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+00 pdb=" C THR L 70 " 0.019 2.00e-02 2.50e+03 pdb=" O THR L 70 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP L 71 " -0.006 2.00e-02 2.50e+03 ... (remaining 517 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 261 2.74 - 3.28: 2966 3.28 - 3.82: 4973 3.82 - 4.36: 5861 4.36 - 4.90: 10233 Nonbonded interactions: 24294 Sorted by model distance: nonbonded pdb=" OG SER L 64 " pdb=" O LYS L 75 " model vdw 2.198 3.040 nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 103 " model vdw 2.212 3.040 nonbonded pdb=" OG SER H 54 " pdb=" OD1 ASP A 83 " model vdw 2.262 3.040 nonbonded pdb=" OG SER A 43 " pdb=" OE2 GLU A 74 " model vdw 2.274 3.040 nonbonded pdb=" OD2 ASP A 83 " pdb=" NZ LYS A 147 " model vdw 2.305 3.120 ... (remaining 24289 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.630 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.540 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 5.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 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 0.035 3006 Z= 0.200 Angle : 0.675 9.789 4081 Z= 0.357 Chirality : 0.040 0.157 439 Planarity : 0.004 0.055 520 Dihedral : 17.640 86.029 1038 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.19 % Favored : 90.54 % Rotamer: Outliers : 1.66 % Allowed : 33.77 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.23 (0.42), residues: 370 helix: 0.53 (0.68), residues: 61 sheet: -0.54 (0.50), residues: 112 loop : -2.85 (0.38), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.011 0.001 TYR A 124 PHE 0.011 0.001 PHE H 68 TRP 0.014 0.001 TRP L 36 HIS 0.002 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.20 ( 3003) covalent geometry : angle 0.67396 / 0.36 ( 4075) SS BOND : bond 0.00258 / 0.13 ( 3) SS BOND : angle 1.18012 / 0.86 ( 6) hydrogen bonds : bond 0.25622 / 16.38 ( 105) hydrogen bonds : angle 8.41343 / 5.92 ( 315) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.106 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 55 average time/residue: 0.0602 time to fit residues: 4.1250 Evaluate side-chains 52 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.0470 chunk 2 optimal weight: 0.0270 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.4315 r_free = 0.4315 target = 0.197807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.185557 restraints weight = 3978.917| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 1.89 r_work: 0.4117 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4003 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3006 Z= 0.123 Angle : 0.631 8.751 4081 Z= 0.323 Chirality : 0.041 0.152 439 Planarity : 0.004 0.061 520 Dihedral : 5.884 50.886 420 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 3.97 % Allowed : 31.79 % Favored : 64.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.15 (0.42), residues: 370 helix: 0.94 (0.66), residues: 61 sheet: -0.72 (0.49), residues: 114 loop : -2.79 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.010 0.001 TYR L 50 PHE 0.008 0.001 PHE H 29 TRP 0.014 0.001 TRP L 36 HIS 0.000 0.000 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 3003) covalent geometry : angle 0.63090 / 0.32 ( 4075) SS BOND : bond 0.00153 / 0.08 ( 3) SS BOND : angle 0.91633 / 0.50 ( 6) hydrogen bonds : bond 0.04612 / 2.91 ( 105) hydrogen bonds : angle 6.00802 / 4.36 ( 315) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.107 Fit side-chains REVERT: A 8 TYR cc_start: 0.5432 (m-10) cc_final: 0.5168 (m-10) outliers start: 12 outliers final: 9 residues processed: 62 average time/residue: 0.0565 time to fit residues: 4.3991 Evaluate side-chains 63 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4285 r_free = 0.4285 target = 0.195155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.183104 restraints weight = 4024.703| |-----------------------------------------------------------------------------| r_work (start): 0.4164 rms_B_bonded: 1.87 r_work: 0.4093 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3977 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3006 Z= 0.149 Angle : 0.641 8.272 4081 Z= 0.328 Chirality : 0.041 0.145 439 Planarity : 0.004 0.062 520 Dihedral : 5.947 51.295 420 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 4.97 % Allowed : 33.11 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.27 (0.41), residues: 370 helix: 0.70 (0.63), residues: 61 sheet: -0.88 (0.46), residues: 122 loop : -2.81 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.012 0.002 TYR L 50 PHE 0.009 0.002 PHE A 101 TRP 0.022 0.001 TRP L 36 HIS 0.001 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 3003) covalent geometry : angle 0.64005 / 0.33 ( 4075) SS BOND : bond 0.00230 / 0.12 ( 3) SS BOND : angle 1.06521 / 0.73 ( 6) hydrogen bonds : bond 0.04494 / 2.83 ( 105) hydrogen bonds : angle 5.66764 / 4.11 ( 315) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.064 Fit side-chains REVERT: A 78 MET cc_start: 0.6440 (mmm) cc_final: 0.6071 (mmm) outliers start: 15 outliers final: 15 residues processed: 63 average time/residue: 0.0480 time to fit residues: 3.7448 Evaluate side-chains 67 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 177 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4290 r_free = 0.4290 target = 0.195700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.183342 restraints weight = 4039.756| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 1.92 r_work: 0.4098 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3006 Z= 0.128 Angle : 0.612 7.977 4081 Z= 0.313 Chirality : 0.041 0.153 439 Planarity : 0.004 0.060 520 Dihedral : 5.886 50.594 420 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 6.95 % Allowed : 30.79 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.26 (0.41), residues: 370 helix: 0.74 (0.63), residues: 61 sheet: -0.87 (0.46), residues: 122 loop : -2.82 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.012 0.001 TYR A 124 PHE 0.007 0.002 PHE A 77 TRP 0.014 0.001 TRP L 36 HIS 0.001 0.000 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 3003) covalent geometry : angle 0.61104 / 0.31 ( 4075) SS BOND : bond 0.00199 / 0.10 ( 3) SS BOND : angle 1.21611 / 0.90 ( 6) hydrogen bonds : bond 0.04052 / 2.56 ( 105) hydrogen bonds : angle 5.40920 / 3.91 ( 315) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.105 Fit side-chains REVERT: L 64 SER cc_start: 0.7489 (OUTLIER) cc_final: 0.7155 (p) outliers start: 21 outliers final: 14 residues processed: 69 average time/residue: 0.0386 time to fit residues: 3.3916 Evaluate side-chains 67 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.4235 r_free = 0.4235 target = 0.190401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.178594 restraints weight = 4011.765| |-----------------------------------------------------------------------------| r_work (start): 0.4115 rms_B_bonded: 1.84 r_work: 0.4045 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3006 Z= 0.210 Angle : 0.704 7.936 4081 Z= 0.361 Chirality : 0.044 0.144 439 Planarity : 0.004 0.062 520 Dihedral : 6.484 52.619 420 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.43 % Favored : 87.57 % Rotamer: Outliers : 8.94 % Allowed : 28.15 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.53 (0.40), residues: 370 helix: 0.24 (0.62), residues: 61 sheet: -0.86 (0.45), residues: 121 loop : -3.02 (0.37), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 40 TYR 0.014 0.002 TYR L 50 PHE 0.013 0.002 PHE A 101 TRP 0.015 0.002 TRP L 36 HIS 0.001 0.001 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 ( 3003) covalent geometry : angle 0.70126 / 0.36 ( 4075) SS BOND : bond 0.00672 / 0.32 ( 3) SS BOND : angle 1.62762 / 1.19 ( 6) hydrogen bonds : bond 0.04880 / 3.08 ( 105) hydrogen bonds : angle 5.70095 / 4.12 ( 315) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.076 Fit side-chains REVERT: A 53 LEU cc_start: 0.4915 (OUTLIER) cc_final: 0.4225 (mt) outliers start: 27 outliers final: 20 residues processed: 70 average time/residue: 0.0465 time to fit residues: 4.0814 Evaluate side-chains 72 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 177 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 11 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.192825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.180945 restraints weight = 4036.283| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.87 r_work: 0.4067 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3006 Z= 0.153 Angle : 0.653 7.675 4081 Z= 0.334 Chirality : 0.042 0.155 439 Planarity : 0.004 0.061 520 Dihedral : 6.451 51.936 420 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 6.95 % Allowed : 29.80 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.48 (0.40), residues: 370 helix: 0.47 (0.62), residues: 60 sheet: -0.83 (0.45), residues: 123 loop : -3.06 (0.38), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.011 0.002 TYR L 50 PHE 0.008 0.002 PHE L 99 TRP 0.010 0.001 TRP L 36 HIS 0.001 0.000 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 3003) covalent geometry : angle 0.65164 / 0.33 ( 4075) SS BOND : bond 0.00241 / 0.12 ( 3) SS BOND : angle 1.33967 / 0.98 ( 6) hydrogen bonds : bond 0.04328 / 2.74 ( 105) hydrogen bonds : angle 5.50565 / 3.98 ( 315) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.109 Fit side-chains REVERT: A 40 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.5142 (ptp-170) REVERT: A 78 MET cc_start: 0.6460 (mmm) cc_final: 0.6059 (mmm) outliers start: 21 outliers final: 17 residues processed: 68 average time/residue: 0.0615 time to fit residues: 5.0790 Evaluate side-chains 69 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.191931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.179697 restraints weight = 4075.488| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.91 r_work: 0.4055 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3006 Z= 0.159 Angle : 0.662 7.438 4081 Z= 0.336 Chirality : 0.043 0.164 439 Planarity : 0.004 0.059 520 Dihedral : 6.525 53.822 420 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 7.62 % Allowed : 28.81 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.50 (0.40), residues: 370 helix: 0.47 (0.62), residues: 60 sheet: -0.82 (0.45), residues: 123 loop : -3.10 (0.38), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.011 0.002 TYR L 50 PHE 0.009 0.002 PHE A 101 TRP 0.010 0.001 TRP L 36 HIS 0.000 0.000 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 3003) covalent geometry : angle 0.65939 / 0.34 ( 4075) SS BOND : bond 0.00289 / 0.14 ( 3) SS BOND : angle 1.62376 / 1.26 ( 6) hydrogen bonds : bond 0.04359 / 2.75 ( 105) hydrogen bonds : angle 5.44022 / 3.92 ( 315) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.095 Fit side-chains REVERT: A 40 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.5168 (ptp-170) REVERT: A 53 LEU cc_start: 0.4855 (OUTLIER) cc_final: 0.4287 (mt) outliers start: 23 outliers final: 20 residues processed: 71 average time/residue: 0.0516 time to fit residues: 4.5118 Evaluate side-chains 75 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.190431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.178252 restraints weight = 4099.533| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.91 r_work: 0.4044 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3928 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3006 Z= 0.179 Angle : 0.705 9.881 4081 Z= 0.356 Chirality : 0.043 0.150 439 Planarity : 0.004 0.060 520 Dihedral : 6.439 52.830 420 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 7.95 % Allowed : 28.81 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.53 (0.40), residues: 370 helix: 0.53 (0.63), residues: 60 sheet: -0.90 (0.45), residues: 121 loop : -3.09 (0.37), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 67 TYR 0.011 0.002 TYR A 124 PHE 0.010 0.002 PHE A 101 TRP 0.023 0.002 TRP L 36 HIS 0.000 0.000 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 3003) covalent geometry : angle 0.70245 / 0.35 ( 4075) SS BOND : bond 0.00361 / 0.18 ( 3) SS BOND : angle 1.84059 / 1.43 ( 6) hydrogen bonds : bond 0.04528 / 2.86 ( 105) hydrogen bonds : angle 5.53213 / 4.00 ( 315) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.081 Fit side-chains REVERT: L 4 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7465 (mmm) REVERT: H 3 GLN cc_start: 0.3325 (OUTLIER) cc_final: 0.3040 (mt0) REVERT: A 40 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.5127 (ptp-170) REVERT: A 53 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4216 (mt) REVERT: A 78 MET cc_start: 0.6121 (mmm) cc_final: 0.5637 (mmm) outliers start: 24 outliers final: 20 residues processed: 70 average time/residue: 0.0426 time to fit residues: 3.7582 Evaluate side-chains 75 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 79 VAL Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 34 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.196055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.184301 restraints weight = 4077.129| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 