Starting phenix.real_space_refine on Fri Aug 22 22:49:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sbd_40305/08_2025/8sbd_40305.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sbd_40305/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sbd_40305/08_2025/8sbd_40305.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sbd_40305/08_2025/8sbd_40305.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sbd_40305/08_2025/8sbd_40305.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sbd_40305/08_2025/8sbd_40305.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8864 Number of models: 1 Model: "" Number of chains: 4 Chain: "p" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "o" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 355 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "P" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 288 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "O" 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: n, l, j, h, f, d, b, m, k, i, g, e, c, a, N, L, J, H, F, D, B, M, K, I, G, E, C, A Time building chain proxies: 0.89, per 1000 atoms: 0.10 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: 0.78 Conformation dependent library (CDL) restraints added in 338.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.24 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: 1.91 Time building geometry restraints manager: 1.11 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 0.00 0.00 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: 0.02 Found NCS groups: ncs_group { reference = chain 'p' selection = chain 'n' selection = chain 'l' selection = chain 'j' selection = chain 'h' selection = chain 'f' selection = chain 'd' selection = chain 'b' } ncs_group { reference = chain 'o' selection = chain 'm' selection = chain 'k' selection = chain 'i' selection = chain 'g' selection = chain 'e' selection = chain 'c' selection = chain 'a' } ncs_group { reference = chain 'P' selection = chain 'N' selection = chain 'L' selection = chain 'J' selection = chain 'H' selection = chain 'F' selection = chain 'D' selection = chain 'B' } ncs_group { reference = chain 'O' selection = chain 'M' selection = chain 'K' selection = chain 'I' selection = chain 'G' selection = chain 'E' selection = chain 'C' selection = chain 'A' } 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: 0.800 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: 0.060 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.190 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.001 0.000 ARG o 22 TYR 0.007 0.001 TYR i 16 PHE 0.007 0.002 PHE m 24 HIS 0.001 0.001 HIS b 10 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4656) covalent geometry : angle 0.72544 ( 6280) hydrogen bonds : bond 0.15498 ( 46) hydrogen bonds : angle 8.82717 ( 138) *********************** 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 : 0.229 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: N 18 ASN cc_start: 0.6673 (m110) cc_final: 0.6321 (m110) 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: 0.7521 (m) outliers start: 32 outliers final: 15 residues processed: 109 average time/residue: 0.0709 time to fit residues: 12.3967 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 : 0.254 ------------------------------------------------------------------------------- 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 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.5482 r_free = 0.5482 target = 0.416561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.5968 r_free = 0.5968 target = 0.342119 restraints weight = 17183.137| |-----------------------------------------------------------------------------| r_work (start): 0.5398 rms_B_bonded: 1.21 r_work: 0.5884 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.5829 rms_B_bonded: 0.92 restraints_weight: 0.2500 r_work: 0.5532 rms_B_bonded: 3.61 restraints_weight: 0.1250 r_work (final): 0.5532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1808 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= 0.180 Angle : 0.657 6.001 6280 Z= 0.351 Chirality : 0.047 0.136 736 Planarity : 0.003 0.021 760 Dihedral : 8.556 50.675 633 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 5.97 % Allowed : 13.99 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.003 0.001 ARG e 22 TYR 0.011 0.002 TYR e 16 PHE 0.006 0.001 PHE g 24 HIS 0.003 0.001 HIS b 10 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4656) covalent geometry : angle 0.65665 ( 6280) hydrogen bonds : bond 0.02740 ( 46) hydrogen bonds : angle 5.87778 ( 138) *********************** 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: 32 poor density : 82 time to evaluate : 0.188 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: 0.5648 (OUTLIER) cc_final: 0.4752 (m) REVERT: l 7 CYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6887 (m) REVERT: j 7 CYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7163 (m) REVERT: J 12 SER cc_start: 0.8337 (m) cc_final: 0.7981 (m) outliers start: 32 outliers final: 17 residues processed: 110 average time/residue: 0.0688 time to fit residues: 12.2896 Evaluate side-chains 79 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.5427 r_free = 0.5427 target = 0.410430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.5984 