Starting phenix.real_space_refine on Wed Sep 17 03:20:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k0d_61944/09_2025/9k0d_61944.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k0d_61944/09_2025/9k0d_61944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k0d_61944/09_2025/9k0d_61944.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k0d_61944/09_2025/9k0d_61944.map" model { file = "/net/cci-nas-00/data/ceres_data/9k0d_61944/09_2025/9k0d_61944.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k0d_61944/09_2025/9k0d_61944.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 1878 2.51 5 N 486 2.21 5 O 498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2874 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 256 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "D" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 110 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 112 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Restraints were copied for chains: G, M, U, N, V, H, O, W, P, X, F, K, S, L, T Time building chain proxies: 0.52, per 1000 atoms: 0.18 Number of scatterers: 2874 At special positions: 0 Unit cell: (97.11, 95.45, 35.69, 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 498 8.00 N 486 7.00 C 1878 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: 0.24 Conformation dependent library (CDL) restraints added in 98.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'M' and resid 12 through 13 removed outlier: 6.261A pdb=" N VAL C 12 " --> pdb=" O HIS N 13 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 16 through 19 removed outlier: 6.358A pdb=" N LEU C 17 " --> pdb=" O VAL M 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 31 through 33 removed outlier: 6.392A pdb=" N ILE C 31 " --> pdb=" O ILE M 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 39 through 41 removed outlier: 6.756A pdb=" N VAL C 40 " --> pdb=" O ILE M 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 30 through 36 removed outlier: 8.863A pdb=" N ILE D 31 " --> pdb=" O ILE O 32 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N LEU O 34 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLY D 33 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL O 36 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET D 35 " --> pdb=" O VAL O 36 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE P 31 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE D 32 " --> pdb=" O ILE P 31 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY P 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'O' and resid 39 through 41 removed outlier: 6.484A pdb=" N VAL D 40 " --> pdb=" O ILE O 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 16 through 19 removed outlier: 6.917A pdb=" N LYS B 16 " --> pdb=" O LEU K 17 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N PHE K 19 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 18 " --> pdb=" O PHE K 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'U' and resid 12 through 13 removed outlier: 6.258A pdb=" N VAL G 12 " --> pdb=" O HIS V 13 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 16 through 19 removed outlier: 6.363A pdb=" N LEU G 17 " --> pdb=" O VAL U 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 31 through 33 removed outlier: 6.392A pdb=" N ILE G 31 " --> pdb=" O ILE U 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 39 through 41 removed outlier: 6.754A pdb=" N VAL G 40 " --> pdb=" O ILE U 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 30 through 36 removed outlier: 8.871A pdb=" N ILE H 31 " --> pdb=" O ILE W 32 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU W 34 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLY H 33 " --> pdb=" O LEU W 34 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N VAL W 36 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET H 35 " --> pdb=" O VAL W 36 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE X 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE H 32 " --> pdb=" O ILE X 31 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLY X 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 39 through 41 removed outlier: 6.488A pdb=" N VAL H 40 " --> pdb=" O ILE W 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 16 through 19 removed outlier: 6.923A pdb=" N LYS F 16 " --> pdb=" O LEU S 17 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N PHE S 19 " --> pdb=" O LYS F 16 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL F 18 " --> pdb=" O PHE S 19 " (cutoff:3.500A) 32 hydrogen bonds defined for protein. 