Starting phenix.real_space_refine on Wed Sep 17 03:39:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jlx_22383/09_2025/7jlx_22383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlx_22383/09_2025/7jlx_22383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jlx_22383/09_2025/7jlx_22383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlx_22383/09_2025/7jlx_22383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jlx_22383/09_2025/7jlx_22383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlx_22383/09_2025/7jlx_22383.map" } resolution = 4.6 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: 3 Type Number sf(0) Gaussians C 1960 2.51 5 N 664 2.21 5 O 664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3288 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 822 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 2, 'TRANS': 163} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'TYR:plan': 5, 'ASP:plan': 12, 'PHE:plan': 12, 'ARG:plan': 9, 'GLU:plan': 14, 'HIS:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 315 Chain: "A" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 822 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 2, 'TRANS': 163} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 557 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'TYR:plan': 5, 'ASP:plan': 12, 'PHE:plan': 12, 'ARG:plan': 9, 'GLU:plan': 14, 'HIS:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 315 Restraints were copied for chains: B, D Time building chain proxies: 1.18, per 1000 atoms: 0.36 Number of scatterers: 3288 At special positions: 0 Unit cell: (95.7372, 93.86, 53.5002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 664 8.00 N 664 7.00 C 1960 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: 0.34 Conformation dependent library (CDL) restraints added in 205.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 57.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 56 through 65 Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 136 through 149 Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.523A pdb=" N ILE B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 39 Processing helix chain 'C' and resid 55 through 66 Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 80 through 97 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'C' and resid 136 through 151 removed outlier: 3.635A pdb=" N ARG C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 4.446A pdb=" N PHE C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 39 Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 80 through 97 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 118 through 127 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 164 through 176 removed outlier: 3.524A pdb=" N ILE A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 39 Processing helix chain 'D' and resid 55 through 66 Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 80 through 97 Processing helix chain 'D' and resid 109 through 115 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 136 through 151 removed outlier: 3.634A pdb=" N ARG D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 176 removed outlier: 4.447A pdb=" N PHE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 14 through 17 removed outlier: 3.835A pdb=" N VAL B 70 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 72 " --> pdb=" O SER B 17 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 102 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 71 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 14 through 17 removed outlier: 3.649A pdb=" N VAL C 70 " --> pdb=" O PHE C 15 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 71 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N HIS C 154 " --> pdb=" O VAL C 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 17 removed outlier: 3.835A pdb=" N VAL A 70 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 72 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 102 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 71 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 14 through 17 removed outlier: 3.649A pdb=" N VAL D 70 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL D 71 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N HIS D 154 " --> pdb=" O VAL D 101 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 804 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: 0.48 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 664 1.29 - 1.36: 660 1.36 - 1.42: 0 1.42 - 1.48: 664 1.48 - 1.55: 1296 Bond restraints: 3284 Sorted by residual: bond pdb=" C VAL B 102 " pdb=" O VAL B 102 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.57e-01 bond pdb=" C VAL A 102 " pdb=" O VAL A 102 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.01e-02 9.80e+03 6.58e-01 bond pdb=" CA ASP D 163 " pdb=" C ASP D 163 " ideal model delta sigma weight residual 1.523 1.517 0.006 1.10e-02 8.26e+03 2.83e-01 bond pdb=" CA VAL B 102 " pdb=" CB VAL B 102 " ideal model delta sigma weight residual 1.540 1.535 0.005 9.00e-03 1.23e+04 2.77e-01 