Starting phenix.real_space_refine on Sun May 11 20:54:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sbd_40305/05_2025/8sbd_40305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sbd_40305/05_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_40305/05_2025/8sbd_40305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sbd_40305/05_2025/8sbd_40305.map" model { file = "/net/cci-nas-00/data/ceres_data/8sbd_40305/05_2025/8sbd_40305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sbd_40305/05_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-5687/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: 2.70, per 1000 atoms: 0.30 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: 2.36 Conformation dependent library (CDL) restraints added in 727.4 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: 0.73 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: 2.81 Time building geometry restraints manager: 2.71 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 39.59 39.59 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: 0.460 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: 0.150 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.260 Find NCS groups from input model: 0.140 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.470 ------------------------------------------------------------------------------- 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= 0.186 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 Details of bonding type rmsd hydrogen bonds : bond 0.15498 ( 46) hydrogen bonds : angle 8.82717 ( 138) covalent geometry : bond 0.00323 ( 4656) covalent geometry : angle 0.72544 ( 6280) *********************** 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 : 0.765 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: 0.1694 time to fit residues: 28.9838 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 : 0.737 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.3990 ------------------------------------------------------------------------------- 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 = 0.5462 r_free = 0.5462 target = 0.414718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.5985 r_free = 0.5985 target = 0.338871 restraints weight = 17011.148| |-----------------------------------------------------------------------------| r_work (start): 0.5378 rms_B_bonded: 1.20 r_work: 0.5853 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.5804 rms_B_bonded: 0.91 restraints_weight: 0.2500 r_work: 0.5520 rms_B_bonded: 3.45 restraints_weight: 0.1250 r_work (final): 0.5520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 4656 Z= 0.194 Angle : 0.667 6.440 6280 Z= 0.357 Chirality : 0.047 0.138 736 Planarity : 0.003 0.022 760 Dihedral : 8.688 50.749 633 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 6.16 % Allowed : 14.55 % Favored : 79.29 % 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: -4.29 (0.25), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.19), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 10 PHE 0.006 0.001 PHE g 24 TYR 0.013 0.002 TYR G 19 ARG 0.003 0.001 ARG e 22 Details of bonding type rmsd hydrogen bonds : bond 0.02806 ( 46) hydrogen bonds : angle 5.93674 ( 138) covalent geometry : bond 0.00414 ( 4656) covalent geometry : angle 0.66666 ( 6280) *********************** 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 113 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.684 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: n 7 CYS cc_start: 0.5495 (OUTLIER) cc_final: 0.4566 (m) REVERT: l 7 CYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6935 (m) REVERT: J 12 SER cc_start: 0.8353 (m) cc_final: 0.7994 (m) REVERT: G 8 THR cc_start: 0.8530 (t) cc_final: 0.8271 (m) outliers start: 33 outliers final: 17 residues processed: 108 average time/residue: 0.1582 time to fit residues: 27.1121 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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 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 L residue 8 THR 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: 3.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5398 r_free = 0.5398 target = 0.357797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.5866 r_free = 0.5866 target = 0.298564 restraints weight = 15648.012| |-----------------------------------------------------------------------------| r_work (start): 0.5352 rms_B_bonded: 1.11 r_work: 0.5910 rms_B_bonded: 0.49 restraints_weight: 0.5000 r_work: 0.5833 rms_B_bonded: 0.90 restraints_weight: 0.2500 r_work: 0.5539 rms_B_bonded: 3.41 restraints_weight: 0.1250 r_work (final): 0.5539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 4656 Z= 0.182 Angle : 0.631 5.970 6280 Z= 0.337 Chirality : 0.046 0.123 736 Planarity : 0.002 0.015 760 Dihedral : 7.296 45.703 626 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 5.41 % Allowed : 16.60 % Favored : 77.99 % 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: -4.69 (0.24), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.18), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS l 10 PHE 0.006 0.001 PHE e 24 TYR 0.009 0.002 TYR i 16 ARG 0.001 0.000 ARG e 22 Details of bonding type rmsd hydrogen bonds : bond 0.02115 ( 46) hydrogen