Starting phenix.real_space_refine on Wed Mar 12 23:47:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sbd_40305/03_2025/8sbd_40305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sbd_40305/03_2025/8sbd_40305.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sbd_40305/03_2025/8sbd_40305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sbd_40305/03_2025/8sbd_40305.map" model { file = "/net/cci-nas-00/data/ceres_data/8sbd_40305/03_2025/8sbd_40305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sbd_40305/03_2025/8sbd_40305.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 96 5.16 5 C 2912 2.51 5 N 720 2.21 5 O 856 1.98 5 H 4280 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8864 Number of models: 1 Model: "" Number of chains: 4 Chain: "b" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "a" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "B" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 288 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 238 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Restraints were copied for chains: D, F, H, J, L, N, P, c, e, g, i, k, m, o, C, E, G, I, K, M, O, d, f, h, j, l, n, p Time building chain proxies: 2.90, per 1000 atoms: 0.33 Number of scatterers: 8864 At special positions: 0 Unit cell: (75.53, 95.45, 56.44, 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 96 16.00 O 856 8.00 N 720 7.00 C 2912 6.00 H 4280 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" CA LEU m 11 " - pdb=" HB3 LEU m 11 " distance=2.05 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: 2.27 Conformation dependent library (CDL) restraints added in 832.6 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'n' and resid 15 through 17 removed outlier: 6.137A pdb=" N TYR p 16 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR l 16 " --> pdb=" O LEU f 17 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR h 16 " --> pdb=" O LEU b 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'm' and resid 12 through 19 removed outlier: 6.503A pdb=" N VAL o 12 " --> pdb=" O GLU m 13 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N LEU m 15 " --> pdb=" O VAL o 12 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA o 14 " --> pdb=" O LEU m 15 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU m 17 " --> pdb=" O ALA o 14 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR o 16 " --> pdb=" O LEU m 17 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS m 19 " --> pdb=" O TYR o 16 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL o 18 " --> pdb=" O CYS m 19 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL k 12 " --> pdb=" O GLU i 13 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N LEU i 15 " --> pdb=" O VAL k 12 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA k 14 " --> pdb=" O LEU i 15 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU i 17 " --> pdb=" O ALA k 14 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR k 16 " --> pdb=" O LEU i 17 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS i 19 " --> pdb=" O TYR k 16 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL k 18 " --> pdb=" O CYS i 19 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU k 13 " --> pdb=" O ALA e 14 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR e 16 " --> pdb=" O GLU k 13 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU k 15 " --> pdb=" O TYR e 16 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL e 18 " --> pdb=" O LEU k 15 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU k 17 " --> pdb=" O VAL e 18 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL g 12 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N LEU e 15 " --> pdb=" O VAL g 12 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA g 14 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU e 17 " --> pdb=" O ALA g 14 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR g 16 " --> pdb=" O LEU e 17 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS e 19 " --> pdb=" O TYR g 16 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL g 18 " --> pdb=" O CYS e 19 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL c 12 " --> pdb=" O GLU a 13 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N LEU a 15 " --> pdb=" O VAL c 12 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA c 14 " --> pdb=" O LEU a 15 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU a 17 " --> pdb=" O ALA c 14 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR c 16 " --> pdb=" O