Starting phenix.real_space_refine on Tue Feb 11 05:10:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r4r_4727/02_2025/6r4r_4727.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r4r_4727/02_2025/6r4r_4727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r4r_4727/02_2025/6r4r_4727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r4r_4727/02_2025/6r4r_4727.map" model { file = "/net/cci-nas-00/data/ceres_data/6r4r_4727/02_2025/6r4r_4727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r4r_4727/02_2025/6r4r_4727.cif" } resolution = 3.4 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= 0.011 sd= 0.467 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 7 5.16 5 C 2723 2.51 5 N 686 2.21 5 O 896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4312 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 1.83, per 1000 atoms: 0.42 Number of scatterers: 4312 At special positions: 0 Unit cell: (90.695, 115.005, 44.88, 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 7 16.00 O 896 8.00 N 686 7.00 C 2723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 479.2 milliseconds 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.618A pdb=" N LYS A 16 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLU C 19 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG A 18 " --> pdb=" O GLU C 19 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS C 16 " --> pdb=" O GLU E 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU E 19 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG C 18 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS E 16 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU G 19 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG E 18 " --> pdb=" O GLU G 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25 removed outlier: 6.538A pdb=" N ASP A 23 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP C 23 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP E 23 " --> pdb=" O LEU G 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 37 through 41 Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 56 removed outlier: 6.149A pdb=" N GLU A 51 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLY C 54 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 53 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU C 56 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP A 55 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU C 51 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY E 54 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE C 53 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU E 56 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TRP C 55 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU E 51 " --> pdb=" O GLU G 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY G 54 " --> pdb=" O GLU E 51 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE E 53 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU G 56 " --> pdb=" O ILE E 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP E 55 " --> pdb=" O LEU G 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 61 through 68 Processing sheet with id=AA8, first strand: chain 'A' and resid 71 through 76 Processing sheet with id=AA9, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.617A pdb=" N LYS B 16 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU D 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 18 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS D 16 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU F 19 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG D 18 " --> pdb=" O GLU F 19 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 23 through 25 removed outlier: 6.538A pdb=" N ASP B 23 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP D 23 " --> pdb=" O LEU F 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 29 through 34 Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 41 Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.151A pdb=" N GLU B 51 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY D 54 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE B 53 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU D 56 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N TRP B 55 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU D 51 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N GLY F 54 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 53 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU F 56 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N TRP D 55 " --> pdb=" O LEU F 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 61 through 68 Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 76 110 hydrogen bonds defined for protein. 