96 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: 0.30 Time building geometry restraints manager: 0.28 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: 900 1.34 - 1.45: 423 1.45 - 1.57: 1563 1.57 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 2910 Sorted by residual: bond pdb=" C ASP N 23 " pdb=" N VAL N 24 " ideal model delta sigma weight residual 1.329 1.303 0.026 1.69e-02 3.50e+03 2.35e+00 bond pdb=" C ASP V 23 " pdb=" N VAL V 24 " ideal model delta sigma weight residual 1.329 1.303 0.025 1.69e-02 3.50e+03 2.26e+00 bond pdb=" C ASP G 23 " pdb=" N VAL G 24 " ideal model delta sigma weight residual 1.329 1.303 0.025 1.69e-02 3.50e+03 2.25e+00 bond pdb=" C ASP M 23 " pdb=" N VAL M 24 " ideal model delta sigma weight residual 1.329 1.303 0.025 1.69e-02 3.50e+03 2.25e+00 bond pdb=" C ASP U 23 " pdb=" N VAL U 24 " ideal model delta sigma weight residual 1.329 1.304 0.025 1.69e-02 3.50e+03 2.21e+00 ... (remaining 2905 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 3586 1.27 - 2.54: 230 2.54 - 3.80: 42 3.80 - 5.07: 18 5.07 - 6.34: 18 Bond angle restraints: 3894 Sorted by residual: angle pdb=" C GLU G 22 " pdb=" N ASP G 23 " pdb=" CA ASP G 23 " ideal model delta sigma weight residual 122.76 118.13 4.63 1.63e+00 3.76e-01 8.06e+00 angle pdb=" C GLU C 22 " pdb=" N ASP C 23 " pdb=" CA ASP C 23 " ideal model delta sigma weight residual 122.76 118.17 4.59 1.63e+00 3.76e-01 7.92e+00 angle pdb=" C GLU V 22 " pdb=" N ASP V 23 " pdb=" CA ASP V 23 " ideal model delta sigma weight residual 122.76 118.18 4.58 1.63e+00 3.76e-01 7.88e+00 angle pdb=" C GLU U 22 " pdb=" N ASP U 23 " pdb=" CA ASP U 23 " ideal model delta sigma weight residual 122.76 118.20 4.56 1.63e+00 3.76e-01 7.83e+00 angle pdb=" C GLU N 22 " pdb=" N ASP N 23 " pdb=" CA ASP N 23 " ideal model delta sigma weight residual 122.76 118.20 4.56 1.63e+00 3.76e-01 7.83e+00 ... (remaining 3889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.32: 1452 18.32 - 36.65: 138 36.65 - 54.97: 12 54.97 - 73.29: 0 73.29 - 91.61: 12 Dihedral angle restraints: 1614 sinusoidal: 582 harmonic: 1032 Sorted by residual: dihedral pdb=" CA ALA M 21 " pdb=" C ALA M 21 " pdb=" N GLU M 22 " pdb=" CA GLU M 22 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA C 21 " pdb=" C ALA C 21 " pdb=" N GLU C 22 " pdb=" CA GLU C 22 " ideal model delta harmonic sigma weight residual -180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA ALA V 21 " pdb=" C ALA V 21 " pdb=" N GLU V 22 " pdb=" CA GLU V 22 " ideal model delta harmonic sigma weight residual -180.00 -155.76 -24.24 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 1611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 180 0.028 - 0.057: 151 0.057 - 0.085: 23 0.085 - 0.113: 67 0.113 - 0.141: 29 Chirality restraints: 450 Sorted by residual: chirality pdb=" CA VAL T 12 " pdb=" N VAL T 12 " pdb=" C VAL T 12 " pdb=" CB VAL T 12 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL S 12 " pdb=" N VAL S 12 " pdb=" C VAL S 12 " pdb=" CB VAL S 12 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA VAL B 12 " pdb=" N VAL B 12 " pdb=" C VAL B 12 " pdb=" CB VAL B 12 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 447 not shown) Planarity restraints: 480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP M 23 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C ASP M 23 " -0.022 2.00e-02 2.50e+03 pdb=" O ASP M 23 " 0.008 2.00e-02 2.50e+03 pdb=" N VAL M 24 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP V 23 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C ASP V 23 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP V 23 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL V 24 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP U 23 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C ASP U 23 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP U 23 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL U 24 " -0.007 2.00e-02 2.50e+03 ... (remaining 477 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 984 2.88 - 3.38: 2349 3.38 - 3.89: 4633 3.89 - 4.39: 4942 4.39 - 4.90: 9912 Nonbonded interactions: 22820 Sorted by model distance: nonbonded pdb=" O SER D 26 " pdb=" N SER O 26 " model vdw 2.369 3.120 nonbonded pdb=" OE1 GLN U 15 " pdb=" ND1 HIS S 13 " model vdw 2.373 3.120 nonbonded pdb=" OE1 GLN C 15 " pdb=" ND1 HIS B 13 " model vdw 2.373 3.120 nonbonded pdb=" OE1 GLN V 15 " pdb=" ND1 HIS T 13 " model vdw 2.374 3.120 nonbonded pdb=" OE1 GLN G 15 " pdb=" ND1 HIS F 13 " model vdw 2.374 3.120 ... (remaining 22815 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'M' selection = chain 'U' selection = chain 'N' selection = chain 'V' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'O' selection = chain 'W' selection = chain 'P' selection = chain 'X' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' selection = chain 'S' selection = chain 'L' selection = chain 'T' } 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: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.270 Find NCS groups from input model: 0.040 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:9.