LEU a 17 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N CYS a 19 " --> pdb=" O TYR c 16 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL c 18 " --> pdb=" O CYS a 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'm' and resid 24 through 25 removed outlier: 6.417A pdb=" N PHE o 24 " --> pdb=" O PHE i 25 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N PHE k 24 " --> pdb=" O PHE e 25 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE g 24 " --> pdb=" O PHE a 25 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 15 through 19 removed outlier: 6.721A pdb=" N LEU P 16 " --> pdb=" O GLU J 17 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR J 19 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN P 18 " --> pdb=" O TYR J 19 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU L 16 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR F 19 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASN L 18 " --> pdb=" O TYR F 19 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU H 16 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N TYR B 19 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN H 18 " --> pdb=" O TYR B 19 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 15 through 16 removed outlier: 6.433A pdb=" N GLN O 15 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLN K 15 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN G 15 " --> pdb=" O LEU A 16 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 138 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: 3.02 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4280 1.04 - 1.23: 184 1.23 - 1.43: 1864 1.43 - 1.63: 2512 1.63 - 1.82: 96 Bond restraints: 8936 Sorted by residual: bond pdb=" N VAL J 3 " pdb=" CA VAL J 3 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.31e+00 bond pdb=" N VAL D 3 " pdb=" CA VAL D 3 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.21e+00 bond pdb=" N VAL H 3 " pdb=" CA VAL H 3 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.20e+00 bond pdb=" N VAL L 3 " pdb=" CA VAL L 3 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.20e+00 bond pdb=" N VAL P 3 " pdb=" CA VAL P 3 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.15e+00 ... (remaining 8931 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 13993 0.93 - 1.85: 1720 1.85 - 2.78: 199 2.78 - 3.70: 32 3.70 - 4.63: 8 Bond angle restraints: 15952 Sorted by residual: angle pdb=" N VAL g 18 " pdb=" CA VAL g 18 " pdb=" C VAL g 18 " ideal model delta sigma weight residual 106.53 111.16 -4.63 1.41e+00 5.03e-01 1.08e+01 angle pdb=" N VAL m 18 " pdb=" CA VAL m 18 " pdb=" C VAL m 18 " ideal model delta sigma weight residual 106.53 111.15 -4.62 1.41e+00 5.03e-01 1.08e+01 angle pdb=" N VAL k 18 " pdb=" CA VAL k 18 " pdb=" C VAL k 18 " ideal model delta sigma weight residual 106.53 111.15 -4.62 1.41e+00 5.03e-01 1.07e+01 angle pdb=" N VAL e 18 " pdb=" CA VAL e 18 " pdb=" C VAL e 18 " ideal model delta sigma weight residual 106.53 111.14 -4.61 1.41e+00 5.03e-01 1.07e+01 angle pdb=" N VAL c 18 " pdb=" CA VAL c 18 " pdb=" C VAL c 18 " ideal model delta sigma weight residual 106.53 111.13 -4.60 1.41e+00 5.03e-01 1.07e+01 ... (remaining 15947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 3824 17.20 - 34.40: 328 34.40 - 51.60: 88 51.60 - 68.80: 16 68.80 - 86.00: 3 Dihedral angle restraints: 4259 sinusoidal: 2131 harmonic: 2128 Sorted by residual: dihedral pdb=" CB LEU m 11 " pdb=" CA LEU m 11 " pdb=" HB3 LEU m 11 " pdb=" CB LEU m 11 " ideal model delta sinusoidal sigma weight residual -86.00 -0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CA LEU m 11 " pdb=" CA LEU m 11 " pdb=" CB LEU m 11 " pdb=" HB3 LEU m 11 " ideal model delta sinusoidal sigma weight residual 41.68 41.68 0.00 1 2.00e+01 2.50e-03 0.00e+00 dihedral pdb=" CA LEU m 11 " pdb=" CB LEU m 11 " pdb=" HB3 LEU m 11 " pdb=" CA LEU m 11 " ideal model delta sinusoidal sigma weight residual -73.00 -0.00 -73.00 1 2.00e+01 2.50e-03 1.70e+01 ... (remaining 4256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 434 0.028 - 0.056: 178 0.056 - 0.084: 59 0.084 - 0.111: 55 0.111 - 0.139: 10 Chirality restraints: 736 Sorted by residual: chirality pdb=" CA THR L 8 " pdb=" N THR L 8 " pdb=" C THR L 8 " pdb=" CB THR L 8 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA THR P 8 " pdb=" N THR P 8 " pdb=" C THR P 8 " pdb=" CB THR P 8 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA THR H 8 " pdb=" N THR H 8 " pdb=" C THR H 8 " pdb=" CB THR H 8 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 