330 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: 1.08 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1415 1.34 - 1.45: 707 1.45 - 1.57: 2267 1.57 - 1.69: 0 1.69 - 1.80: 14 Bond restraints: 4403 Sorted by residual: bond pdb=" CG LEU C 30 " pdb=" CD1 LEU C 30 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.98e+00 bond pdb=" CG LEU G 30 " pdb=" CD1 LEU G 30 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 bond pdb=" CG LEU E 30 " pdb=" CD1 LEU E 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CG LEU A 30 " pdb=" CD1 LEU A 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CG LEU D 30 " pdb=" CD1 LEU D 30 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.89e+00 ... (remaining 4398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 5708 3.12 - 6.23: 207 6.23 - 9.35: 7 9.35 - 12.47: 14 12.47 - 15.58: 7 Bond angle restraints: 5943 Sorted by residual: angle pdb=" C GLU C 20 " pdb=" N ASP C 21 " pdb=" CA ASP C 21 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLU F 20 " pdb=" N ASP F 21 " pdb=" CA ASP F 21 " ideal model delta sigma weight residual 121.54 131.22 -9.68 1.91e+00 2.74e-01 2.57e+01 angle pdb=" C GLU E 20 " pdb=" N ASP E 21 " pdb=" CA ASP E 21 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLU G 20 " pdb=" N ASP G 21 " pdb=" CA ASP G 21 " ideal model delta sigma weight residual 121.54 131.20 -9.66 1.91e+00 2.74e-01 2.56e+01 angle pdb=" C GLU D 20 " pdb=" N ASP D 21 " pdb=" CA ASP D 21 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 ... (remaining 5938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.72: 1867 7.72 - 15.43: 499 15.43 - 23.15: 119 23.15 - 30.87: 35 30.87 - 38.59: 35 Dihedral angle restraints: 2555 sinusoidal: 1036 harmonic: 1519 Sorted by residual: dihedral pdb=" CA GLY E 5 " pdb=" C GLY E 5 " pdb=" N TYR E 6 " pdb=" CA TYR E 6 " ideal model delta harmonic sigma weight residual -180.00 -159.56 -20.44 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLY G 5 " pdb=" C GLY G 5 " pdb=" N TYR G 6 " pdb=" CA TYR G 6 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA GLY C 5 " pdb=" C GLY C 5 " pdb=" N TYR C 6 " pdb=" CA TYR C 6 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 2552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 405 0.069 - 0.137: 162 0.137 - 0.206: 21 0.206 - 0.275: 0 0.275 - 0.344: 7 Chirality restraints: 595 Sorted by residual: chirality pdb=" CA ASP F 21 " pdb=" N ASP F 21 " pdb=" C ASP F 21 " pdb=" CB ASP F 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ASP D 21 " pdb=" N ASP D 21 " pdb=" C ASP D 21 " pdb=" CB ASP D 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASP A 21 " pdb=" N ASP A 21 " pdb=" C ASP A 21 " pdb=" CB ASP A 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 592 not shown) Planarity restraints: 791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 48 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C ALA C 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA C 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS C 49 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 48 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C ALA E 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA E 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS E 49 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 48 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C ALA G 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ALA G 48 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS G 49 " -0.018 2.00e-02 2.50e+03 ... (remaining 788 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1211 2.83 - 3.34: 3397 3.34 - 3.86: 7837 3.86 - 4.38: 8251 4.38 - 4.90: 15637 Nonbonded