Starting phenix.real_space_refine on Tue Mar 3 19:11:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nsl_12570/03_2026/7nsl_12570.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nsl_12570/03_2026/7nsl_12570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nsl_12570/03_2026/7nsl_12570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nsl_12570/03_2026/7nsl_12570.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nsl_12570/03_2026/7nsl_12570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nsl_12570/03_2026/7nsl_12570.map" } resolution = 3.1 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= 1.000 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: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2667 2.51 5 N 679 2.21 5 O 910 1.98 5 H 4053 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8323 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1189 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Restraints were copied for chains: E, F, C, B, A, G Time building chain proxies: 0.95, per 1000 atoms: 0.11 Number of scatterers: 8323 At special positions: 0 Unit cell: (64.48, 98.8, 58.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 910 8.00 N 679 7.00 C 2667 6.00 H 4053 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 89 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 89 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 89 " distance=2.02 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 89 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.02 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: 0.72 Conformation dependent library (CDL) restraints added in 158.1 milliseconds 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 34 Processing sheet with id=AA4, first strand: chain 'A' and resid 37 through 39 Processing sheet with id=AA5, first strand: chain 'A' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 43 through 44 current: chain 'B' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 43 through 44 current: chain 'C' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 43 through 44 current: chain 'D' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 43 through 44 current: chain 'E' and resid 43 through 44 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 43 through 44 current: chain 'F' and resid 43 through 44 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 45 through 51 Processing sheet with id=AA7, first strand: chain 'A' and resid 70 through 74 Processing sheet with id=AA8, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'A' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 88 through 89 current: chain 'B' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 88 through 89 current: chain 'C' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 88 through 89 current: chain 'D' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 88 through 89 current: chain 'E' and resid 88 through 89 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 88 through 89 current: chain 'F' and resid 88 through 89 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 107 180 hydrogen bonds defined for protein. 540 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: 1.77 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4053 1.03 - 1.23: 125 1.23 - 1.42: 1730 1.42 - 1.61: 2478 1.61 - 1.81: 14 Bond restraints: 8400 Sorted by residual: bond pdb=" CA ALA G 44 " pdb=" CB ALA G 44 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.17e-02 7.31e+03 5.56e+01 bond pdb=" CA ALA A 44 " pdb=" CB ALA A 44 " ideal model delta sigma weight residual 1.528 1.441 0.087 1.17e-02 7.31e+03 5.56e+01 bond pdb=" CA ALA B 44 " pdb=" CB ALA B 44 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.17e-02 7.31e+03 5.48e+01 bond pdb=" CA ALA E 44 " pdb=" CB ALA E 44 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.17e-02 7.31e+03 5.47e+01 bond pdb=" CA ALA F 44 " pdb=" CB ALA F 44 " ideal model delta sigma weight residual 1.528 1.442 0.086 1.17e-02 7.31e+03 5.46e+01 ... (remaining 8395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 13451 2.12 - 4.23: 1160 4.23 - 6.35: 328 6.35 - 8.47: 104 8.47 - 10.58: 14 Bond angle restraints: 15057 Sorted by residual: angle pdb=" CA GLY G 90 " pdb=" C GLY G 90 " pdb=" O GLY G 90 " ideal model delta sigma weight residual 120.91 114.30 6.61 6.90e-01 2.10e+00 9.18e+01 angle pdb=" CA GLY C 90 " pdb=" C GLY C 90 " pdb=" O GLY C 90 " ideal model delta sigma weight residual 120.91 114.34 6.57 6.90e-01 2.10e+00 9.06e+01 angle pdb=" CA GLY E 90 " pdb=" C GLY E 90 " pdb=" O GLY E 90 " ideal model delta sigma weight residual 