r_free = 0.5984 target = 0.332089 restraints weight = 17149.190| |-----------------------------------------------------------------------------| r_work (start): 0.5317 rms_B_bonded: 0.92 r_work: 0.5899 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.5833 rms_B_bonded: 0.72 restraints_weight: 0.2500 r_work: 0.5559 rms_B_bonded: 2.56 restraints_weight: 0.1250 r_work (final): 0.5559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2804 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= 0.214 Angle : 0.661 6.522 6280 Z= 0.353 Chirality : 0.047 0.124 736 Planarity : 0.003 0.017 760 Dihedral : 7.572 44.833 626 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.31 % Favored : 87.69 % Rotamer: Outliers : 5.60 % Allowed : 17.72 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.77 (0.24), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.18), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG e 22 TYR 0.012 0.002 TYR k 16 PHE 0.008 0.002 PHE o 24 HIS 0.003 0.001 HIS l 10 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 4656) covalent geometry : angle 0.66078 ( 6280) hydrogen bonds : bond 0.02229 ( 46) hydrogen bonds : angle 5.76371 ( 138) *********************** 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 101 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.231 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: 0.5796 (OUTLIER) cc_final: 0.5206 (m) REVERT: c 26 TYR cc_start: 0.7488 (m-80) cc_final: 0.7284 (m-80) outliers start: 30 outliers final: 22 residues processed: 95 average time/residue: 0.0697 time to fit residues: 10.7582 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 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 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 7 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 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 = 0.350241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.5792 r_free = 0.5792 target = 0.285762 restraints weight = 16224.271| |-----------------------------------------------------------------------------| r_work (start): 0.5229 rms_B_bonded: 1.27 r_work: 0.5826 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.5753 rms_B_bonded: 0.85 restraints_weight: 0.2500 r_work: 0.5487 rms_B_bonded: 2.96 restraints_weight: 0.1250 r_work (final): 0.5487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 4656 Z= 0.364 Angle : 0.826 9.557 6280 Z= 0.433 Chirality : 0.052 0.156 736 Planarity : 0.004 0.021 760 Dihedral : 8.263 47.393 625 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 32.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.27 % Favored : 81.73 % Rotamer: Outliers : 5.22 % Allowed : 25.00 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.11 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 22 TYR 0.021 0.004 TYR k 16 PHE 0.017 0.003 PHE k 24 HIS 0.004 0.001 HIS b 10 Details of bonding type rmsd covalent geometry : bond 0.00801 ( 4656) covalent geometry : angle 0.82560 ( 6280) hydrogen bonds : bond 0.02201 ( 46) hydrogen bonds : angle 6.29872 ( 138) *********************** 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 98 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 70 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5485 (t) REVERT: F 9 SER cc_start: 0.7819 (p) cc_final: 0.7540 (p) REVERT: B 20 CYS cc_start: 0.6572 (p) cc_final: 0.6142 (t) outliers start: 28 outliers final: 22 residues processed: 93 average time/residue: 0.0887 time to fit residues: 13.1281 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 : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 17 LEU 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 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 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 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 3 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.5421 r_free = 0.5421 target = 0.407199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.6001 r_free = 0.6001 target = 0.329089 restraints weight = 17158.613| |-----------------------------------------------------------------------------| r_work (start): 0.5301 rms_B_bonded: 1.20 r_work: 0.5914 rms_B_bonded: 0.45 restraints_weight: 0.5000 r_work: 0.5854 rms_B_bonded: 0.79 restraints_weight: 0.2500 r_work: 0.5556 rms_B_bonded: 2.87 restraints_weight: 0.1250 r_work (final): 0.5556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 4656 Z= 0.188 Angle : 0.670 7.311 6280 Z= 0.356 Chirality : 0.047 0.143 736 Planarity : 0.002 0.025 760 Dihedral : 7.217 46.298 624 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 4.29 % Allowed : 26.87 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.05 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG k 22 TYR 0.010 0.001 TYR c 26 PHE 0.004 0.001 PHE g 24 HIS 0.003 0.001 HIS j 10 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 4656) covalent geometry : angle 0.66959 ( 6280) hydrogen bonds : bond 0.01717 ( 46) hydrogen bonds : angle 5.71038 ( 138) *********************** 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 78 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5744 (t) REVERT: j 7 CYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7912 (m) REVERT: B 20 CYS cc_start: 