interactions: 36333 Sorted by model distance: nonbonded pdb=" OE2 GLU A 47 " pdb=" NZ LYS A 49 " model vdw 2.308 3.120 nonbonded pdb=" OE2 GLU B 47 " pdb=" NZ LYS B 49 " model vdw 2.309 3.120 nonbonded pdb=" OE2 GLU F 47 " pdb=" NZ LYS F 49 " model vdw 2.310 3.120 nonbonded pdb=" OE2 GLU E 47 " pdb=" NZ LYS E 49 " model vdw 2.310 3.120 nonbonded pdb=" OE2 GLU C 47 " pdb=" NZ LYS C 49 " model vdw 2.310 3.120 ... (remaining 36328 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 'G' 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: 0.540 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.720 Find NCS groups from input model: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 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 : 0.008 0.057 4403 Z= 0.504 Angle : 1.430 15.584 5943 Z= 0.726 Chirality : 0.075 0.344 595 Planarity : 0.008 0.054 791 Dihedral : 10.872 38.585 1617 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -5.16 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 55 HIS 0.018 0.011 HIS A 25 PHE 0.008 0.003 PHE B 69 TYR 0.017 0.004 TYR B 8 ARG 0.003 0.001 ARG G 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.480 Fit side-chains REVERT: A 66 ARG cc_start: 0.7176 (ttm110) cc_final: 0.5303 (tpt170) REVERT: B 66 ARG cc_start: 0.7045 (ttm110) cc_final: 0.5719 (tpt170) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1604 time to fit residues: 39.5741 Evaluate side-chains 116 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 0.0170 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 overall best weight: 3.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 HIS E 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.219933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.202260 restraints weight = 8039.820| |-----------------------------------------------------------------------------| r_work (start): 0.4782 rms_B_bonded: 2.77 r_work: 0.4717 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4403 Z= 0.214 Angle : 0.737 9.336 5943 Z= 0.365 Chirality : 0.046 0.185 595 Planarity : 0.005 0.041 791 Dihedral : 5.968 17.953 602 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.17 % Allowed : 12.02 % Favored : 84.81 % 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: -4.87 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 55 HIS 0.004 0.001 HIS F 25 PHE 0.010 0.002 PHE D 69 TYR 0.018 0.002 TYR E 59 ARG 0.010 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.525 Fit side-chains REVERT: A 51 GLU cc_start: 0.7159 (tt0) cc_final: 0.6857 (tt0) REVERT: A 55 TRP cc_start: 0.6257 (t60) cc_final: 0.6025 (t60) REVERT: A 66 ARG cc_start: 0.7302 (ttm110) cc_final: 0.4946 (tpt170) REVERT: B 28 ASP cc_start: 0.5119 (t70) cc_final: 0.4066 (t0) REVERT: B 29 ILE cc_start: 0.7447 (mm) cc_final: 0.7246 (pt) REVERT: B 44 ASP cc_start: 0.4435 (m-30) cc_final: 0.3714 (m-30) REVERT: B 63 THR cc_start: 0.8533 (m) cc_final: 0.8295 (t) REVERT: D 8 TYR cc_start: 0.7800 (p90) cc_final: 0.7579 (p90) REVERT: D 44 ASP cc_start: 0.6449 (m-30) cc_final: 0.6068 (m-30) REVERT: D 66 ARG cc_start: 0.7480 (ttm110) cc_final: 0.7047 (ttp-110) REVERT: D 69 PHE cc_start: 0.8460 (m-80) cc_final: 0.8241 (m-80) REVERT: E 44 ASP cc_start: 0.6746 (m-30) cc_final: 0.6135 (m-30) REVERT: E 55 TRP cc_start: 0.7913 (t-100) cc_final: 0.7588 (t-100) REVERT: E 69 PHE cc_start: 0.8656 (m-80) cc_final: 0.8134 (m-80) REVERT: E 75 GLU cc_start: 0.8190 (tt0) cc_final: 0.7923 (tt0) REVERT: F 51 GLU cc_start: 0.6654 (tt0) cc_final: 0.6142 (pm20) REVERT: F 63 THR cc_start: 0.8299 (m) cc_final: 0.7855 (t) REVERT: G 63 THR cc_start: 0.8505 (m) cc_final: 0.8133 (t) outliers start: 14 outliers final: 7 residues processed: 142 average time/residue: 0.1517 time to fit residues: 27.0880 Evaluate side-chains 118 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain G residue 56 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 27 optimal weight: 30.0000 chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 16 optimal weight: 5.9990 chunk 6 optimal weight: 0.0870 chunk 14 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 overall best weight: 9.