bond pdb=" CA ASP C 163 " pdb=" C ASP C 163 " ideal model delta sigma weight residual 1.523 1.517 0.006 1.10e-02 8.26e+03 2.60e-01 ... (remaining 3279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.97: 4421 0.97 - 1.95: 132 1.95 - 2.92: 11 2.92 - 3.89: 6 3.89 - 4.87: 2 Bond angle restraints: 4572 Sorted by residual: angle pdb=" N LYS D 47 " pdb=" CA LYS D 47 " pdb=" C LYS D 47 " ideal model delta sigma weight residual 114.04 110.39 3.65 1.24e+00 6.50e-01 8.66e+00 angle pdb=" N LYS C 47 " pdb=" CA LYS C 47 " pdb=" C LYS C 47 " ideal model delta sigma weight residual 114.04 110.41 3.63 1.24e+00 6.50e-01 8.56e+00 angle pdb=" C TYR A 160 " pdb=" N ASN A 161 " pdb=" CA ASN A 161 " ideal model delta sigma weight residual 121.54 126.41 -4.87 1.91e+00 2.74e-01 6.50e+00 angle pdb=" C TYR B 160 " pdb=" N ASN B 161 " pdb=" CA ASN B 161 " ideal model delta sigma weight residual 121.54 126.30 -4.76 1.91e+00 2.74e-01 6.22e+00 angle pdb=" N ASP D 45 " pdb=" CA ASP D 45 " pdb=" C ASP D 45 " ideal model delta sigma weight residual 113.20 109.98 3.22 1.36e+00 5.41e-01 5.61e+00 ... (remaining 4567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 2.66: 1647 2.66 - 5.32: 169 5.32 - 7.97: 74 7.97 - 10.63: 28 10.63 - 13.29: 6 Dihedral angle restraints: 1924 sinusoidal: 0 harmonic: 1924 Sorted by residual: dihedral pdb=" CA TYR D 160 " pdb=" C TYR D 160 " pdb=" N ASN D 161 " pdb=" CA ASN D 161 " ideal model delta harmonic sigma weight residual 180.00 166.71 13.29 0 5.00e+00 4.00e-02 7.06e+00 dihedral pdb=" CA TYR C 160 " pdb=" C TYR C 160 " pdb=" N ASN C 161 " pdb=" CA ASN C 161 " ideal model delta harmonic sigma weight residual 180.00 166.74 13.26 0 5.00e+00 4.00e-02 7.03e+00 dihedral pdb=" CA THR C 26 " pdb=" C THR C 26 " pdb=" N PHE C 27 " pdb=" CA PHE C 27 " ideal model delta harmonic sigma weight residual -180.00 -169.05 -10.95 0 5.00e+00 4.00e-02 4.80e+00 ... (remaining 1921 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.025: 362 0.025 - 0.049: 124 0.049 - 0.073: 85 0.073 - 0.097: 22 0.097 - 0.121: 39 Chirality restraints: 632 Sorted by residual: chirality pdb=" CA VAL D 104 " pdb=" N VAL D 104 " pdb=" C VAL D 104 " pdb=" CB VAL D 104 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA VAL C 104 " pdb=" N VAL C 104 " pdb=" C VAL C 104 " pdb=" CB VAL C 104 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.63e-01 chirality pdb=" CA ILE A 100 " pdb=" N ILE A 100 " pdb=" C ILE A 100 " pdb=" CB ILE A 100 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 629 not shown) Planarity restraints: 660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 76 " -0.003 2.00e-02 2.50e+03 5.65e-03 3.19e-01 pdb=" C ASN B 76 " 0.010 2.00e-02 2.50e+03 pdb=" O ASN B 76 " -0.004 2.00e-02 2.50e+03 pdb=" N TYR B 77 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 76 " 0.003 2.00e-02 2.50e+03 5.57e-03 3.10e-01 pdb=" C ASN A 76 " -0.010 2.00e-02 2.50e+03 pdb=" O ASN A 76 " 0.004 2.00e-02 2.50e+03 pdb=" N TYR A 77 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 135 " -0.002 2.00e-02 2.50e+03 4.33e-03 1.87e-01 pdb=" C ARG D 135 " 0.007 2.00e-02 2.50e+03 pdb=" O ARG D 135 " -0.003 2.00e-02 2.50e+03 pdb=" N ASP D 136 " -0.003 2.00e-02 2.50e+03 ... (remaining 657 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 698 2.77 - 3.30: 3171 3.30 - 3.84: 5199 3.84 - 4.37: 4502 4.37 - 4.90: 7958 Nonbonded interactions: 21528 Sorted by model distance: nonbonded pdb=" O VAL B 132 " pdb=" N ASP B 136 " model vdw 2.240 3.120 nonbonded pdb=" O VAL A 132 " pdb=" N ASP A 136 " model vdw 2.240 3.120 nonbonded pdb=" O ASP A 13 " pdb=" N ARG A 67 " model vdw 2.416 3.120 nonbonded pdb=" O ASP B 13 " pdb=" N ARG B 67 " model vdw 2.416 3.120 nonbonded pdb=" N TYR D 12 " pdb=" O GLU D 65 " model vdw 2.422 3.120 ... (remaining 21523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 8.750 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.870 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 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 : 0.001 0.009 3284 Z= 0.109 Angle : 0.417 4.868 4572 Z= 0.278 Chirality : 0.043 0.121 632 Planarity : 0.001 0.006 660 Dihedral : 3.804 13.288 660 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 1.23 (0.35), residues: 656 helix: 2.61 (0.28), residues: 360 sheet: -1.18 (0.63), residues: 80 loop : -1.61 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00144 ( 3284) covalent geometry : angle 0.41731 ( 4572) hydrogen bonds : bond 0.18033 ( 272) hydrogen bonds : angle 6.35931 ( 804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.025 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0127 time to fit residues: 0.0658 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.111697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.106079 restraints weight = 33561.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.106969 restraints weight = 27190.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.106811 restraints weight = 24545.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.106856 restraints weight = 24380.