733 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS D 7 " -0.003 2.00e-02 2.50e+03 5.96e-03 3.56e-01 pdb=" C CYS D 7 " 0.010 2.00e-02 2.50e+03 pdb=" O CYS D 7 " -0.004 2.00e-02 2.50e+03 pdb=" N THR D 8 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 7 " -0.003 2.00e-02 2.50e+03 5.94e-03 3.53e-01 pdb=" C CYS B 7 " 0.010 2.00e-02 2.50e+03 pdb=" O CYS B 7 " -0.004 2.00e-02 2.50e+03 pdb=" N THR B 8 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS J 7 " -0.003 2.00e-02 2.50e+03 5.92e-03 3.51e-01 pdb=" C CYS J 7 " 0.010 2.00e-02 2.50e+03 pdb=" O CYS J 7 " -0.004 2.00e-02 2.50e+03 pdb=" N THR J 8 " -0.003 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.25: 1404 2.25 - 2.84: 21351 2.84 - 3.43: 23266 3.43 - 4.01: 35173 4.01 - 4.60: 50315 Nonbonded interactions: 131509 Sorted by model distance: nonbonded pdb="HE21 GLN N 15 " pdb=" OE1 GLU N 17 " model vdw 1.666 2.450 nonbonded pdb="HE21 GLN B 15 " pdb=" OE1 GLU B 17 " model vdw 1.666 2.450 nonbonded pdb="HE21 GLN J 15 " pdb=" OE1 GLU J 17 " model vdw 1.666 2.450 nonbonded pdb="HE21 GLN H 15 " pdb=" OE1 GLU H 17 " model vdw 1.667 2.450 nonbonded pdb="HE21 GLN P 15 " pdb=" OE1 GLU P 17 " model vdw 1.667 2.450 ... (remaining 131504 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: 0.05 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' selection = chain 'm' selection = chain 'o' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' selection = chain 'n' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.170 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 21.570 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 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 : 0.003 0.020 4656 Z= 0.206 Angle : 0.725 4.629 6280 Z= 0.437 Chirality : 0.043 0.139 736 Planarity : 0.002 0.006 760 Dihedral : 12.978 52.500 1576 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.97 % Allowed : 8.96 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.24), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.19), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS b 10 PHE 0.007 0.002 PHE m 24 TYR 0.007 0.001 TYR i 16 ARG 0.001 0.000 ARG o 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 8 THR cc_start: 0.8017 (t) cc_final: 0.7790 (m) REVERT: B 8 THR cc_start: 0.7919 (t) cc_final: 0.7518 (m) outliers start: 32 outliers final: 15 residues processed: 109 average time/residue: 0.1888 time to fit residues: 32.3825 Evaluate side-chains 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 7 CYS Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain h residue 7 CYS Chi-restraints excluded: chain f residue 7 CYS Chi-restraints excluded: chain c residue 17 LEU Chi-restraints excluded: chain b residue 7 CYS Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain B residue 6 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.0010 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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 = 0.5480 r_free = 0.5480 target = 0.416376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.6022 r_free = 0.6022 target = 0.342080 restraints weight = 17060.749| |-----------------------------------------------------------------------------| r_work (start): 0.5400 rms_B_bonded: 1.22 r_work: 0.5881 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.5836 rms_B_bonded: 0.83 restraints_weight: 0.2500 r_work: 0.5573 rms_B_bonded: 3.09 restraints_weight: 0.1250 r_work (final): 0.5573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 4656 Z= 0.243 Angle : 0.648 5.974 6280 Z= 0.348 Chirality : 0.047 0.127 736 Planarity : 0.003 0.020 760 Dihedral : 8.587 50.882 633 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 5.78 % Allowed : 13.99 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.22 (0.25), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.19), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 10 PHE 0.005 0.001 PHE g 24 TYR 0.011 0.002 TYR G 19 ARG 0.002 0.001 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.5483 (OUTLIER) cc_final: 0.4517 (m) REVERT: l 7 CYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6820 (m) REVERT: j 7 CYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7104 (m) REVERT: J 12 SER cc_start: 0.8319 (m) cc_final: 0.7954 (m) outliers start: 31 outliers final: 16 residues processed: 110 average time/residue: 0.1595 time to fit residues: 27.7237 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain j residue 7 CYS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain J residue 6 CYS Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 ASN Chi-restraints excluded: chain B residue 6 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 27 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.5340 r_free = 0.5340 target = 0.354081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.5823 r_free = 0.5823 target = 0.291816 restraints weight = 15829.365| |-----------------------------------------------------------------------------| r_work (start): 0.5287 rms_B_bonded: 1.11 r_work: 0.5863 rms_B_bonded: 0.49 restraints_weight: 0.5000 r_work: 0.5810 rms_B_bonded: 0.82 restraints_weight: 0.2500 r_work: 0.5600 rms_B_bonded: 2.79 restraints_weight: 0.1250 r_work (final): 0.5600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 4656 Z= 0.344 Angle : 0.700 7.455 6280 Z= 0.372 Chirality : 0.048 0.119 736 Planarity : 0.003 0.019 760 Dihedral : 7.745 45.902 626 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.62 % Favored : 85.38 % Rotamer: Outliers : 5.97 % Allowed : 18.84 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.18), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS l 10 PHE 0.010 0.002 PHE m 24 TYR 0.015 0.002 TYR k 16 ARG 0.002 0.001 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5327 (m) REVERT: G 8 THR cc_start: 0.8435 (t) cc_final: 0.8178 (m) outliers start: 32 outliers final: 23 residues processed: 95 average time/residue: 0.1711 time to fit residues: 25.4989 Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain J residue 18 ASN Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain A residue 20 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5302 r_free = 0.5302 target = 0.350535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.5803 r_free = 0.5803 target = 0.284332 restraints weight = 16065.974| |-----------------------------------------------------------------------------| r_work (start): 0.5242 rms_B_bonded: 1.06 r_work: 0.5843 rms_B_bonded: 0.45 restraints_weight: 0.5000 r_work: 0.5774 rms_B_bonded: 0.80 restraints_weight: 0.2500 r_work: 0.5516 rms_B_bonded: 2.76 restraints_weight: 0.1250 r_work (final): 0.5516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 4656 Z= 0.464 Angle : 0.781 9.204 6280 Z= 0.410 Chirality : 0.050 0.140 736 Planarity : 0.003 0.020 760 Dihedral : 7.925 47.367 624 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 29.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.69 % Favored : 82.31 % Rotamer: Outliers : 5.41 % Allowed : 25.93 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.17 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.93 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS h 10 PHE 0.014 0.003 PHE k 24 TYR 0.019 0.003 TYR k 16 ARG 0.002 0.000 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.6027 (OUTLIER) cc_final: 0.5516 (t) REVERT: F 9 SER cc_start: 0.7709 (p) cc_final: 0.7507 (p) REVERT: B 20 CYS cc_start: 0.6622 (p) cc_final: 0.6177 (t) outliers start: 29 outliers final: 20 residues processed: 91 average time/residue: 0.1714 time to fit residues: 24.3417 Evaluate side-chains 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 20 CYS Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain H residue 6 CYS Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain F residue 6 CYS Chi-restraints excluded: chain F residue 7 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 5 GLN E 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5337 r_free = 0.5337 target = 0.347346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.5813 r_free = 0.5813 target = 0.282659 restraints weight = 15923.198| |-----------------------------------------------------------------------------| r_work (start): 0.5278 rms_B_bonded: 1.07 r_work: 0.5841 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.5784 rms_B_bonded: 0.83 restraints_weight: 0.2500 r_work: 0.5577 rms_B_bonded: 2.67 restraints_weight: 0.1250 r_work (final): 0.5577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 4656 Z= 0.389 Angle : 0.723 8.643 6280 Z= 0.384 Chirality : 0.049 0.128 736 Planarity : 0.003 0.022 760 Dihedral : 7.604 46.396 623 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.50 % Favored : 82.50 % Rotamer: Outliers : 5.60 % Allowed : 28.17 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.00 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS j 10 PHE 0.008 0.002 PHE m 24 TYR 0.013 0.002 TYR i 16 ARG 0.002 0.001 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5764 (t) REVERT: B 20 CYS cc_start: 0.6692 (p) cc_final: 