Starting phenix.real_space_refine on Fri Aug 22 13:58:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r47_18881/08_2025/8r47_18881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r47_18881/08_2025/8r47_18881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r47_18881/08_2025/8r47_18881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r47_18881/08_2025/8r47_18881.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r47_18881/08_2025/8r47_18881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r47_18881/08_2025/8r47_18881.map" } resolution = 2.25 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= 0.005 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 12 5.16 5 C 2376 2.51 5 N 636 2.21 5 O 756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3780 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.55, per 1000 atoms: 0.15 Number of scatterers: 3780 At special positions: 0 Unit cell: (77.522, 81.258, 45.766, 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 12 16.00 O 756 8.00 N 636 7.00 C 2376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 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: 0.28 Conformation dependent library (CDL) restraints added in 114.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.776A pdb=" N CYS B 22 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS C 22 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS D 22 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS E 22 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS F 22 " --> pdb=" O THR E 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 31 removed outlier: 6.803A pdb=" N LEU A 27 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG B 28 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 28 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C 27 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG D 28 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU D 27 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 28 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU E 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG F 28 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.409A pdb=" N TYR A 35 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 35 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR C 35 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR D 35 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR E 35 " --> pdb=" O GLN F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 48 removed outlier: 6.591A pdb=" N LEU A 44 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE B 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL A 46 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 44 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE C 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL B 46 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 44 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE D 47 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL C 46 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 44 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE E 47 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL D 46 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU E 44 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE F 47 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL E 46 " --> pdb=" O ILE F 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.542A pdb=" N ALA A 70 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR B 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 72 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 70 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR C 73 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU B 72 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA C 70 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR D 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU C 72 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 70 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR E 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU D 72 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA E 70 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR F 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 72 " --> pdb=" O THR F 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 86 Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'A' and resid 104 through 105 60 hydrogen bonds defined for protein. 