bonds : angle 5.68648 ( 138) covalent geometry : bond 0.00392 ( 4656) covalent geometry : angle 0.63056 ( 6280) *********************** 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 104 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.5698 (OUTLIER) cc_final: 0.5027 (m) REVERT: c 26 TYR cc_start: 0.7554 (m-80) cc_final: 0.7180 (m-80) outliers start: 29 outliers final: 21 residues processed: 98 average time/residue: 0.1621 time to fit residues: 25.1460 Evaluate side-chains 82 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 P residue 6 CYS Chi-restraints excluded: chain P residue 7 CYS 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 6 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 E residue 20 CYS 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 Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 chunk 7 optimal weight: 0.7980 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 = 0.5316 r_free = 0.5316 target = 0.351451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.5809 r_free = 0.5809 target = 0.287649 restraints weight = 15930.566| |-----------------------------------------------------------------------------| r_work (start): 0.5261 rms_B_bonded: 1.09 r_work: 0.5845 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.5780 rms_B_bonded: 0.83 restraints_weight: 0.2500 r_work: 0.5508 rms_B_bonded: 2.87 restraints_weight: 0.1250 r_work (final): 0.5508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3505 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= 0.295 Angle : 0.740 8.499 6280 Z= 0.390 Chirality : 0.049 0.129 736 Planarity : 0.003 0.014 760 Dihedral : 7.947 46.607 626 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 28.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.73 % Favored : 83.27 % Rotamer: Outliers : 5.22 % Allowed : 22.01 % Favored : 72.76 % 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: -5.04 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS l 10 PHE 0.011 0.002 PHE m 24 TYR 0.017 0.003 TYR k 16 ARG 0.001 0.000 ARG k 22 Details of bonding type rmsd hydrogen bonds : bond 0.01991 ( 46) hydrogen bonds : angle 6.00928 ( 138) covalent geometry : bond 0.00653 ( 4656) covalent geometry : angle 0.73956 ( 6280) *********************** 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 92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.5975 (OUTLIER) cc_final: 0.5158 (m) outliers start: 28 outliers final: 22 residues processed: 87 average time/residue: 0.1690 time to fit residues: 23.2461 Evaluate side-chains 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain c 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 L 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 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 6 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 38 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.5390 r_free = 0.5390 target = 0.362228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.5888 r_free = 0.5888 target = 0.303267 restraints weight = 15610.868| |-----------------------------------------------------------------------------| r_work (start): 0.5339 rms_B_bonded: 0.87 r_work: 0.5962 rms_B_bonded: 0.40 restraints_weight: 0.5000 r_work: 0.5906 rms_B_bonded: 0.70 restraints_weight: 0.2500 r_work: 0.5610 rms_B_bonded: 2.56 restraints_weight: 0.1250 r_work (final): 0.5610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3754 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= 0.143 Angle : 0.603 5.575 6280 Z= 0.324 Chirality : 0.046 0.132 736 Planarity : 0.002 0.022 760 Dihedral : 6.923 46.368 625 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 3.92 % Allowed : 22.76 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.02 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS l 10 PHE 0.004 0.001 PHE g 25 TYR 0.012 0.001 TYR c 26 ARG 0.002 0.001 ARG e 22 Details of bonding type rmsd hydrogen bonds : bond 0.01550 ( 46) hydrogen bonds : angle 5.39499 ( 138) covalent geometry : bond 0.00308 ( 4656) covalent geometry : angle 0.60262 ( 6280) *********************** 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 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.5765 (OUTLIER) cc_final: 0.5368 (t) REVERT: C 11 CYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5681 (t) REVERT: B 20 CYS cc_start: 0.6473 (p) cc_final: 0.5890 (t) outliers start: 21 outliers final: 18 residues processed: 74 average time/residue: 0.1561 time to fit residues: 18.6640 Evaluate side-chains 73 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain d residue 10 HIS 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 L residue 6 CYS Chi-restraints excluded: chain K residue 20 CYS Chi-restraints excluded: chain I residue 20 CYS 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 G residue 20 CYS Chi-restraints excluded: chain F residue 6 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 11 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: 8.