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 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 0.037 2910 Z= 0.337 Angle : 0.851 6.340 3894 Z= 0.441 Chirality : 0.058 0.141 450 Planarity : 0.003 0.013 480 Dihedral : 16.067 91.614 966 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.32), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.24), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR S 10 PHE 0.005 0.002 PHE N 19 HIS 0.005 0.002 HIS V 14 Details of bonding type rmsd covalent geometry : bond 0.00775 ( 2910) covalent geometry : angle 0.85089 ( 3894) hydrogen bonds : bond 0.13396 ( 32) hydrogen bonds : angle 7.61873 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.084 Fit side-chains REVERT: N 14 HIS cc_start: 0.7820 (t70) cc_final: 0.7559 (t70) REVERT: V 14 HIS cc_start: 0.7766 (t70) cc_final: 0.7533 (t70) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.4034 time to fit residues: 26.6410 Evaluate side-chains 50 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 13 optimal weight: 0.0570 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 HIS G 13 HIS K 14 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 HIS L 14 HIS V 13 HIS ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.177603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.131334 restraints weight = 3106.175| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.68 r_work: 0.3899 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2910 Z= 0.092 Angle : 0.527 4.924 3894 Z= 0.260 Chirality : 0.055 0.124 450 Planarity : 0.001 0.006 480 Dihedral : 4.562 21.120 384 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.74 % Allowed : 23.61 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.35), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.26), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR S 10 PHE 0.009 0.001 PHE F 19 HIS 0.008 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 2910) covalent geometry : angle 0.52653 ( 3894) hydrogen bonds : bond 0.01498 ( 32) hydrogen bonds : angle 4.85767 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.112 Fit side-chains REVERT: B 16 LYS cc_start: 0.8377 (mppt) cc_final: 0.8164 (mptp) REVERT: G 14 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7550 (m-70) REVERT: N 14 HIS cc_start: 0.8277 (t70) cc_final: 0.7992 (t70) REVERT: L 14 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7189 (p90) REVERT: V 14 HIS cc_start: 0.8250 (t70) cc_final: 0.7997 (t70) outliers start: 5 outliers final: 0 residues processed: 43 average time/residue: 0.5960 time to fit residues: 26.2972 Evaluate side-chains 43 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain L residue 14 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 14 HIS M 13 HIS U 13 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN L 14 HIS ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.171853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.124030 restraints weight = 3184.906| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.79 r_work: 0.3807 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2910 Z= 0.179 Angle : 0.593 5.323 3894 Z= 0.298 Chirality : 0.057 0.130 450 Planarity : 0.002 0.011 480 Dihedral : 4.872 23.105 384 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.47 % Allowed : 27.08 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.36), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR K 10 PHE 0.009 0.001 PHE F 19 HIS 0.004 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 2910) covalent geometry : angle 0.59346 ( 3894) hydrogen bonds : bond 0.01595 ( 32) hydrogen bonds : angle 4.93237 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.154 Fit side-chains REVERT: G 14 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7513 (m-70) REVERT: F 16 LYS cc_start: 0.8477 (mptp) cc_final: 0.8219 (mptp) REVERT: K 14 HIS cc_start: 0.8096 (OUTLIER) cc_final: 0.7464 (p90) outliers start: 10 outliers final: 2 residues processed: 51 average time/residue: 0.4281 time to fit residues: 22.5122 Evaluate side-chains 50 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain T residue 14 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS U 13 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN N 14 HIS ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.168545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.121363 restraints weight = 3230.071| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.79 r_work: 0.3751 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 2910 Z= 0.305 Angle : 0.695 5.697 3894 Z= 0.350 Chirality : 0.059 0.133 450 Planarity : 0.003 0.015 480 Dihedral : 5.301 25.588 384 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 6.94 % Allowed : 25.35 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.36), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR M 10 PHE 0.012 0.002 PHE F 19 HIS 0.005 0.002 HIS T 14 Details of bonding type rmsd covalent geometry : bond 0.00724 ( 2910) covalent geometry : angle 0.69450 ( 3894) hydrogen bonds : bond 0.01718 ( 32) hydrogen bonds : angle 4.92925 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.115 Fit side-chains REVERT: G 14 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.7466 (m90) REVERT: F 14 HIS cc_start: 0.7740 (OUTLIER) cc_final: 0.7237 (p90) REVERT: F 16 LYS cc_start: 0.8482 (mptp) cc_final: 0.8019 (mptp) REVERT: K 14 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7423 (p90) REVERT: L 14 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7446 (p-80) outliers start: 20 outliers final: 5 residues processed: 56 average time/residue: 0.4224 time to fit residues: 24.4476 Evaluate side-chains 56 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain L residue 