Starting phenix.real_space_refine on Sat Apr 26 22:58:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r47_18881/04_2025/8r47_18881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r47_18881/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8r47_18881/04_2025/8r47_18881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r47_18881/04_2025/8r47_18881.map" model { file = "/net/cci-nas-00/data/ceres_data/8r47_18881/04_2025/8r47_18881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r47_18881/04_2025/8r47_18881.cif" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: C, B, E, D, F Time building chain proxies: 1.69, per 1000 atoms: 0.45 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 C 22 " - pdb=" SG CYS C 87 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 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: 0.76 Conformation dependent library (CDL) restraints added in 409.0 milliseconds 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: 0.54 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: 0.88 Time building geometry restraints manager: 0.93 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.700 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP E 97 PHE 0.008 0.001 PHE C 61 TYR 0.004 0.001 TYR C 30 ARG 0.002 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.13813 ( 60) hydrogen bonds : angle 7.44321 ( 180) SS BOND : bond 0.01099 ( 6) SS BOND : angle 5.94105 ( 12) covalent geometry : bond 0.01280 ( 3858) covalent geometry : angle 2.03594 ( 5238) *********************** 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 : 0.413 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: 0.5256 time to fit residues: 42.2578 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 : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 F 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.141423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.122901 restraints weight = 3990.158| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.42 r_work: 0.3767 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3864 Z= 0.167 Angle : 0.652 8.081 5250 Z= 0.339 Chirality : 0.045 0.154 576 Planarity : 0.005 0.053 672 Dihedral : 6.156 15.019 534 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 15.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.25), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.19), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 97 PHE 0.008 0.002 PHE B 99 TYR 0.011 0.002 TYR B 48 ARG 0.005 0.001 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 60) hydrogen bonds : angle 5.62216 ( 180) SS BOND : bond 0.00074 ( 6) SS BOND : angle 0.79218 ( 12) covalent geometry : bond 0.00352 ( 3858) covalent geometry : angle 0.65180 ( 5238) *********************** 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 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.377 Fit side-chains REVERT: B 82 GLU cc_start: 0.8216 (tp30) cc_final: 0.7980 (mm-30) REVERT: C 82 GLU cc_start: 0.8181 (tp30) cc_final: 0.7953 (mm-30) REVERT: E 90 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7275 (mtt90) REVERT: F 69 THR cc_start: 0.8254 (m) cc_final: 0.7880 (t) outliers start: 3 outliers final: 3 residues processed: 75 average time/residue: 0.6326 time to fit residues: 50.3147 Evaluate side-chains 68 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN F 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.133345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.115781 restraints weight = 4056.109| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.38 r_work: 0.3677 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 3864 Z= 0.407 Angle : 0.895 10.821 5250 Z= 0.463 Chirality : 0.055 0.194 576 Planarity : 0.006 0.057 672 Dihedral : 7.154 18.890 534 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.03 % Allowed : 13.89 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 97 PHE 0.009 0.002 PHE F 99 TYR 0.019 0.003 TYR F 48 ARG 0.011 0.002 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 60) hydrogen bonds : angle 5.90588 ( 180) SS BOND : bond 0.00726 ( 6) SS BOND : angle 0.99131 ( 12) covalent geometry : bond 0.00873 ( 3858) covalent geometry : angle 0.89527 ( 5238) *********************** 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 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.381 Fit side-chains REVERT: D 69 THR cc_start: 0.8433 (m) cc_final: 0.8145 (t) REVERT: F 69 THR cc_start: 0.8378 (m) cc_final: 0.8123 (t) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.8475 time to fit residues: 60.2231 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER 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 46 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 66 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 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.0060 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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 = 0.4069 r_free = 0.4069 target = 0.141102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.124194 restraints weight = 4102.517| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.36 r_work: 0.3782 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3864 Z= 0.109 Angle : 0.578 6.852 5250 Z= 0.297 Chirality : 0.043 0.146 576 Planarity : 0.005 0.056 672 Dihedral : 5.989 15.285 534 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.26 % Allowed : 16.16 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.010 0.001 TYR C 48 ARG 0.001 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.02904 ( 