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 HIS ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.177922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.169447 restraints weight = 8378.524| |-----------------------------------------------------------------------------| r_work (start): 0.4692 rms_B_bonded: 2.95 r_work: 0.4628 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4403 Z= 0.358 Angle : 0.808 11.297 5943 Z= 0.412 Chirality : 0.049 0.162 595 Planarity : 0.006 0.052 791 Dihedral : 6.116 19.705 602 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 4.54 % Allowed : 12.93 % Favored : 82.54 % 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: -4.72 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 55 HIS 0.002 0.001 HIS B 25 PHE 0.022 0.002 PHE A 69 TYR 0.022 0.003 TYR B 8 ARG 0.005 0.002 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.480 Fit side-chains REVERT: A 11 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8619 (pt) REVERT: A 28 ASP cc_start: 0.5991 (t0) cc_final: 0.5448 (t0) REVERT: A 66 ARG cc_start: 0.7966 (ttm110) cc_final: 0.5198 (tpt170) REVERT: B 63 THR cc_start: 0.8367 (m) cc_final: 0.8068 (t) REVERT: D 47 GLU cc_start: 0.5936 (tp30) cc_final: 0.5462 (tp30) REVERT: D 63 THR cc_start: 0.8549 (m) cc_final: 0.8074 (t) REVERT: D 69 PHE cc_start: 0.8496 (m-80) cc_final: 0.8230 (m-80) REVERT: E 44 ASP cc_start: 0.6821 (m-30) cc_final: 0.6478 (m-30) REVERT: E 47 GLU cc_start: 0.5871 (tp30) cc_final: 0.4981 (tp30) REVERT: E 55 TRP cc_start: 0.8143 (t-100) cc_final: 0.7763 (t-100) REVERT: F 51 GLU cc_start: 0.7240 (tt0) cc_final: 0.6659 (pm20) REVERT: F 63 THR cc_start: 0.8431 (m) cc_final: 0.8164 (t) REVERT: G 66 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7781 (ttp-110) outliers start: 20 outliers final: 12 residues processed: 133 average time/residue: 0.1415 time to fit residues: 24.0311 Evaluate side-chains 120 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 30.0000 chunk 47 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 10 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 37 optimal weight: 0.0270 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.223174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.198303 restraints weight = 8211.095| |-----------------------------------------------------------------------------| r_work (start): 0.4852 rms_B_bonded: 2.49 r_work: 0.4912 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.4832 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.4832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.5575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4403 Z= 0.174 Angle : 0.592 6.648 5943 Z= 0.298 Chirality : 0.042 0.168 595 Planarity : 0.004 0.033 791 Dihedral : 5.219 15.339 602 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.31 % Allowed : 14.74 % Favored : 80.95 % 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: -4.66 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 55 HIS 0.002 0.001 HIS F 25 PHE 0.021 0.002 PHE B 69 TYR 0.016 0.002 TYR B 8 ARG 0.005 0.001 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.516 Fit side-chains REVERT: A 28 ASP cc_start: 0.5298 (t0) cc_final: 0.4810 (t0) REVERT: A 29 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6561 (pt) REVERT: A 36 SER cc_start: 0.7371 (m) cc_final: 0.7155 (t) REVERT: B 28 ASP cc_start: 0.4638 (t70) cc_final: 0.3320 (t0) REVERT: B 29 ILE cc_start: 0.7393 (mm) cc_final: 0.6748 (pt) REVERT: B 30 LEU cc_start: 0.7936 (tt) cc_final: 0.7608 (mm) REVERT: C 47 GLU cc_start: 0.6038 (tp30) cc_final: 0.5410 (tp30) REVERT: C 69 PHE cc_start: 0.8530 (m-80) cc_final: 0.8245 (m-80) REVERT: D 30 LEU cc_start: 0.8005 (tt) cc_final: 0.7789 (tp) REVERT: D 63 THR cc_start: 0.8461 (m) cc_final: 0.8147 (t) REVERT: E 47 GLU cc_start: 0.5142 (tp30) cc_final: 0.4898 (tp30) REVERT: F 51 GLU cc_start: 0.6809 (tt0) cc_final: 0.6489 (pm20) REVERT: G 66 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7740 (ttp-110) outliers start: 19 outliers final: 10 residues processed: 135 average time/residue: 0.1569 time to fit residues: 26.8208 Evaluate side-chains 121 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 27 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.200139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.176766 restraints