1.81 r_work: 0.4107 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3994 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3006 Z= 0.117 Angle : 0.635 8.419 4081 Z= 0.319 Chirality : 0.041 0.159 439 Planarity : 0.004 0.057 520 Dihedral : 6.098 50.776 420 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 5.63 % Allowed : 32.12 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.38 (0.41), residues: 370 helix: 0.81 (0.64), residues: 61 sheet: -0.91 (0.45), residues: 125 loop : -3.02 (0.39), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.010 0.001 TYR A 124 PHE 0.008 0.001 PHE A 77 TRP 0.018 0.001 TRP L 36 HIS 0.000 0.000 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 3003) covalent geometry : angle 0.63284 / 0.32 ( 4075) SS BOND : bond 0.00263 / 0.13 ( 3) SS BOND : angle 1.52965 / 1.16 ( 6) hydrogen bonds : bond 0.03709 / 2.37 ( 105) hydrogen bonds : angle 5.22018 / 3.77 ( 315) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.065 Fit side-chains REVERT: L 4 MET cc_start: 0.7672 (mtp) cc_final: 0.7230 (mmm) outliers start: 17 outliers final: 13 residues processed: 63 average time/residue: 0.0479 time to fit residues: 3.7165 Evaluate side-chains 66 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4279 r_free = 0.4279 target = 0.194699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.183239 restraints weight = 4022.299| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.76 r_work: 0.4095 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3006 Z= 0.132 Angle : 0.672 12.107 4081 Z= 0.334 Chirality : 0.041 0.141 439 Planarity : 0.004 0.061 520 Dihedral : 6.060 51.160 420 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 5.63 % Allowed : 31.46 % Favored : 62.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.33 (0.41), residues: 370 helix: 0.84 (0.65), residues: 61 sheet: -0.78 (0.45), residues: 123 loop : -3.04 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 19 TYR 0.013 0.002 TYR L 37 PHE 0.008 0.002 PHE A 77 TRP 0.035 0.002 TRP L 36 HIS 0.000 0.000 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 3003) covalent geometry : angle 0.66958 / 0.33 ( 4075) SS BOND : bond 0.00286 / 0.14 ( 3) SS BOND : angle 1.65720 / 1.32 ( 6) hydrogen bonds : bond 0.03908 / 2.47 ( 105) hydrogen bonds : angle 5.08874 / 3.65 ( 315) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 740 Ramachandran restraints generated. 370 Oldfield, 0 Emsley, 370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.129 Fit side-chains REVERT: L 4 MET cc_start: 0.7675 (mtp) cc_final: 0.7219 (mmm) REVERT: A 53 LEU cc_start: 0.4728 (OUTLIER) cc_final: 0.4230 (mt) outliers start: 17 outliers final: 14 residues processed: 66 average time/residue: 0.0576 time to fit residues: 4.7911 Evaluate side-chains 69 residues out of total 328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 156 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.0020 chunk 37 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 6 GLN ** 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 = 0.4300 r_free = 0.4300 target = 0.196600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.185014 restraints weight = 4019.468| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.80 r_work: 0.4109 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3999 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3006 Z= 0.121 Angle : 0.640 8.595 4081 Z= 0.322 Chirality : 0.041 0.156 439 Planarity : 0.004 0.059 520 Dihedral : 5.937 50.126 420 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 6.29 % Allowed : 30.46 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 8.33 % 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: -2.31 (0.41), residues: 370 helix: 0.88 (0.64), residues: 61 sheet: -0.77 (0.45), residues: 123 loop : -3.03 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.010 0.001 TYR A 124 PHE 0.008 0.001 PHE A 77 TRP 0.029 0.002 TRP L 36 HIS 0.000 0.000 HIS A 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 3003) covalent geometry : angle 0.63783 / 0.32 ( 4075) SS BOND : bond 0.00295 / 0.14 ( 3) SS BOND : angle 1.52992 / 1.18 ( 6) hydrogen bonds : bond 0.03756 / 2.38 ( 105) hydrogen bonds : angle 4.97001 / 3.57 ( 315) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 958.39 seconds wall clock time: 17 minutes 1.11 seconds (1021.11 seconds total)