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.106878 restraints weight = 23755.962| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5245 moved from start: 1.0114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3284 Z= 0.362 Angle : 0.794 4.671 4572 Z= 0.542 Chirality : 0.048 0.129 632 Planarity : 0.006 0.022 660 Dihedral : 7.768 38.445 660 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 1.83 % Allowed : 8.54 % Favored : 89.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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 aren not related in a simple way. whole: -1.69 (0.31), residues: 656 helix: -0.05 (0.26), residues: 388 sheet: -2.03 (0.48), residues: 80 loop : -2.81 (0.38), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 3284) covalent geometry : angle 0.79393 ( 4572) hydrogen bonds : bond 0.06885 ( 272) hydrogen bonds : angle 7.22434 ( 804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0058 time to fit residues: 0.0695 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 60 optimal weight: 0.1980 chunk 45 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 overall best weight: 14.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.110584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104554 restraints weight = 34435.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.105379 restraints weight = 27641.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.105770 restraints weight = 23101.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.105617 restraints weight = 24036.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.105690 restraints weight = 22425.446| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5247 moved from start: 1.0171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.013 3284 Z= 0.272 Angle : 0.719 4.674 4572 Z= 0.484 Chirality : 0.045 0.120 632 Planarity : 0.005 0.033 660 Dihedral : 6.632 33.629 660 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.61 % Allowed : 11.59 % Favored : 87.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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 aren not related in a simple way. whole: -1.66 (0.32), residues: 656 helix: -0.08 (0.26), residues: 368 sheet: -1.76 (0.62), residues: 72 loop : -2.56 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3284) covalent geometry : angle 0.71948 ( 4572) hydrogen bonds : bond 0.06709 ( 272) hydrogen bonds : angle 7.08223 ( 804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.031 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0056 time to fit residues: 0.0650 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 40 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.109678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.102803 restraints weight = 35082.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.102774 restraints weight = 29384.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.103437 restraints weight = 26642.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.103675 restraints weight = 24550.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.103792 restraints weight = 25035.704| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5302 moved from start: 1.0488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 3284 Z= 0.335 Angle : 0.768 4.664 4572 Z= 0.523 Chirality : 0.046 0.121 632 Planarity : 0.005 0.034 660 Dihedral : 7.297 32.632 660 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.61 % Allowed : 12.80 % Favored : 86.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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 aren not related in a simple way. whole: -2.62 (0.30), residues: 656 helix: -0.82 (0.24), residues: 384 sheet: -2.33 (0.61), residues: 72 loop : -3.13 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 3284) covalent geometry : angle 0.76812 ( 4572) hydrogen bonds : bond 0.07644 ( 272) hydrogen bonds : angle 7.76460 ( 804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0059 time to fit residues: 0.0620 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 41 optimal weight: 30.0000 chunk 8 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 28 optimal weight: 30.0000 chunk 30 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 11 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 overall best weight: 17.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107727 restraints weight = 3566.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107723 restraints weight = 2669.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107721 restraints weight = 2333.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107721 restraints weight = 2485.