weight = 8368.493| |-----------------------------------------------------------------------------| r_work (start): 0.4706 rms_B_bonded: 2.88 r_work: 0.4637 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.4637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4403 Z= 0.360 Angle : 0.730 6.632 5943 Z= 0.377 Chirality : 0.047 0.160 595 Planarity : 0.005 0.060 791 Dihedral : 5.638 16.021 602 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 7.03 % Allowed : 14.74 % Favored : 78.23 % 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: -4.67 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 55 HIS 0.001 0.000 HIS G 25 PHE 0.028 0.003 PHE E 69 TYR 0.015 0.003 TYR G 8 ARG 0.003 0.001 ARG D 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: B 28 ASP cc_start: 0.4517 (t70) cc_final: 0.3478 (t0) REVERT: B 29 ILE cc_start: 0.7783 (mm) cc_final: 0.7200 (pt) REVERT: C 55 TRP cc_start: 0.7717 (t-100) cc_final: 0.7291 (t-100) REVERT: D 47 GLU cc_start: 0.5938 (tp30) cc_final: 0.5704 (mm-30) REVERT: D 63 THR cc_start: 0.8588 (m) cc_final: 0.8222 (t) REVERT: E 55 TRP cc_start: 0.8471 (t-100) cc_final: 0.7744 (t-100) REVERT: F 51 GLU cc_start: 0.7208 (tt0) cc_final: 0.6754 (pm20) REVERT: G 44 ASP cc_start: 0.6011 (m-30) cc_final: 0.5666 (m-30) REVERT: G 66 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7846 (ttp-110) outliers start: 31 outliers final: 20 residues processed: 117 average time/residue: 0.1341 time to fit residues: 20.4208 Evaluate side-chains 116 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 66 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 20.0000 chunk 17 optimal weight: 40.0000 chunk 46 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 45 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.205731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.183586 restraints weight = 7996.182| |-----------------------------------------------------------------------------| r_work (start): 0.4788 rms_B_bonded: 2.84 r_work: 0.4719 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.6249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4403 Z= 0.189 Angle : 0.605 7.747 5943 Z= 0.305 Chirality : 0.043 0.158 595 Planarity : 0.004 0.036 791 Dihedral : 5.142 17.341 602 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 5.67 % Allowed : 16.78 % Favored : 77.55 % 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: -4.66 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 55 HIS 0.001 0.001 HIS G 25 PHE 0.014 0.002 PHE E 69 TYR 0.018 0.002 TYR B 8 ARG 0.002 0.000 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.6129 (t0) cc_final: 0.5838 (t0) REVERT: B 18 ARG cc_start: 0.5964 (mtt180) cc_final: 0.5361 (mtm110) REVERT: B 28 ASP cc_start: 0.4641 (t70) cc_final: 0.3548 (t0) REVERT: D 1 MET cc_start: 0.5802 (mtm) cc_final: 0.5559 (mtm) REVERT: D 63 THR cc_start: 0.8639 (m) cc_final: 0.8367 (t) REVERT: D 66 ARG cc_start: 0.7532 (ttp-110) cc_final: 0.7114 (ttp-110) REVERT: D 69 PHE cc_start: 0.8377 (m-80) cc_final: 0.8041 (m-80) REVERT: E 24 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8095 (pp) REVERT: E 44 ASP cc_start: 0.6385 (m-30) cc_final: 0.6024 (m-30) REVERT: E 47 GLU cc_start: 0.5314 (tp30) cc_final: 0.4875 (tp30) REVERT: F 51 GLU cc_start: 0.7111 (tt0) cc_final: 0.6679 (pm20) REVERT: G 51 GLU cc_start: 0.6777 (tt0) cc_final: 0.6420 (pm20) REVERT: G 69 PHE cc_start: 0.6990 (m-80) cc_final: 0.6022 (m-80) outliers start: 25 outliers final: 13 residues processed: 132 average time/residue: 0.1624 time to fit residues: 26.7271 Evaluate side-chains 119 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 33 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 40.0000 chunk 42 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.246097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.223129 restraints weight = 9277.144| |-----------------------------------------------------------------------------| r_work (start): 0.4861 rms_B_bonded: 1.19 r_work: 0.4892 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.4842 rms_B_bonded: 2.33 restraints_weight: 0.2500 r_work (final): 0.4842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4403 Z= 0.238 Angle : 0.655 7.877 5943 Z= 0.333 