120.91 114.35 6.56 6.90e-01 2.10e+00 9.03e+01 angle pdb=" CA GLY B 90 " pdb=" C GLY B 90 " pdb=" O GLY B 90 " ideal model delta sigma weight residual 120.91 114.36 6.55 6.90e-01 2.10e+00 9.01e+01 angle pdb=" CA GLY F 90 " pdb=" C GLY F 90 " pdb=" O GLY F 90 " ideal model delta sigma weight residual 120.91 114.37 6.54 6.90e-01 2.10e+00 8.97e+01 ... (remaining 15052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 3444 16.17 - 32.34: 413 32.34 - 48.51: 105 48.51 - 64.68: 91 64.68 - 80.86: 7 Dihedral angle restraints: 4060 sinusoidal: 2163 harmonic: 1897 Sorted by residual: dihedral pdb=" N LEU F 97 " pdb=" CA LEU F 97 " pdb=" CB LEU F 97 " pdb=" CG LEU F 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.63 53.63 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LEU C 97 " pdb=" CA LEU C 97 " pdb=" CB LEU C 97 " pdb=" CG LEU C 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 dihedral pdb=" N LEU B 97 " pdb=" CA LEU B 97 " pdb=" CB LEU B 97 " pdb=" CG LEU B 97 " ideal model delta sinusoidal sigma weight residual -60.00 -113.61 53.61 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 4057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 390 0.056 - 0.111: 188 0.111 - 0.167: 67 0.167 - 0.222: 34 0.222 - 0.278: 14 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA LEU A 47 " pdb=" N LEU A 47 " pdb=" C LEU A 47 " pdb=" CB LEU A 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LEU B 47 " pdb=" N LEU B 47 " pdb=" C LEU B 47 " pdb=" CB LEU B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA LEU F 47 " pdb=" N LEU F 47 " pdb=" C LEU F 47 " pdb=" CB LEU F 47 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 690 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN E 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN E 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN E 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN E 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN E 16 " -0.546 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN G 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN G 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN G 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN G 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN G 16 " -0.546 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 16 " -0.240 2.00e-02 2.50e+03 3.43e-01 1.77e+03 pdb=" CD GLN D 16 " 0.009 2.00e-02 2.50e+03 pdb=" OE1 GLN D 16 " 0.236 2.00e-02 2.50e+03 pdb=" NE2 GLN D 16 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN D 16 " 0.544 2.00e-02 2.50e+03 pdb="HE22 GLN D 16 " -0.546 2.00e-02 2.50e+03 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 427 2.18 - 2.78: 16305 2.78 - 3.39: 22336 3.39 - 3.99: 32827 3.99 - 4.60: 47613 Nonbonded interactions: 119508 Sorted by model distance: nonbonded pdb=" HG1 THR A 81 " pdb=" OD1 ASP A 83 " model vdw 1.572 2.450 nonbonded pdb=" HG1 THR E 81 " pdb=" OD1 ASP E 83 " model vdw 1.573 2.450 nonbonded pdb=" HG1 THR F 81 " pdb=" OD1 ASP F 83 " model vdw 1.573 2.450 nonbonded pdb=" HG1 THR G 81 " pdb=" OD1 ASP G 83 " model vdw 1.573 2.450 nonbonded pdb=" HG1 THR D 81 " pdb=" OD1 ASP D 83 " model vdw 1.573 2.450 ... (remaining 119503 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'C' selection = chain 'B' selection = chain 'A' selection = chain 'G' } 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: 1.080 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: 0.050 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.050 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.012 0.087 4354 Z= 0.885 Angle : 1.844 8.934 5943 Z= 1.281 Chirality : 0.084 0.278 693 Planarity : 0.014 0.039 749 Dihedral : 14.483 80.856 1442 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % 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 are not related in a simple way. whole: -5.51 (0.17), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.13), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.024 0.002 TYR E 88 PHE 0.018 0.006 PHE C 101 TRP 0.013 0.002 TRP D 36 Details of bonding type rmsd covalent geometry : bond 0.01233 ( 4347) covalent geometry : angle 1.84497 ( 5929) SS BOND : bond 0.00827 ( 7) SS BOND : angle 1.35679 ( 14) hydrogen bonds : bond 0.14488 ( 180) hydrogen bonds : angle 7.47783 ( 540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 GLN cc_start: 0.9084 (pt0) cc_final: 0.8778 (pt0) REVERT: F 31 ASN cc_start: 0.8659 (m-40) cc_final: 0.8330 (m-40) REVERT: C 48 LEU cc_start: 0.8864 (mp) cc_final: 0.8450 (mp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.0984 time to fit residues: 26.6541 Evaluate