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.5319 r_free = 0.5319 target = 0.353244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.5824 r_free = 0.5824 target = 0.288564 restraints weight = 15753.965| |-----------------------------------------------------------------------------| r_work (start): 0.5256 rms_B_bonded: 1.23 r_work: 0.5855 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.5791 rms_B_bonded: 0.84 restraints_weight: 0.2500 r_work: 0.5529 rms_B_bonded: 2.92 restraints_weight: 0.1250 r_work (final): 0.5529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4161 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= 0.264 Angle : 0.695 8.121 6280 Z= 0.370 Chirality : 0.048 0.121 736 Planarity : 0.003 0.016 760 Dihedral : 7.296 47.041 623 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.12 % Favored : 82.88 % Rotamer: Outliers : 4.48 % Allowed : 25.19 % Favored : 70.34 % 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: -5.15 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.92 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 10 PHE 0.010 0.002 PHE m 24 TYR 0.016 0.003 TYR J 14 ARG 0.002 0.000 ARG e 22 Details of bonding type rmsd hydrogen bonds : bond 0.01757 ( 46) hydrogen bonds : angle 5.77792 ( 138) covalent geometry : bond 0.00583 ( 4656) covalent geometry : angle 0.69537 ( 6280) *********************** 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 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.5945 (OUTLIER) cc_final: 0.5489 (t) REVERT: C 11 CYS cc_start: 0.6493 (t) cc_final: 0.6184 (t) REVERT: B 20 CYS cc_start: 0.6676 (p) cc_final: 0.6308 (t) outliers start: 24 outliers final: 18 residues processed: 71 average time/residue: 0.1653 time to fit residues: 18.9545 Evaluate side-chains 69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain k 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 K residue 20 CYS Chi-restraints excluded: chain I residue 20 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.5427 r_free = 0.5427 target = 0.406912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 136)---------------| | r_work = 0.6089 r_free = 0.6089 target = 0.327799 restraints weight = 17082.835| |-----------------------------------------------------------------------------| r_work (start): 0.5292 rms_B_bonded: 1.25 r_work: 0.5904 rms_B_bonded: 0.45 restraints_weight: 0.5000 r_work: 0.5851 rms_B_bonded: 0.78 restraints_weight: 0.2500 r_work: 0.5575 rms_B_bonded: 2.73 restraints_weight: 0.1250 r_work (final): 0.5575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 4656 Z= 0.200 Angle : 0.651 7.057 6280 Z= 0.346 Chirality : 0.047 0.126 736 Planarity : 0.002 0.015 760 Dihedral : 6.863 46.680 621 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 4.29 % Allowed : 25.56 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.16 (0.22), 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 0.002 0.000 HIS h 10 PHE 0.006 0.001 PHE m 24 TYR 0.010 0.002 TYR i 16 ARG 0.002 0.000 ARG c 22 Details of bonding type rmsd hydrogen bonds : bond 0.01603 ( 46) hydrogen bonds : angle 5.62996 ( 138) covalent geometry : bond 0.00437 ( 4656) covalent geometry : angle 0.65080 ( 6280) *********************** 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 77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5595 (t) REVERT: B 20 CYS cc_start: 0.6849 (p) cc_final: 0.6494 (t) outliers start: 23 outliers final: 19 residues processed: 70 average time/residue: 0.1597 time to fit residues: 18.1290 Evaluate side-chains 71 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain d residue 10 HIS 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 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 G residue 20 CYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.5420 r_free = 0.5420 target = 0.406071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.5972 r_free = 0.5972 target = 0.327508 restraints weight = 17170.489| |-----------------------------------------------------------------------------| r_work (start): 0.5277 rms_B_bonded: 1.25 r_work: 0.5899 rms_B_bonded: 0.49 restraints_weight: 0.5000 r_work: 0.5833 rms_B_bonded: 0.85 restraints_weight: 0.2500 r_work: 0.5535 rms_B_bonded: 3.10 restraints_weight: 0.1250 r_work (final): 0.5535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 4656 Z= 0.209 Angle : 0.653 7.213 6280 Z= 0.349 Chirality : 0.047 0.136 736 Planarity : 0.002 0.012 760 Dihedral : 6.861 46.687 621 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.92 % Favored : 83.08 % Rotamer: Outliers : 3.73 % Allowed : 25.56 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.28 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS f 5 PHE 0.005 0.002 PHE e 24 TYR 0.011 0.002 TYR i 16 ARG 0.002 0.000 ARG e 22 Details of bonding type rmsd hydrogen bonds : bond 0.01561 ( 46) hydrogen bonds : angle 5.68765 ( 138) covalent geometry : bond 0.00461 ( 4656) covalent geometry : angle 0.65338 ( 6280) *********************** 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 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.6151 (OUTLIER) cc_final: 0.5773 (t) REVERT: B 20 CYS cc_start: 0.7051 (p) cc_final: 0.6695 (t) outliers start: 20 outliers final: 19 residues processed: 73 average time/residue: 0.1628 time to fit residues: 19.1647 Evaluate side-chains 75 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 11 LEU Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain d residue 10 HIS 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 11 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 