14 HIS Chi-restraints excluded: chain X residue 34 LEU Chi-restraints excluded: chain T residue 14 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 13 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN N 14 HIS ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.172062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125316 restraints weight = 3158.660| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.76 r_work: 0.3816 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2910 Z= 0.161 Angle : 0.566 5.166 3894 Z= 0.284 Chirality : 0.056 0.128 450 Planarity : 0.002 0.010 480 Dihedral : 4.834 23.114 384 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.12 % Allowed : 29.17 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR F 10 PHE 0.009 0.001 PHE F 19 HIS 0.007 0.001 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2910) covalent geometry : angle 0.56641 ( 3894) hydrogen bonds : bond 0.01378 ( 32) hydrogen bonds : angle 4.54520 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.065 Fit side-chains REVERT: G 14 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7471 (m90) REVERT: F 16 LYS cc_start: 0.8448 (mptp) cc_final: 0.8081 (mptp) REVERT: K 14 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7405 (p90) REVERT: L 14 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7480 (p-80) outliers start: 9 outliers final: 1 residues processed: 51 average time/residue: 0.4764 time to fit residues: 25.0038 Evaluate side-chains 51 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain L residue 14 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN N 14 HIS ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.168054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.120845 restraints weight = 3224.704| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.79 r_work: 0.3749 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.035 2910 Z= 0.325 Angle : 0.710 5.909 3894 Z= 0.357 Chirality : 0.059 0.147 450 Planarity : 0.003 0.015 480 Dihedral : 5.284 25.634 384 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 5.90 % Allowed : 27.78 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.37), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR K 10 PHE 0.013 0.002 PHE B 19 HIS 0.006 0.002 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00770 ( 2910) covalent geometry : angle 0.70980 ( 3894) hydrogen bonds : bond 0.01588 ( 32) hydrogen bonds : angle 4.73854 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.157 Fit side-chains REVERT: G 14 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7445 (m90) REVERT: F 14 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7251 (p90) REVERT: F 16 LYS cc_start: 0.8440 (mptp) cc_final: 0.7956 (mptp) REVERT: K 14 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7480 (p90) REVERT: L 14 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7480 (p-80) outliers start: 17 outliers final: 5 residues processed: 55 average time/residue: 0.4517 time to fit residues: 25.6049 Evaluate side-chains 55 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain K residue 14 HIS Chi-restraints excluded: chain U residue 23 ASP Chi-restraints excluded: chain L residue 14 HIS Chi-restraints excluded: chain X residue 34 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN N 14 HIS ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.173101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.126497 restraints weight = 3189.522| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.77 r_work: 0.3823 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2910 Z= 0.137 Angle : 0.530 4.992 3894 Z= 0.271 Chirality : 0.056 0.129 450 Planarity : 0.002 0.010 480 Dihedral : 4.696 22.292 384 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.82 % Allowed : 30.90 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR G 10 PHE 0.009 0.001 PHE B 19 HIS 0.004 0.001 HIS B 14 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 2910) covalent geometry : angle 0.53015 ( 3894) hydrogen bonds : bond 0.01159 ( 32) hydrogen bonds : angle 4.35129 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.105 Fit side-chains REVERT: G 14 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7465 (m90) outliers start: 11 outliers final: 0 residues processed: 54 average time/residue: 0.4629 time to fit residues: 25.7098 Evaluate side-chains 46 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 45 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN N 14 HIS ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.170642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.123596 restraints weight = 3254.212| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.80 r_work: 0.3782 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.021 2910 Z= 0.200 Angle : 0.593 5.591 3894 Z= 0.300 Chirality : 0.057 0.130 450 Planarity : 0.002 0.012 480 Dihedral : 4.934 24.105 384 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.82 % Allowed : 30.56 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR N 10 PHE 0.011 0.002 PHE B 19 HIS 0.003 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 2910) covalent