side-chains 154 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 32 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 = 0.4158 r_free = 0.4158 target = 0.142719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.126591 restraints weight = 17374.062| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.69 r_work: 0.3873 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4354 Z= 0.167 Angle : 0.665 4.366 5943 Z= 0.357 Chirality : 0.046 0.149 693 Planarity : 0.003 0.024 749 Dihedral : 6.457 17.504 616 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.90 % Allowed : 14.50 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.94 (0.19), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.15), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR E 37 PHE 0.014 0.003 PHE E 101 TRP 0.004 0.001 TRP C 36 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 4347) covalent geometry : angle 0.66502 ( 5929) SS BOND : bond 0.00137 ( 7) SS BOND : angle 0.50053 ( 14) hydrogen bonds : bond 0.04466 ( 180) hydrogen bonds : angle 4.90890 ( 540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6501 (tt0) outliers start: 18 outliers final: 12 residues processed: 166 average time/residue: 0.1095 time to fit residues: 24.6365 Evaluate side-chains 163 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 GLN C 32 ASN B 32 ASN A 16 GLN A 32 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.138633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.123199 restraints weight = 17646.897| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.69 r_work: 0.3844 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4354 Z= 0.137 Angle : 0.632 5.709 5943 Z= 0.330 Chirality : 0.045 0.141 693 Planarity : 0.003 0.022 749 Dihedral : 6.158 15.204 616 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.55 % Allowed : 16.45 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.57 (0.22), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.16), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.001 TYR B 37 PHE 0.025 0.005 PHE D 101 TRP 0.003 0.001 TRP G 92 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 4347) covalent geometry : angle 0.63250 ( 5929) SS BOND : bond 0.00123 ( 7) SS BOND : angle 0.40598 ( 14) hydrogen bonds : bond 0.03235 ( 180) hydrogen bonds : angle 4.70626 ( 540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.4987 (pm20) cc_final: 0.4778 (pm20) outliers start: 21 outliers final: 16 residues processed: 151 average time/residue: 0.1062 time to fit residues: 21.8685 Evaluate side-chains 156 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.135602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.120282 restraints weight = 18082.252| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.70 r_work: 0.3818 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4354 Z= 0.128 Angle : 0.587 4.176 5943 Z= 0.309 Chirality : 0.044 0.136 693 Planarity : 0.003 0.025 749 Dihedral : 6.020 16.310 616 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.90 % Allowed : 16.88 % Favored : 79.22 % 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 are not related in a simple way. whole: -4.39 (0.23), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.18), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.001 TYR B 37 PHE 0.020 0.004 PHE D 101 TRP 0.003 0.000 TRP G 92 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 4347) covalent geometry : angle 0.58746 ( 5929) SS BOND : bond 0.00106 ( 7) SS BOND : angle 0.41681 ( 14) hydrogen bonds : bond 0.02775 ( 180) hydrogen bonds : angle 4.63624 ( 540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: D 101 PHE cc_start: 0.8688 (m-80) cc_final: 0.8394 (m-80) REVERT: C 46 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8275 (ttmt) REVERT: C 101 PHE cc_start: 0.8750 (m-80) cc_final: 0.8129 (m-80) REVERT: B 84 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6698 (tt0) REVERT: G 46 LYS cc_start: 0.7980 (ttmt) cc_final: 0.7701 (tppt) outliers start: 18 outliers final: 17 residues processed: 150 average time/residue: 0.1259 time to fit residues: 24.7522 Evaluate side-chains 157 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN E 38 GLN F 38 GLN C 38 GLN G 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.131375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.115857 restraints weight = 17718.595| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.75 r_work: 0.3785 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4354 Z= 0.133 Angle : 0.586 5.418 5943 Z= 0.306 Chirality : 0.044 0.132 693 Planarity : 0.003 0.027 749 Dihedral : 5.853 