G residue 20 CYS 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 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: 3.9990 chunk 0 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN F 5 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5325 r_free = 0.5325 target = 0.357037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.5847 r_free = 0.5847 target = 0.292374 restraints weight = 15829.206| |-----------------------------------------------------------------------------| r_work (start): 0.5267 rms_B_bonded: 1.09 r_work: 0.5901 rms_B_bonded: 0.42 restraints_weight: 0.5000 r_work: 0.5852 rms_B_bonded: 0.71 restraints_weight: 0.2500 r_work: 0.5574 rms_B_bonded: 2.50 restraints_weight: 0.1250 r_work (final): 0.5574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 4656 Z= 0.233 Angle : 0.680 7.562 6280 Z= 0.361 Chirality : 0.048 0.131 736 Planarity : 0.002 0.012 760 Dihedral : 6.935 47.883 621 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.12 % Favored : 82.88 % Rotamer: Outliers : 4.10 % Allowed : 25.93 % Favored : 69.96 % 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: -5.34 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS h 10 PHE 0.007 0.002 PHE m 24 TYR 0.012 0.002 TYR J 14 ARG 0.002 0.000 ARG e 22 Details of bonding type rmsd hydrogen bonds : bond 0.01602 ( 46) hydrogen bonds : angle 5.84060 ( 138) covalent geometry : bond 0.00516 ( 4656) covalent geometry : angle 0.67989 ( 6280) *********************** 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 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 CYS cc_start: 0.6963 (p) cc_final: 0.6740 (t) outliers start: 22 outliers final: 20 residues processed: 75 average time/residue: 0.1750 time to fit residues: 21.0749 Evaluate side-chains 76 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain d residue 10 HIS 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 K residue 11 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 G residue 20 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.5385 r_free = 0.5385 target = 0.366371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.5929 r_free = 0.5929 target = 0.301793 restraints weight = 15885.664| |-----------------------------------------------------------------------------| r_work (start): 0.5326 rms_B_bonded: 1.16 r_work: 0.5966 rms_B_bonded: 0.46 restraints_weight: 0.5000 r_work: 0.5906 rms_B_bonded: 0.80 restraints_weight: 0.2500 r_work: 0.5633 rms_B_bonded: 2.79 restraints_weight: 0.1250 r_work (final): 0.5633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4796 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= 0.146 Angle : 0.612 5.553 6280 Z= 0.327 Chirality : 0.045 0.127 736 Planarity : 0.002 0.014 760 Dihedral : 6.182 37.650 620 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 3.54 % Allowed : 26.31 % Favored : 70.15 % 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: -5.31 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.04 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS n 5 PHE 0.004 0.001 PHE a 25 TYR 0.010 0.001 TYR c 26 ARG 0.002 0.000 ARG e 22 Details of bonding type rmsd hydrogen bonds : bond 0.01492 ( 46) hydrogen bonds : angle 5.49117 ( 138) covalent geometry : bond 0.00313 ( 4656) covalent geometry : angle 0.61171 ( 6280) ********************** 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 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 18 residues processed: 71 average time/residue: 0.1685 time to fit residues: 19.7943 Evaluate side-chains 77 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 11 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 G residue 20 CYS 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 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 Chi-restraints excluded: chain A residue 20 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.5395 r_free = 0.5395 target = 0.366564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.5939 r_free = 0.5939 target = 0.299300 restraints weight = 15802.044| |-----------------------------------------------------------------------------| r_work (start): 0.5332 rms_B_bonded: 0.91 r_work: 0.6001 rms_B_bonded: 0.40 restraints_weight: 0.5000 r_work: 0.5948 rms_B_bonded: 0.70 restraints_weight: 0.2500 r_work: 0.5687 rms_B_bonded: 2.45 restraints_weight: 0.1250 r_work (final): 0.5687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4853 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= 0.152 Angle : 0.609 5.693 6280 Z= 0.325 Chirality : 0.045 0.128 736 Planarity : 0.002 0.026 760 Dihedral : 6.005 35.195 618 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 3.17 % Allowed : 27.61 % Favored : 69.22 % 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: -5.25 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.18), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS e 5 PHE 0.006 0.001 PHE c 25 TYR 0.009 0.001 TYR c 26 ARG 0.002 0.000 ARG e 22 Details of bonding type rmsd hydrogen bonds : bond 0.01412 ( 46) hydrogen bonds : angle 5.40952 ( 138) covalent geometry : bond 0.00330 ( 4656) covalent geometry : angle 0.60923 ( 6280) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5160.69 seconds wall clock time: 90 minutes 10.06 seconds (5410.06 seconds total)