180 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: 0.35 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 648 1.31 - 1.44: 1116 1.44 - 1.57: 2082 1.57 - 1.69: 0 1.69 - 1.82: 12 Bond restraints: 3858 Sorted by residual: bond pdb=" C GLN F 16 " pdb=" O GLN F 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN A 16 " pdb=" O GLN A 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN C 16 " pdb=" O GLN C 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN D 16 " pdb=" O GLN D 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN B 16 " pdb=" O GLN B 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.24e+01 ... (remaining 3853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 3849 1.97 - 3.94: 989 3.94 - 5.91: 328 5.91 - 7.88: 54 7.88 - 9.85: 18 Bond angle restraints: 5238 Sorted by residual: angle pdb=" CA GLY E 94 " pdb=" C GLY E 94 " pdb=" O GLY E 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY C 94 " pdb=" C GLY C 94 " pdb=" O GLY C 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY F 94 " pdb=" C GLY F 94 " pdb=" O GLY F 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY A 94 " pdb=" C GLY A 94 " pdb=" O GLY A 94 " ideal model delta sigma weight residual 121.04 115.89 5.15 7.90e-01 1.60e+00 4.24e+01 angle pdb=" CA GLY D 94 " pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 121.04 115.90 5.14 7.90e-01 1.60e+00 4.23e+01 ... (remaining 5233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 1926 16.00 - 32.00: 210 32.00 - 48.00: 42 48.00 - 64.00: 24 64.00 - 80.00: 6 Dihedral angle restraints: 2208 sinusoidal: 828 harmonic: 1380 Sorted by residual: dihedral pdb=" CA PRO D 39 " pdb=" C PRO D 39 " pdb=" N GLY D 40 " pdb=" CA GLY D 40 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO F 39 " pdb=" C PRO F 39 " pdb=" N GLY F 40 " pdb=" CA GLY F 40 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO A 39 " pdb=" C PRO A 39 " pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 399 0.083 - 0.165: 135 0.165 - 0.248: 30 0.248 - 0.330: 6 0.330 - 0.413: 6 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA ILE F 65 " pdb=" N ILE F 65 " pdb=" C ILE F 65 " pdb=" CB ILE F 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ILE D 65 " pdb=" N ILE D 65 " pdb=" C ILE D 65 " pdb=" CB ILE D 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA ILE C 65 " pdb=" N ILE C 65 " pdb=" C ILE C 65 " pdb=" CB ILE C 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 573 not shown) Planarity restraints: 672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 63 " 0.024 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C GLY B 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY B 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER B 64 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 63 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLY A 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY A 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER A 64 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 63 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLY D 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY D 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER D 64 " 0.029 2.00e-02 2.50e+03 ... (remaining 669 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 1806 2.95 - 3.44: 3291 3.44 - 3.93: 7281 3.93 - 4.41: 7950 4.41 - 4.90: 15330 Nonbonded interactions: 35658 Sorted by model distance: nonbonded pdb=" O GLY E 101 " pdb=" O GLY F 100 " model vdw 2.468 3.040 nonbonded pdb=" O GLY C 101 " pdb=" O GLY D 100 " model vdw 2.468 3.040 nonbonded pdb=" O GLY A 101 " pdb=" O GLY B 100 " model vdw 2.468 3.040 nonbonded pdb=" O GLY D 101 " pdb=" O GLY E 100 " model vdw 2.468 3.040 nonbonded pdb=" O GLY B 101 " pdb=" O GLY C 100 " model vdw 2.469 3.040 ... (remaining 35653 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' selection = chain 'E' selection = chain 'F' } 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: 0.460 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.013 0.054 3864 Z= 0.961 Angle : 2.053 9.847 5250 Z= 1.472 Chirality : 0.097 0.413 576 Planarity : 0.016 0.070 672 Dihedral : 15.668 79.999 1326 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 18.43 % Favored : 81.57 % 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: -4.59 (0.21), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.16), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 19 TYR 0.004 0.001 TYR C 30 PHE 0.008 0.001 PHE C 61 TRP 0.006 0.001 TRP E 97 Details of bonding type rmsd covalent geometry : bond 0.01280 ( 3858) covalent geometry : angle 2.03594 ( 5238) SS BOND : bond 0.01099 ( 6) SS BOND : angle 5.94105 ( 12) hydrogen bonds : bond 0.13813 ( 60) hydrogen bonds : angle 7.44321 ( 180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.129 Fit side-chains REVERT: B 66 SER cc_start: 0.8301 (p) cc_final: 0.8059 (t) REVERT: D 90 ARG cc_start: 0.6960 (ttm170) cc_final: 0.6716 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.2252 time to fit residues: 18.0190 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN B 23 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 23 GLN E 23 