15.012 616 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.41 % Allowed : 16.88 % Favored : 77.71 % 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 are not related in a simple way. whole: -4.19 (0.24), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR E 88 PHE 0.016 0.003 PHE E 101 TRP 0.002 0.001 TRP A 92 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4347) covalent geometry : angle 0.58683 ( 5929) SS BOND : bond 0.00081 ( 7) SS BOND : angle 0.36718 ( 14) hydrogen bonds : bond 0.02631 ( 180) hydrogen bonds : angle 4.47558 ( 540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 96 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8285 (tp) REVERT: B 84 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6884 (tt0) REVERT: G 46 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7680 (tppt) outliers start: 25 outliers final: 18 residues processed: 151 average time/residue: 0.1139 time to fit residues: 22.7718 Evaluate side-chains 154 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 38 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.0870 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.130222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.114661 restraints weight = 17712.636| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.78 r_work: 0.3774 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4354 Z= 0.143 Angle : 0.604 4.793 5943 Z= 0.319 Chirality : 0.045 0.134 693 Planarity : 0.003 0.026 749 Dihedral : 5.844 14.967 616 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.90 % Allowed : 18.40 % Favored : 77.71 % 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 are not related in a simple way. whole: -4.12 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR E 88 PHE 0.012 0.002 PHE E 101 TRP 0.003 0.001 TRP D 36 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4347) covalent geometry : angle 0.60477 ( 5929) SS BOND : bond 0.00080 ( 7) SS BOND : angle 0.35772 ( 14) hydrogen bonds : bond 0.02872 ( 180) hydrogen bonds : angle 4.46707 ( 540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6954 (tt0) REVERT: G 46 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7643 (tppt) outliers start: 18 outliers final: 14 residues processed: 139 average time/residue: 0.1103 time to fit residues: 20.3626 Evaluate side-chains 147 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.129326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.113715 restraints weight = 18059.264| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.82 r_work: 0.3760 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3670 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4354 Z= 0.130 Angle : 0.587 6.603 5943 Z= 0.305 Chirality : 0.044 0.133 693 Planarity : 0.003 0.027 749 Dihedral : 5.713 15.527 616 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.25 % Allowed : 19.48 % Favored : 77.27 % 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 are not related in a simple way. whole: -4.09 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR C 37 PHE 0.011 0.002 PHE F 101 TRP 0.003 0.001 TRP E 36 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4347) covalent geometry : angle 0.58742 ( 5929) SS BOND : bond 0.00068 ( 7) SS BOND : angle 0.32411 ( 14) hydrogen bonds : bond 0.02830 ( 180) hydrogen bonds : angle 4.46455 ( 540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: B 84 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6956 (tt0) REVERT: G 46 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7630 (tppt) outliers start: 15 outliers final: 12 residues processed: 140 average time/residue: 0.1133 time to fit residues: 21.1200 Evaluate side-chains 149 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.128737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.113587 restraints weight = 18011.043| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.74 r_work: 0.3745 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4354 Z= 0.164 Angle : 0.603 5.166 5943 Z= 0.314 Chirality : 0.044 0.134 693 Planarity : 0.003 0.026 749 Dihedral : 5.764 16.025 616 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.46 % Allowed : 19.48 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR E 37 PHE 0.010 0.002 PHE G 101 TRP 0.002 0.001 TRP C 36 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 4347) covalent geometry : angle 0.60305 ( 5929) SS BOND : bond 0.00101 ( 7) SS BOND : angle 0.37120 ( 14) hydrogen bonds : bond 0.02772 ( 180) hydrogen bonds : angle 4.47115 ( 540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: C 96 LEU cc_start: 0.8681 (tp) cc_final: 