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.107721 restraints weight = 2485.593| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 moved from start: 1.0575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 3284 Z= 0.329 Angle : 0.764 4.437 4572 Z= 0.519 Chirality : 0.046 0.117 632 Planarity : 0.005 0.034 660 Dihedral : 7.374 32.716 660 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.41 % Favored : 85.98 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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 aren not related in a simple way. whole: -2.71 (0.30), residues: 656 helix: -0.90 (0.24), residues: 384 sheet: -2.59 (0.60), residues: 72 loop : -3.03 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3284) covalent geometry : angle 0.76418 ( 4572) hydrogen bonds : bond 0.07744 ( 272) hydrogen bonds : angle 7.84714 ( 804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.037 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0064 time to fit residues: 0.0767 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 0 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 10 optimal weight: 8.9990 chunk 4 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.108159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.101652 restraints weight = 36832.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102338 restraints weight = 29558.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.102919 restraints weight = 26556.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.102911 restraints weight = 25509.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.103040 restraints weight = 23921.997| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5338 moved from start: 1.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 3284 Z= 0.329 Angle : 0.777 5.171 4572 Z= 0.528 Chirality : 0.045 0.119 632 Planarity : 0.005 0.032 660 Dihedral : 7.457 34.313 660 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.61 % Allowed : 17.07 % Favored : 82.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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 aren not related in a simple way. whole: -2.64 (0.31), residues: 656 helix: -0.94 (0.24), residues: 384 sheet: -2.53 (0.65), residues: 72 loop : -2.80 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3284) covalent geometry : angle 0.77657 ( 4572) hydrogen bonds : bond 0.08016 ( 272) hydrogen bonds : angle 7.92117 ( 804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0069 time to fit residues: 0.0893 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 20.0000 chunk 39 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.108139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.102128 restraints weight = 35286.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.103038 restraints weight = 28558.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.103605 restraints weight = 24573.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.103434 restraints weight = 22948.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103532 restraints weight = 23229.799| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5319 moved from start: 1.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 3284 Z= 0.329 Angle : 0.788 4.909 4572 Z= 0.534 Chirality : 0.046 0.116 632 Planarity : 0.005 0.031 660 Dihedral : 7.397 36.578 660 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.24 % Favored : 84.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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 aren not related in a simple way. whole: -2.77 (0.30), residues: 656 helix: -0.93 (0.24), residues: 376 sheet: -3.01 (0.59), residues: 72 loop : -2.86 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 3284) covalent geometry : angle 0.78840 ( 4572) hydrogen bonds : bond 0.07992 ( 272) hydrogen bonds : angle 7.82372 ( 804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0058 time to fit residues: 0.0667 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 30.0000 chunk 13 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 chunk 37 optimal weight: 20.0000 chunk 56 optimal weight: 40.0000 chunk 47 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.107221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101104 restraints weight = 35071.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102109 restraints weight = 28838.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.102408 restraints weight = 25466.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102416 restraints weight = 23935.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.102431 restraints weight = 23803.741| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5346 moved from start: 1.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 3284 Z= 0.331 Angle : 0.781 5.142 4572 Z= 0.531 Chirality : 0.046 0.117 632 Planarity : 0.005 0.033 660 Dihedral : 7.437 37.099 660 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.61 % Allowed : 16.46 % Favored : 82.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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 aren not related in a simple way. whole: -2.80 (0.31), residues: 656 helix: -1.11 (0.24), residues: 380 sheet: -3.22 (0.58), residues: 72 loop : -2.48 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 3284) covalent geometry : angle 0.78069 ( 4572) hydrogen bonds : bond 0.08065 ( 272) hydrogen bonds : angle 7.77694 ( 804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.028 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0040 time to fit residues: 0.0500 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 59 optimal weight: 40.0000 chunk 17 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 45 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 61 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.107522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.102051 restraints weight = 35203.