GLN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.147544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.128961 restraints weight = 4081.483| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.42 r_work: 0.3837 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3864 Z= 0.115 Angle : 0.593 8.682 5250 Z= 0.304 Chirality : 0.043 0.148 576 Planarity : 0.005 0.052 672 Dihedral : 5.782 14.609 534 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.25 % Allowed : 16.41 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.17 (0.25), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.19), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 19 TYR 0.010 0.001 TYR E 48 PHE 0.006 0.001 PHE D 61 TRP 0.007 0.001 TRP F 97 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 3858) covalent geometry : angle 0.59294 ( 5238) SS BOND : bond 0.00075 ( 6) SS BOND : angle 0.76373 ( 12) hydrogen bonds : bond 0.03154 ( 60) hydrogen bonds : angle 5.44675 ( 180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.107 Fit side-chains REVERT: B 82 GLU cc_start: 0.8166 (tp30) cc_final: 0.7952 (mm-30) REVERT: C 82 GLU cc_start: 0.8124 (tp30) cc_final: 0.7879 (mm-30) REVERT: E 90 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7163 (mtt90) REVERT: F 66 SER cc_start: 0.8369 (p) cc_final: 0.8154 (p) REVERT: F 69 THR cc_start: 0.8149 (m) cc_final: 0.7764 (t) outliers start: 1 outliers final: 1 residues processed: 81 average time/residue: 0.2578 time to fit residues: 22.0904 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 33 ASN B 33 ASN C 16 GLN C 95 ASN D 95 ASN E 95 ASN F 16 GLN F 95 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.141953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123861 restraints weight = 4051.428| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.40 r_work: 0.3773 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3864 Z= 0.153 Angle : 0.608 6.775 5250 Z= 0.317 Chirality : 0.045 0.154 576 Planarity : 0.005 0.049 672 Dihedral : 6.020 15.383 534 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.26 % Allowed : 18.18 % Favored : 80.56 % 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: -4.01 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 19 TYR 0.010 0.002 TYR B 48 PHE 0.008 0.002 PHE B 99 TRP 0.009 0.001 TRP F 97 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3858) covalent geometry : angle 0.60751 ( 5238) SS BOND : bond 0.00191 ( 6) SS BOND : angle 0.60642 ( 12) hydrogen bonds : bond 0.03357 ( 60) hydrogen bonds : angle 5.49371 ( 180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.085 Fit side-chains REVERT: C 82 GLU cc_start: 0.8193 (tp30) cc_final: 0.7964 (mm-30) REVERT: D 69 THR cc_start: 0.8397 (m) cc_final: 0.8049 (t) REVERT: F 66 SER cc_start: 0.8321 (p) cc_final: 0.7973 (p) REVERT: F 69 THR cc_start: 0.8235 (m) cc_final: 0.7908 (t) REVERT: F 103 THR cc_start: 0.8360 (OUTLIER) cc_final: 0.8041 (m) outliers start: 5 outliers final: 2 residues processed: 69 average time/residue: 0.3201 time to fit residues: 23.1391 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.140369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122732 restraints weight = 4075.517| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.39 r_work: 0.3763 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3864 Z= 0.164 Angle : 0.600 5.265 5250 Z= 0.316 Chirality : 0.046 0.151 576 Planarity : 0.005 0.046 672 Dihedral : 6.117 16.272 534 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.53 % Allowed : 16.41 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.04 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 19 TYR 0.010 0.002 TYR E 48 PHE 0.007 0.001 PHE B 99 TRP 0.009 0.001 TRP F 97 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3858) covalent geometry : angle 0.60004 ( 5238) SS BOND : bond 0.00240 ( 6) SS BOND : angle 0.54277 ( 12) hydrogen bonds : bond 0.03226 ( 60) hydrogen bonds : angle 5.52839 ( 180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.154 Fit side-chains REVERT: C 82 GLU cc_start: 0.8125 (tp30) cc_final: 0.7913 (mm-30) REVERT: C 90 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.7343 (mtp85) REVERT: D 69 THR cc_start: 0.8391 (m) cc_final: 0.8043 (t) REVERT: E 80 GLU cc_start: 0.7408 (tt0) cc_final: 0.7031 (tt0) REVERT: E 103 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8101 (m) REVERT: F 69 THR cc_start: 0.8273 (m) cc_final: 0.7975 (t) REVERT: F 103 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8032 (m) outliers start: 10 outliers final: 5 residues processed: 73 average time/residue: 0.3460 time to fit residues: 26.4103 Evaluate side-chains 70 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 0.0670 chunk 10 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.146989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.130123 restraints weight = 4063.145| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.36 