0.8363 (tp) REVERT: B 84 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6998 (tt0) REVERT: G 46 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7641 (tppt) outliers start: 16 outliers final: 16 residues processed: 136 average time/residue: 0.1058 time to fit residues: 19.2443 Evaluate side-chains 145 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.127179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.112187 restraints weight = 18096.600| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.73 r_work: 0.3744 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4354 Z= 0.154 Angle : 0.590 5.466 5943 Z= 0.308 Chirality : 0.044 0.138 693 Planarity : 0.003 0.027 749 Dihedral : 5.732 16.217 616 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.03 % Allowed : 19.91 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.05 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.001 TYR C 37 PHE 0.010 0.002 PHE F 101 TRP 0.003 0.001 TRP G 92 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 4347) covalent geometry : angle 0.59024 ( 5929) SS BOND : bond 0.00094 ( 7) SS BOND : angle 0.32257 ( 14) hydrogen bonds : bond 0.02704 ( 180) hydrogen bonds : angle 4.41690 ( 540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: F 29 ILE cc_start: 0.8933 (mm) cc_final: 0.8678 (mp) REVERT: B 84 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7198 (tt0) REVERT: G 46 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7779 (tppt) outliers start: 14 outliers final: 12 residues processed: 136 average time/residue: 0.1081 time to fit residues: 19.6150 Evaluate side-chains 139 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.0470 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.127003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.111856 restraints weight = 18175.020| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.78 r_work: 0.3735 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3646 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4354 Z= 0.151 Angle : 0.594 5.123 5943 Z= 0.309 Chirality : 0.044 0.136 693 Planarity : 0.003 0.027 749 Dihedral : 5.723 16.431 616 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.25 % Allowed : 20.78 % Favored : 75.97 % 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 are not related in a simple way. whole: -4.07 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR C 37 PHE 0.010 0.002 PHE F 101 TRP 0.003 0.001 TRP G 92 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4347) covalent geometry : angle 0.59455 ( 5929) SS BOND : bond 0.00093 ( 7) SS BOND : angle 0.35525 ( 14) hydrogen bonds : bond 0.02647 ( 180) hydrogen bonds : angle 4.38677 ( 540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1134 Ramachandran restraints generated. 567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: F 29 ILE cc_start: 0.8883 (mm) cc_final: 0.8644 (mp) REVERT: B 84 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7133 (tt0) REVERT: G 46 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7781 (tppt) outliers start: 15 outliers final: 15 residues processed: 126 average time/residue: 0.1132 time to fit residues: 18.8492 Evaluate side-chains 136 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 86 ASP Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain C residue 84 GLU Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain G residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.128143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113174 restraints weight = 18068.463| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.77 r_work: 0.3742 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.6180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4354 Z= 0.138 Angle : 0.582 5.119 5943 Z= 0.303 Chirality : 0.044 0.136 693 Planarity : 0.003 0.026 749 Dihedral : 5.666 16.759 616 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.25 % Allowed : 21.43 % Favored : 75.32 % 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 are not related in a simple way. whole: -4.09 (0.25), residues: 567 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.19), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.001 TYR C 37 PHE 0.011 0.002 PHE F 101 TRP 0.003 0.001 TRP G 92 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4347) covalent geometry : angle 0.58287 ( 5929) SS BOND : bond 0.00082 ( 7) SS BOND : angle 0.36437 ( 14) hydrogen bonds : bond 0.02571 ( 180) hydrogen bonds : angle 4.33526 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2457.59 seconds wall clock time: 42 minutes 15.21 seconds (2535.21 seconds total)