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102051 restraints weight = 29222.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102195 restraints weight = 28251.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.102474 restraints weight = 24586.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.102525 restraints weight = 23785.259| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5357 moved from start: 1.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.016 3284 Z= 0.368 Angle : 0.822 5.421 4572 Z= 0.558 Chirality : 0.046 0.118 632 Planarity : 0.005 0.034 660 Dihedral : 7.806 37.711 660 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.61 % Allowed : 15.85 % Favored : 83.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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 aren not related in a simple way. whole: -3.17 (0.29), residues: 656 helix: -1.37 (0.23), residues: 380 sheet: -3.55 (0.59), residues: 72 loop : -2.65 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 3284) covalent geometry : angle 0.82162 ( 4572) hydrogen bonds : bond 0.08710 ( 272) hydrogen bonds : angle 8.05920 ( 804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0065 time to fit residues: 0.0695 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 62 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 56 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 27 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 overall best weight: 17.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.107405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.101293 restraints weight = 36321.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.101716 restraints weight = 30265.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101846 restraints weight = 26830.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.102153 restraints weight = 25612.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.102224 restraints weight = 25135.061| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 moved from start: 1.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 3284 Z= 0.335 Angle : 0.804 5.329 4572 Z= 0.546 Chirality : 0.046 0.117 632 Planarity : 0.005 0.033 660 Dihedral : 7.777 37.721 660 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.61 % Allowed : 16.46 % Favored : 82.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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 aren not related in a simple way. whole: -3.19 (0.29), residues: 656 helix: -1.37 (0.23), residues: 380 sheet: -3.60 (0.59), residues: 72 loop : -2.65 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00447 ( 3284) covalent geometry : angle 0.80447 ( 4572) hydrogen bonds : bond 0.08677 ( 272) hydrogen bonds : angle 8.04062 ( 804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1312 Ramachandran restraints generated. 656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.0062 time to fit residues: 0.0717 Evaluate side-chains 2 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 60 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 34 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 overall best weight: 16.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.107564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.101406 restraints weight = 36151.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.101518 restraints weight = 31634.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.101768 restraints weight = 27655.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.102152 restraints weight = 26561.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102196 restraints weight = 26395.771| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 moved from start: 1.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.014 3284 Z= 0.319 Angle : 0.799 5.368 4572 Z= 0.541 Chirality : 0.045 0.114 632 Planarity : 0.005 0.033 660 Dihedral : 7.771 37.721 660 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.61 % Allowed : 17.07 % Favored : 82.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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 aren not related in a simple way. whole: -3.18 (0.29), residues: 656 helix: -1.36 (0.23), residues: 380 sheet: -3.62 (0.59), residues: 72 loop : -2.64 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR B 12 PHE 0.000 0.000 PHE B 15 TRP 0.000 0.000 TRP B 82 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 3284) covalent geometry : angle 0.79899 ( 4572) hydrogen bonds : bond 0.08640 ( 272) hydrogen bonds : angle 8.02681 ( 804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 553.25 seconds wall clock time: 10 minutes 13.27 seconds (613.27 seconds total)