0.6331 (t) outliers start: 30 outliers final: 23 residues processed: 81 average time/residue: 0.1727 time to fit residues: 21.8391 Evaluate side-chains 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain g residue 11 LEU Chi-restraints excluded: chain d residue 10 HIS Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 20 CYS Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain M residue 20 CYS Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 7 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 CYS Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5342 r_free = 0.5342 target = 0.348557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5817 r_free = 0.5817 target = 0.283897 restraints weight = 15862.493| |-----------------------------------------------------------------------------| r_work (start): 0.5277 rms_B_bonded: 1.25 r_work: 0.5844 rms_B_bonded: 0.50 restraints_weight: 0.5000 r_work: 0.5790 rms_B_bonded: 0.86 restraints_weight: 0.2500 r_work: 0.5514 rms_B_bonded: 2.97 restraints_weight: 0.1250 r_work (final): 0.5514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 4656 Z= 0.379 Angle : 0.716 8.752 6280 Z= 0.381 Chirality : 0.048 0.137 736 Planarity : 0.003 0.018 760 Dihedral : 7.285 46.692 621 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 29.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.04 % Favored : 80.96 % Rotamer: Outliers : 5.60 % Allowed : 28.92 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 10 PHE 0.008 0.002 PHE a 24 TYR 0.013 0.002 TYR k 16 ARG 0.002 0.000 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5633 (t) REVERT: E 5 GLN cc_start: 0.5905 (tt0) cc_final: 0.5540 (mp10) REVERT: B 20 CYS cc_start: 0.6870 (p) cc_final: 0.6579 (t) outliers start: 30 outliers final: 24 residues processed: 81 average time/residue: 0.1794 time to fit residues: 23.0343 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 24 PHE Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain l residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain g residue 11 LEU Chi-restraints excluded: chain d residue 10 HIS Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 20 CYS Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain M residue 20 CYS Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 7 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5440 r_free = 0.5440 target = 0.408300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.6039 r_free = 0.6039 target = 0.329662 restraints weight = 17111.972| |-----------------------------------------------------------------------------| r_work (start): 0.5309 rms_B_bonded: 0.90 r_work: 0.5951 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.5886 rms_B_bonded: 0.70 restraints_weight: 0.2500 r_work: 0.5614 rms_B_bonded: 2.47 restraints_weight: 0.1250 r_work (final): 0.5614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 4656 Z= 0.227 Angle : 0.627 6.378 6280 Z= 0.336 Chirality : 0.046 0.132 736 Planarity : 0.002 0.015 760 Dihedral : 6.672 47.143 621 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 3.73 % Allowed : 29.10 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS j 10 PHE 0.004 0.001 PHE a 24 TYR 0.010 0.001 TYR c 26 ARG 0.002 0.001 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.6160 (OUTLIER) cc_final: 0.5647 (t) REVERT: B 20 CYS cc_start: 0.6871 (p) cc_final: 0.6579 (t) outliers start: 20 outliers final: 17 residues processed: 72 average time/residue: 0.1749 time to fit residues: 20.3079 Evaluate side-chains 76 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 20 CYS Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 7 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain E residue 20 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5408 r_free = 0.5408 target = 0.397850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5689 r_free = 0.5689 target = 0.316750 restraints weight = 17538.958| |-----------------------------------------------------------------------------| r_work (start): 0.5248 rms_B_bonded: 2.33 r_work: 0.5746 rms_B_bonded: 0.91 restraints_weight: 0.5000 r_work: 0.5664 rms_B_bonded: 1.55 restraints_weight: 0.2500 r_work (final): 0.5664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 4656 Z= 0.526 Angle : 0.801 9.730 6280 Z= 0.424 Chirality : 0.052 0.156 736 Planarity : 0.004 0.028 760 Dihedral : 7.569 49.372 621 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 33.