Chirality : 0.044 0.148 595 Planarity : 0.004 0.037 791 Dihedral : 5.193 19.622 602 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 6.80 % Allowed : 17.46 % Favored : 75.74 % 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: -4.66 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 55 HIS 0.002 0.001 HIS B 25 PHE 0.016 0.002 PHE E 69 TYR 0.016 0.002 TYR G 8 ARG 0.003 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6737 (t0) REVERT: B 28 ASP cc_start: 0.4517 (t70) cc_final: 0.3436 (t0) REVERT: C 43 SER cc_start: 0.8449 (p) cc_final: 0.7655 (m) REVERT: C 47 GLU cc_start: 0.6185 (tp30) cc_final: 0.5528 (tp30) REVERT: D 63 THR cc_start: 0.8552 (m) cc_final: 0.8315 (t) REVERT: D 66 ARG cc_start: 0.7768 (ttp-110) cc_final: 0.7283 (ttp-110) REVERT: E 55 TRP cc_start: 0.7956 (t-100) cc_final: 0.7670 (t-100) REVERT: F 18 ARG cc_start: 0.6553 (mtt180) cc_final: 0.6034 (mtm110) REVERT: G 69 PHE cc_start: 0.6576 (m-80) cc_final: 0.5984 (m-80) outliers start: 30 outliers final: 21 residues processed: 121 average time/residue: 0.1604 time to fit residues: 24.6530 Evaluate side-chains 122 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 14 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.246231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.5121 r_free = 0.5121 target = 0.223400 restraints weight = 9165.374| |-----------------------------------------------------------------------------| r_work (start): 0.4872 rms_B_bonded: 1.21 r_work: 0.4888 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.4835 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.6625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4403 Z= 0.250 Angle : 0.679 8.361 5943 Z= 0.344 Chirality : 0.044 0.146 595 Planarity : 0.004 0.038 791 Dihedral : 5.185 21.013 602 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 7.03 % Allowed : 18.14 % Favored : 74.83 % 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: -4.66 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 55 HIS 0.001 0.001 HIS B 25 PHE 0.029 0.002 PHE B 69 TYR 0.016 0.002 TYR F 8 ARG 0.003 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.532 Fit side-chains REVERT: A 57 ASN cc_start: 0.7387 (OUTLIER) cc_final: 0.6716 (t0) REVERT: B 28 ASP cc_start: 0.4259 (t70) cc_final: 0.3351 (t0) REVERT: C 47 GLU cc_start: 0.6087 (tp30) cc_final: 0.5738 (tp30) REVERT: D 63 THR cc_start: 0.8587 (m) cc_final: 0.8373 (t) REVERT: D 66 ARG cc_start: 0.7682 (ttp-110) cc_final: 0.7377 (ttp-110) REVERT: E 24 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8061 (pp) REVERT: E 47 GLU cc_start: 0.5266 (tp30) cc_final: 0.4830 (tp30) REVERT: E 55 TRP cc_start: 0.8017 (t-100) cc_final: 0.7806 (t-100) REVERT: F 18 ARG cc_start: 0.6458 (mtt180) cc_final: 0.5966 (mtm110) outliers start: 31 outliers final: 21 residues processed: 118 average time/residue: 0.1519 time to fit residues: 22.9636 Evaluate side-chains 119 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.243319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.219950 restraints weight = 9336.302| |-----------------------------------------------------------------------------| r_work (start): 0.4847 rms_B_bonded: 1.20 r_work: 0.4874 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.4823 rms_B_bonded: 2.38 restraints_weight: 0.2500 r_work (final): 0.4823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4403 Z= 0.305 Angle : 0.721 8.385 5943 Z= 0.368 Chirality : 0.046 0.154 595 Planarity : 0.004 0.043 791 Dihedral : 5.399 21.842 602 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 6.35 % Allowed : 19.27 % Favored : 74.38 % 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: -4.67 (0.25), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 55 HIS 0.002 0.001 HIS B 25 PHE 0.033 0.002 PHE B 69 TYR 0.016 0.002 TYR G 8 ARG 0.003 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.470 Fit side-chains REVERT: A 28 ASP cc_start: 0.6400 (t0) cc_final: 0.6171 (t0) REVERT: B 28 ASP cc_start: 0.3925 (t70) cc_final: 0.3009 (t0) REVERT: B 68 ASP cc_start: 0.7832 (m-30) cc_final: 0.7619 (t0) REVERT: C 43 SER cc_start: 0.8651 (m) cc_final: 0.8385 (p) REVERT: C 47 GLU cc_start: 0.5964 (tp30) cc_final: 0.5388 (tp30) REVERT: D 18 ARG