60) hydrogen bonds : angle 5.56852 ( 180) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.45471 ( 12) covalent geometry : bond 0.00240 ( 3858) covalent geometry : angle 0.57848 ( 5238) *********************** 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 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.421 Fit side-chains REVERT: C 90 ARG cc_start: 0.7653 (ttm170) cc_final: 0.7168 (mmm160) REVERT: D 69 THR cc_start: 0.8436 (m) cc_final: 0.8125 (t) REVERT: F 69 THR cc_start: 0.8269 (m) cc_final: 0.7992 (t) outliers start: 5 outliers final: 2 residues processed: 69 average time/residue: 0.7524 time to fit residues: 54.5839 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain D residue 62 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3992 r_free = 0.3992 target = 0.133706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.116103 restraints weight = 4136.102| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.39 r_work: 0.3683 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3864 Z= 0.309 Angle : 0.780 7.288 5250 Z= 0.407 Chirality : 0.052 0.186 576 Planarity : 0.006 0.061 672 Dihedral : 6.875 18.845 534 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.78 % Allowed : 15.91 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 97 PHE 0.008 0.002 PHE B 99 TYR 0.013 0.002 TYR D 48 ARG 0.007 0.001 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 60) hydrogen bonds : angle 5.73625 ( 180) SS BOND : bond 0.00531 ( 6) SS BOND : angle 0.74548 ( 12) covalent geometry : bond 0.00667 ( 3858) covalent geometry : angle 0.78006 ( 5238) *********************** 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 72 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.432 Fit side-chains REVERT: C 80 GLU cc_start: 0.7668 (tt0) cc_final: 0.7307 (tm-30) REVERT: D 69 THR cc_start: 0.8430 (m) cc_final: 0.8122 (t) REVERT: D 80 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: E 80 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: F 69 THR cc_start: 0.8411 (m) cc_final: 0.8149 (t) outliers start: 11 outliers final: 5 residues processed: 70 average time/residue: 0.8982 time to fit residues: 65.5454 Evaluate side-chains 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.139547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.122295 restraints weight = 4080.897| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 1.39 r_work: 0.3756 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3864 Z= 0.137 Angle : 0.619 7.495 5250 Z= 0.317 Chirality : 0.045 0.148 576 Planarity : 0.005 0.060 672 Dihedral : 6.219 15.980 534 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.011 0.001 TYR B 48 ARG 0.002 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 60) hydrogen bonds : angle 5.55784 ( 180) SS BOND : bond 0.00183 ( 6) SS BOND : angle 0.39465 ( 12) covalent geometry : bond 0.00301 ( 3858) covalent geometry : angle 0.61934 ( 5238) *********************** 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 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.440 Fit side-chains REVERT: C 80 GLU cc_start: 0.7526 (tt0) cc_final: 0.7220 (tm-30) REVERT: C 90 ARG cc_start: 0.7712 (ttm170) cc_final: 0.7405 (mtp85) REVERT: D 69 THR cc_start: 0.8403 (m) cc_final: 0.8072 (t) REVERT: F 69 THR cc_start: 0.8373 (m) cc_final: 0.8076 (t) REVERT: F 103 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8038 (m) outliers start: 6 outliers final: 1 residues processed: 64 average time/residue: 0.8894 time to fit residues: 59.5447 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3998 r_free = 0.3998 target = 0.134331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.116872 restraints weight = 4082.393| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.39 r_work: 0.3693 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3864 Z= 0.278 Angle : 0.758 6.911 5250 Z= 0.393 Chirality : 0.050 0.181 576 Planarity : 0.006 0.063 672 Dihedral : 6.797 19.459 534 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.77 % Allowed : 17.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 97 PHE 0.007 0.002 PHE B 99 TYR 0.014 0.002 TYR A 48 ARG 0.006 0.001 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 60) hydrogen bonds : angle 5.65632 ( 180) SS BOND : bond 0.00459 ( 6) SS BOND : angle 0.67930 ( 12) covalent geometry : bond 0.00598 ( 3858) covalent geometry : angle 0.75776 ( 5238) *********************** 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 66 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.410 Fit side-chains REVERT: C 80 GLU cc_start: 0.7727 (tt0) cc_final: 0.7362 (tm-30) REVERT: C 90 ARG cc_start: 0.7746 (ttm170) cc_final: 0.7441 (mtp85) REVERT: D 69 THR cc_start: 0.8412 (m) cc_final: 0.8101 (t) REVERT: D 80 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: F 69 THR cc_start: 0.8424 (m) cc_final: 0.8142 (t) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.9071 time to fit residues: 60.6082 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 : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 80 GLU 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 20 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 0.0870 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 34 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.140258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.123241 restraints weight = 4073.982| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.40 r_work: 0.3770 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3864 Z= 0.121 Angle : 0.629 8.719 5250 Z= 0.314 Chirality : 0.044 0.148 576 Planarity : 0.005 0.062 672 Dihedral : 6.106 15.465 534 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.01 % Allowed : 18.