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.31 % Favored : 77.69 % Rotamer: Outliers : 3.54 % Allowed : 31.34 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.54 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS h 10 PHE 0.011 0.003 PHE k 24 TYR 0.019 0.003 TYR J 14 ARG 0.003 0.000 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 5 GLN cc_start: 0.6299 (OUTLIER) cc_final: 0.5958 (tt0) outliers start: 19 outliers final: 15 residues processed: 74 average time/residue: 0.1707 time to fit residues: 19.9485 Evaluate side-chains 70 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 20 CYS Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain H residue 7 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 7 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain E residue 5 GLN Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.5417 r_free = 0.5417 target = 0.364219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.5960 r_free = 0.5960 target = 0.299411 restraints weight = 15876.489| |-----------------------------------------------------------------------------| r_work (start): 0.5363 rms_B_bonded: 1.32 r_work: 0.5968 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.5907 rms_B_bonded: 0.83 restraints_weight: 0.2500 r_work: 0.5657 rms_B_bonded: 2.87 restraints_weight: 0.1250 r_work (final): 0.5657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 4656 Z= 0.200 Angle : 0.648 6.357 6280 Z= 0.346 Chirality : 0.046 0.128 736 Planarity : 0.002 0.032 760 Dihedral : 6.346 31.338 620 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.43 % Allowed : 32.09 % Favored : 65.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.46 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS n 10 PHE 0.006 0.001 PHE g 25 TYR 0.011 0.001 TYR c 26 ARG 0.002 0.001 ARG c 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 67 average time/residue: 0.1784 time to fit residues: 18.8651 Evaluate side-chains 66 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 20 CYS Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5431 r_free = 0.5431 target = 0.402925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.6096 r_free = 0.6096 target = 0.322398 restraints weight = 17235.547| |-----------------------------------------------------------------------------| r_work (start): 0.5291 rms_B_bonded: 1.14 r_work: 0.5934 rms_B_bonded: 0.42 restraints_weight: 0.5000 r_work: 0.5878 rms_B_bonded: 0.74 restraints_weight: 0.2500 r_work: 0.5602 rms_B_bonded: 2.61 restraints_weight: 0.1250 r_work (final): 0.5602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 4656 Z= 0.314 Angle : 0.680 7.945 6280 Z= 0.360 Chirality : 0.047 0.128 736 Planarity : 0.002 0.016 760 Dihedral : 6.591 37.292 620 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.08 % Favored : 81.92 % Rotamer: Outliers : 2.43 % Allowed : 32.28 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.56 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS h 10 PHE 0.006 0.002 PHE e 24 TYR 0.012 0.002 TYR J 14 ARG 0.002 0.000 ARG e 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 9 SER cc_start: 0.7197 (p) cc_final: 0.6963 (p) outliers start: 13 outliers final: 12 residues processed: 60 average time/residue: 0.2037 time to fit residues: 19.5515 Evaluate side-chains 64 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain f residue 6 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain O residue 20 CYS Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.5404 r_free = 0.5404 target = 0.366863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.5952 r_free = 0.5952 target = 0.299310 restraints weight = 15872.768| |-----------------------------------------------------------------------------| r_work (start): 0.5340 rms_B_bonded: 0.91 r_work: 0.6013 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.5955 rms_B_bonded: 0.69 restraints_weight: 0.2500 r_work: 0.5681 rms_B_bonded: 2.48 restraints_weight: 0.1250 r_work (final): 0.5681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 4656 Z= 0.204 Angle : 0.615 5.545 6280 Z= 0.329 Chirality : 0.045 0.136 736 Planarity : 0.002 0.015 760 Dihedral : 6.103 29.787 620 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 2.05 % Allowed : 32.28 % Favored : 65.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.44 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.14 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS j 5 PHE 0.005 0.001 PHE g 25 TYR 0.008 0.001 TYR n 16 ARG 0.002 0.000 ARG e 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5419.18 seconds wall clock time: 94 minutes 57.91 seconds (5697.91 seconds total)