cc_start: 0.6064 (mtt180) cc_final: 0.5603 (mtm110) REVERT: D 63 THR cc_start: 0.8558 (m) cc_final: 0.8335 (t) REVERT: D 66 ARG cc_start: 0.7740 (ttp-110) cc_final: 0.7423 (ttp-110) REVERT: E 44 ASP cc_start: 0.6660 (m-30) cc_final: 0.6377 (m-30) REVERT: E 47 GLU cc_start: 0.5287 (tp30) cc_final: 0.4817 (tp30) REVERT: E 55 TRP cc_start: 0.8031 (t-100) cc_final: 0.7757 (t-100) REVERT: F 18 ARG cc_start: 0.6639 (mtt180) cc_final: 0.6019 (mtm110) outliers start: 28 outliers final: 23 residues processed: 109 average time/residue: 0.1680 time to fit residues: 22.8866 Evaluate side-chains 114 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 2 SER Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 30 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.244859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.221894 restraints weight = 9149.463| |-----------------------------------------------------------------------------| r_work (start): 0.4871 rms_B_bonded: 1.18 r_work: 0.4895 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.4842 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.4842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.6911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4403 Z= 0.267 Angle : 0.700 8.684 5943 Z= 0.353 Chirality : 0.045 0.152 595 Planarity : 0.004 0.041 791 Dihedral : 5.293 21.862 602 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 5.44 % Allowed : 20.63 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.65 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.19), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 55 HIS 0.001 0.001 HIS B 25 PHE 0.032 0.002 PHE B 69 TYR 0.016 0.002 TYR G 8 ARG 0.004 0.001 ARG F 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1050 Ramachandran restraints generated. 525 Oldfield, 0 Emsley, 525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.514 Fit side-chains REVERT: A 57 ASN cc_start: 0.7422 (OUTLIER) cc_final: 0.6761 (t0) REVERT: B 28 ASP cc_start: 0.3913 (t70) cc_final: 0.3226 (t0) REVERT: B 68 ASP cc_start: 0.7824 (m-30) cc_final: 0.7612 (t0) REVERT: C 43 SER cc_start: 0.8599 (m) cc_final: 0.8352 (p) REVERT: C 47 GLU cc_start: 0.6011 (tp30) cc_final: 0.5477 (tp30) REVERT: D 18 ARG cc_start: 0.6111 (mtt180) cc_final: 0.5612 (mtm110) REVERT: D 43 SER cc_start: 0.8645 (p) cc_final: 0.8400 (m) REVERT: D 63 THR cc_start: 0.8632 (m) cc_final: 0.8431 (t) REVERT: D 66 ARG cc_start: 0.7658 (ttp-110) cc_final: 0.7285 (ttp-110) REVERT: E 55 TRP cc_start: 0.8033 (t-100) cc_final: 0.7813 (t-100) REVERT: F 18 ARG cc_start: 0.6597 (mtt180) cc_final: 0.6000 (mtm110) outliers start: 24 outliers final: 18 residues processed: 110 average time/residue: 0.1647 time to fit residues: 22.7396 Evaluate side-chains 113 residues out of total 441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain G residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 21 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 42 optimal weight: 20.0000 chunk 9 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4964 r_free = 0.4964 target = 0.243482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5105 r_free = 0.5105 target = 0.220203 restraints weight = 9228.509| |-----------------------------------------------------------------------------| r_work (start): 0.4848 rms_B_bonded: 1.20 r_work: 0.4867 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.4817 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.4817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.7006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4403 Z= 0.309 Angle : 0.739 8.507 5943 Z= 0.373 Chirality : 0.046 0.153 595 Planarity : 0.005 0.044 791 Dihedral : 5.437 21.879 602 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.76 % Allowed : 20.63 % Favored : 74.60 % 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: -4.68 (0.24), residues: 525 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.18), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 55 HIS 0.001 0.001 HIS B 25 PHE 0.031 0.002 PHE B 69 TYR 0.016 0.002 TYR G 8 ARG 0.007 0.001 ARG F 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1920.48 seconds wall clock time: 34 minutes 59.59 seconds (2099.59 seconds total)