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.012 0.001 TYR D 48 ARG 0.001 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.02845 ( 60) hydrogen bonds : angle 5.49568 ( 180) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.36230 ( 12) covalent geometry : bond 0.00267 ( 3858) covalent geometry : angle 0.62932 ( 5238) *********************** 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 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.435 Fit side-chains REVERT: C 80 GLU cc_start: 0.7564 (tt0) cc_final: 0.7149 (tm-30) REVERT: C 90 ARG cc_start: 0.7782 (ttm170) cc_final: 0.7436 (mtp85) REVERT: D 69 THR cc_start: 0.8410 (m) cc_final: 0.8063 (t) REVERT: D 80 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: F 69 THR cc_start: 0.8378 (m) cc_final: 0.8082 (t) REVERT: F 103 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8022 (m) outliers start: 4 outliers final: 2 residues processed: 63 average time/residue: 0.8679 time to fit residues: 57.2220 Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 80 GLU 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 38 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.0870 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.137146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.119788 restraints weight = 4024.314| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.36 r_work: 0.3731 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3864 Z= 0.158 Angle : 0.655 7.846 5250 Z= 0.332 Chirality : 0.045 0.149 576 Planarity : 0.005 0.061 672 Dihedral : 6.232 15.919 534 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.26 % Allowed : 19.19 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.012 0.001 TYR D 48 ARG 0.003 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03066 ( 60) hydrogen bonds : angle 5.48087 ( 180) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.46111 ( 12) covalent geometry : bond 0.00345 ( 3858) covalent geometry : angle 0.65566 ( 5238) *********************** 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 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.433 Fit side-chains REVERT: C 80 GLU cc_start: 0.7594 (tt0) cc_final: 0.7195 (tm-30) REVERT: C 90 ARG cc_start: 0.7790 (ttm170) cc_final: 0.7484 (mtp85) REVERT: D 44 LEU cc_start: 0.8564 (tp) cc_final: 0.8341 (tm) REVERT: D 69 THR cc_start: 0.8396 (m) cc_final: 0.8055 (t) REVERT: D 80 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: F 69 THR cc_start: 0.8396 (m) cc_final: 0.8100 (t) REVERT: F 103 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8078 (m) outliers start: 5 outliers final: 2 residues processed: 61 average time/residue: 0.9079 time to fit residues: 57.8213 Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 80 GLU 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 13 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.133716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.116180 restraints weight = 4089.807| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.39 r_work: 0.3687 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 3864 Z= 0.304 Angle : 0.798 6.994 5250 Z= 0.411 Chirality : 0.051 0.188 576 Planarity : 0.006 0.062 672 Dihedral : 6.828 19.437 534 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.52 % Allowed : 18.94 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 97 PHE 0.008 0.002 PHE B 99 TYR 0.015 0.002 TYR A 48 ARG 0.007 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 60) hydrogen bonds : angle 5.59219 ( 180) SS BOND : bond 0.00522 ( 6) SS BOND : angle 0.78571 ( 12) covalent geometry : bond 0.00654 ( 3858) covalent geometry : angle 0.79767 ( 5238) ********************** 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 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.388 Fit side-chains REVERT: C 80 GLU cc_start: 0.7721 (tt0) cc_final: 0.7349 (tm-30) REVERT: C 90 ARG cc_start: 0.7756 (ttm170) cc_final: 0.7458 (mtp85) REVERT: D 69 THR cc_start: 0.8417 (m) cc_final: 0.8101 (t) REVERT: D 80 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: F 69 THR cc_start: 0.8423 (m) cc_final: 0.8150 (t) outliers start: 6 outliers final: 4 residues processed: 62 average time/residue: 0.9686 time to fit residues: 62.5714 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 80 GLU 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 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4073 r_free = 0.4073 target = 0.141202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.124310 restraints weight = 4066.919| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.37 r_work: 0.3785 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3458 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= 0.108 Angle : 0.618 8.980 5250 Z= 0.308 Chirality : 0.043 0.146 576 Planarity : 0.005 0.062 672 Dihedral : 5.971 14.805 534 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.52 % Allowed : 18.94 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 97 PHE 0.005 0.001 PHE B 99 TYR 0.013 0.001 TYR E 48 ARG 0.002 0.000 ARG A 28 Details of bonding type rmsd hydrogen bonds : bond 0.02681 ( 60) hydrogen bonds : angle 5.43974 ( 180) SS BOND : bond 0.00144 ( 6) SS BOND : angle 0.34399 ( 12) covalent geometry : bond 0.00241 ( 3858) covalent geometry : angle 0.61839 ( 5238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3153.22 seconds wall clock time: 54 minutes 59.41 seconds (3299.41 seconds total)