geometry : angle 0.59340 ( 3894) hydrogen bonds : bond 0.01159 ( 32) hydrogen bonds : angle 4.44551 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.107 Fit side-chains REVERT: G 14 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7444 (m90) REVERT: F 14 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7107 (p90) REVERT: F 16 LYS cc_start: 0.8498 (mptp) cc_final: 0.8074 (mptp) REVERT: P 34 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8403 (tt) REVERT: L 14 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7495 (p-80) outliers start: 11 outliers final: 2 residues processed: 53 average time/residue: 0.4029 time to fit residues: 22.0064 Evaluate side-chains 52 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain L residue 14 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 14 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN N 14 HIS ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 HIS ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.172490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.125981 restraints weight = 3234.807| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.78 r_work: 0.3812 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2910 Z= 0.151 Angle : 0.547 5.041 3894 Z= 0.279 Chirality : 0.056 0.129 450 Planarity : 0.002 0.010 480 Dihedral : 4.708 22.265 384 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.47 % Allowed : 30.90 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR N 10 PHE 0.009 0.001 PHE B 19 HIS 0.003 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 2910) covalent geometry : angle 0.54733 ( 3894) hydrogen bonds : bond 0.01140 ( 32) hydrogen bonds : angle 4.30043 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.104 Fit side-chains REVERT: G 14 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7494 (m90) REVERT: U 14 HIS cc_start: 0.8107 (t-90) cc_final: 0.7510 (m90) REVERT: P 34 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8358 (tt) REVERT: L 14 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7550 (p-80) outliers start: 10 outliers final: 2 residues processed: 52 average time/residue: 0.4588 time to fit residues: 24.5627 Evaluate side-chains 49 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 HIS Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain L residue 14 HIS Chi-restraints excluded: chain X residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 26 optimal weight: 0.0670 chunk 5 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 14 HIS ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN N 14 HIS ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 HIS ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.170740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.123836 restraints weight = 3247.567| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.81 r_work: 0.3782 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2910 Z= 0.203 Angle : 0.603 5.470 3894 Z= 0.305 Chirality : 0.057 0.129 450 Planarity : 0.002 0.011 480 Dihedral : 4.913 23.930 384 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.43 % Allowed : 31.60 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.001 TYR N 10 PHE 0.010 0.002 PHE B 19 HIS 0.003 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 2910) covalent geometry : angle 0.60271 ( 3894) hydrogen bonds : bond 0.01246 ( 32) hydrogen bonds : angle 4.43951 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.112 Fit side-chains REVERT: G 14 HIS cc_start: 0.8094 (t70) cc_final: 0.7564 (m90) REVERT: F 14 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7133 (p90) REVERT: P 34 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8384 (tt) REVERT: L 14 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7560 (p-80) outliers start: 7 outliers final: 3 residues processed: 48 average time/residue: 0.4410 time to fit residues: 21.8118 Evaluate side-chains 50 residues out of total 288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain F residue 14 HIS Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain L residue 14 HIS Chi-restraints excluded: chain X residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN N 14 HIS ** L 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.169273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.122354 restraints weight = 3205.239| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.79 r_work: 0.3765 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 2910 Z= 0.264 Angle : 0.663 5.725 3894 Z= 0.335 Chirality : 0.058 0.134 450 Planarity : 0.002 0.014 480 Dihedral : 5.094 24.401 384 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.12 % Allowed : 31.25 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.37), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.001 TYR N 10 PHE 0.012 0.002 PHE B 19 HIS 0.004 0.001 HIS T 14 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 2910) covalent geometry : angle 0.66298 ( 3894) hydrogen bonds : bond 0.01389 ( 32) hydrogen bonds : angle 4.55255 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1419.91 seconds wall clock time: 24 minutes 59.10 seconds (1499.10 seconds total)