r_work: 0.3837 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3864 Z= 0.090 Angle : 0.541 7.727 5250 Z= 0.274 Chirality : 0.042 0.144 576 Planarity : 0.004 0.044 672 Dihedral : 5.488 15.418 534 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.51 % Allowed : 18.69 % Favored : 80.81 % 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: -4.04 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 28 TYR 0.009 0.001 TYR C 48 PHE 0.006 0.001 PHE B 99 TRP 0.004 0.000 TRP F 97 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 3858) covalent geometry : angle 0.54074 ( 5238) SS BOND : bond 0.00044 ( 6) SS BOND : angle 0.44311 ( 12) hydrogen bonds : bond 0.02526 ( 60) hydrogen bonds : angle 5.31767 ( 180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.153 Fit side-chains REVERT: C 82 GLU cc_start: 0.8200 (tp30) cc_final: 0.7969 (mm-30) REVERT: C 90 ARG cc_start: 0.7661 (ttm-80) cc_final: 0.7427 (mtp85) REVERT: E 80 GLU cc_start: 0.7334 (tt0) cc_final: 0.7039 (tt0) REVERT: F 69 THR cc_start: 0.8264 (m) cc_final: 0.7935 (t) outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 0.3720 time to fit residues: 23.6812 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain D residue 62 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 13 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.139786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.122170 restraints weight = 4105.854| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 1.40 r_work: 0.3752 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3864 Z= 0.174 Angle : 0.616 5.524 5250 Z= 0.323 Chirality : 0.046 0.149 576 Planarity : 0.005 0.046 672 Dihedral : 6.062 15.666 534 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.77 % Allowed : 18.18 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.00 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 19 TYR 0.008 0.001 TYR A 48 PHE 0.007 0.002 PHE F 99 TRP 0.008 0.001 TRP F 97 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3858) covalent geometry : angle 0.61629 ( 5238) SS BOND : bond 0.00264 ( 6) SS BOND : angle 0.53857 ( 12) hydrogen bonds : bond 0.03199 ( 60) hydrogen bonds : angle 5.51308 ( 180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.089 Fit side-chains REVERT: C 90 ARG cc_start: 0.7692 (ttm170) cc_final: 0.7484 (mtp85) REVERT: D 69 THR cc_start: 0.8402 (m) cc_final: 0.8051 (t) REVERT: E 103 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.8107 (m) REVERT: F 69 THR cc_start: 0.8303 (m) cc_final: 0.7991 (t) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.3563 time to fit residues: 25.3183 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.135564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.117836 restraints weight = 4112.667| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.40 r_work: 0.3705 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3864 Z= 0.258 Angle : 0.711 7.289 5250 Z= 0.373 Chirality : 0.049 0.159 576 Planarity : 0.005 0.047 672 Dihedral : 6.554 16.493 534 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.27 % Allowed : 15.91 % Favored : 81.82 % 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: -3.99 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 19 TYR 0.013 0.002 TYR D 48 PHE 0.008 0.002 PHE F 99 TRP 0.010 0.002 TRP F 97 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 3858) covalent geometry : angle 0.71133 ( 5238) SS BOND : bond 0.00426 ( 6) SS BOND : angle 0.66765 ( 12) hydrogen bonds : bond 0.03559 ( 60) hydrogen bonds : angle 5.66587 ( 180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.101 Fit side-chains REVERT: C 80 GLU cc_start: 0.7514 (tt0) cc_final: 0.7266 (tm-30) REVERT: C 90 ARG cc_start: 0.7699 (ttm170) cc_final: 0.7471 (mtp85) REVERT: D 69 THR cc_start: 0.8422 (m) cc_final: 0.8074 (t) REVERT: F 66 SER cc_start: 0.8355 (p) cc_final: 0.8107 (p) REVERT: F 69 THR cc_start: 0.8302 (m) cc_final: 0.8016 (t) REVERT: F 103 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8050 (m) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.3949 time to fit residues: 29.1781 Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 5 optimal weight: 0.3980 chunk 25 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.142272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.124801 restraints weight = 4096.084| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.40 r_work: 0.3792 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3864 Z= 0.112 Angle : 0.584 8.631 5250 Z= 0.297 Chirality : 0.043 0.146 576 Planarity : 0.004 0.046 672 Dihedral : 5.853 15.826 534 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.52 % Allowed : 17.42 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.99 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 19 TYR 0.009 0.001 TYR B 48 PHE 0.006 0.001 PHE B 99 TRP 0.005 0.001 TRP F 97 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3858) covalent geometry : angle 0.58444 ( 5238) SS BOND : bond 0.00104 ( 6) SS BOND : angle 0.37345 ( 12) hydrogen bonds : bond 0.02756 ( 60) hydrogen bonds : angle 5.47754 ( 180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.147 Fit side-chains REVERT: C 80 GLU cc_start: 0.7313 (tt0) cc_final: 0.7073 (tm-30) REVERT: C 90 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7525 (mtp85) REVERT: D 44 LEU cc_start: 0.8533 (tp) cc_final: 0.8313 (tm) REVERT: D 69 THR cc_start: 0.8383 (m) cc_final: 0.8014 (t) REVERT: E 103 THR cc_start: 0.8337 (OUTLIER) cc_final: 0.8129 (m) REVERT: F 69 THR cc_start: 0.8260 (m) cc_final: 0.7947 (t) REVERT: F 103 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8044 (m) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.3606 time to fit residues: 25.9935 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.0070 chunk 4 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN D 95 ASN E 95 ASN F 95 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.145029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.128100 restraints weight = 4085.531| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.38 r_work: 0.3818 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3864 Z= 0.105 Angle : 0.568 8.145 5250 Z= 0.289 Chirality : 0.043 0.143 576 Planarity : 0.004 0.046 672 Dihedral : 5.640 15.394 534 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.52 % Allowed : 17.93 % Favored : 80.56 % 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: -3.96 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 19 TYR 0.011 0.001 TYR A 48 PHE 0.006 0.001 PHE B 99 TRP 0.006 0.001 TRP F 97 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 3858) covalent geometry : angle 0.56864 ( 5238) SS BOND : bond 0.00097 ( 6) SS BOND : angle 0.38843 ( 12) hydrogen bonds : bond 0.02611 ( 60) hydrogen bonds : angle 5.38964 ( 180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.146 Fit side-chains REVERT: C 90 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7512 (mtp85) REVERT: E 103 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8071 (m) REVERT: F 69 THR cc_start: 0.8265 (m) cc_final: 0.7943 (t) REVERT: F 103 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8038 (m) outliers start: 6 outliers final: 4 residues processed: 65 average time/residue: 0.3167 time to fit residues: 21.5538 Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.133818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.116180 restraints weight = 4160.012| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.41 r_work: 0.3681 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 3864 Z= 0.353 Angle : 0.825 7.854 5250 Z= 0.431 Chirality : 0.053 0.178 576 Planarity : 0.006 0.048 672 Dihedral : 6.802 17.455 534 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.52 % Allowed : 18.43 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.95 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG E 19 TYR 0.012 0.002 TYR C 48 PHE 0.010 0.002 PHE F 61 TRP 0.010 0.002 TRP F 97 Details of bonding type rmsd covalent geometry : bond 0.00763 ( 3858) covalent geometry : angle 0.82434 ( 5238) SS BOND : bond 0.00593 ( 6) SS BOND : angle 0.94565 ( 12) hydrogen bonds : bond 0.03723 ( 60) hydrogen bonds : angle 5.69928 ( 180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.096 Fit side-chains REVERT: C 80 GLU cc_start: 0.7499 (tt0) cc_final: 0.7271 (tm-30) REVERT: C 90 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7517 (mtp85) REVERT: D 69 THR cc_start: 0.8411 (m) cc_final: 0.8092 (t) REVERT: F 69 THR cc_start: 0.8312 (m) cc_final: 0.8034 (t) outliers start: 6 outliers final: 6 residues processed: 66 average time/residue: 0.3855 time to fit residues: 26.4255 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.143173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.126409 restraints weight = 4058.727| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.37 r_work: 0.3801 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3864 Z= 0.111 Angle : 0.593 9.143 5250 Z= 0.302 Chirality : 0.043 0.147 576 Planarity : 0.004 0.046 672 Dihedral : 5.898 15.543 534 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.52 % Allowed : 18.18 % Favored : 80.30 % 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: -3.98 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 19 TYR 0.013 0.001 TYR E 48 PHE 0.006 0.001 PHE B 99 TRP 0.004 0.001 TRP C 97 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 3858) covalent geometry : angle 0.59369 ( 5238) SS BOND : bond 0.00180 ( 6) SS BOND : angle 0.38135 ( 12) hydrogen bonds : bond 0.02726 ( 60) hydrogen bonds : angle 5.50513 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1375.70 seconds wall clock time: 24 minutes 21.08 seconds (1461.08 seconds total)