0.6816 (p) cc_final: 0.6386 (t) outliers start: 23 outliers final: 17 residues processed: 72 average time/residue: 0.0755 time to fit residues: 9.0021 Evaluate side-chains 72 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain j residue 7 CYS 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 6 CYS Chi-restraints excluded: chain H residue 8 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.5377 r_free = 0.5377 target = 0.360934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.5887 r_free = 0.5887 target = 0.300592 restraints weight = 15771.577| |-----------------------------------------------------------------------------| r_work (start): 0.5320 rms_B_bonded: 1.10 r_work: 0.5948 rms_B_bonded: 0.43 restraints_weight: 0.5000 r_work: 0.5887 rms_B_bonded: 0.76 restraints_weight: 0.2500 r_work: 0.5587 rms_B_bonded: 2.77 restraints_weight: 0.1250 r_work (final): 0.5587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4656 Z= 0.179 Angle : 0.637 6.921 6280 Z= 0.338 Chirality : 0.046 0.130 736 Planarity : 0.002 0.014 760 Dihedral : 6.858 45.838 623 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.81 % Favored : 85.19 % Rotamer: Outliers : 4.10 % Allowed : 27.99 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.14 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.91 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 22 TYR 0.008 0.001 TYR i 16 PHE 0.005 0.001 PHE m 24 HIS 0.002 0.000 HIS b 10 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4656) covalent geometry : angle 0.63668 ( 6280) hydrogen bonds : bond 0.01554 ( 46) hydrogen bonds : angle 5.51217 ( 138) *********************** 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 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5696 (t) REVERT: B 20 CYS cc_start: 0.6888 (p) cc_final: 0.6548 (t) outliers start: 22 outliers final: 15 residues processed: 76 average time/residue: 0.0740 time to fit residues: 9.1755 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 : 0.268 ------------------------------------------------------------------------------- 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 7 CYS Chi-restraints excluded: chain P residue 8 THR 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.5372 r_free = 0.5372 target = 0.362364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.5897 r_free = 0.5897 target = 0.298296 restraints weight = 15953.834| |-----------------------------------------------------------------------------| r_work (start): 0.5316 rms_B_bonded: 0.87 r_work: 0.5971 rms_B_bonded: 0.38 restraints_weight: 0.5000 r_work: 0.5919 rms_B_bonded: 0.67 restraints_weight: 0.2500 r_work: 0.5654 rms_B_bonded: 2.28 restraints_weight: 0.1250 r_work (final): 0.5654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.4479 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= 0.188 Angle : 0.640 6.982 6280 Z= 0.341 Chirality : 0.046 0.145 736 Planarity : 0.002 0.016 760 Dihedral : 6.555 46.318 621 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 3.36 % Allowed : 28.92 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.19 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG k 22 TYR 0.010 0.002 TYR L 14 PHE 0.005 0.001 PHE m 24 HIS 0.002 0.001 HIS h 10 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 4656) covalent geometry : angle 0.64015 ( 6280) hydrogen bonds : bond 0.01554 ( 46) hydrogen bonds : angle 5.53227 ( 138) *********************** 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 74 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 7 CYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5648 (t) REVERT: B 20 CYS cc_start: 0.6942 (p) cc_final: 0.6615 (t) outliers start: 18 outliers final: 14 residues processed: 66 average time/residue: 0.0715 time to fit residues: 7.7129 Evaluate side-chains 67 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 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 G residue 20 CYS 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 24 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5400 r_free = 0.5400 target = 0.367016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.5936 r_free = 0.5936 target = 0.301881 restraints weight = 15676.405| |-----------------------------------------------------------------------------| r_work (start): 0.5341 rms_B_bonded: 0.91 r_work: 0.6025 rms_B_bonded: 0.39 restraints_weight: 0.5000 r_work: 0.5951 rms_B_bonded: 0.71 restraints_weight: 0.2500 r_work: 0.5653 rms_B_bonded: 2.54 restraints_weight: 0.1250 r_work (final): 0.5653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.4585 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= 0.149 Angle : 0.606 6.030 6280 Z= 0.323 Chirality : 0.045 0.146 736 Planarity : 0.002 0.011 760 Dihedral : 6.194 45.517 620 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 20.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.92 % Favored : 88.08 % Rotamer: Outliers : 3.36 % Allowed : 28.54 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.21 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 22 TYR 0.009 0.001 TYR c 26 PHE 0.003 0.001 PHE a 25 HIS 0.002 0.000 HIS j 10 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4656) covalent geometry : angle 0.60623 ( 6280) hydrogen bonds : bond 0.01456 ( 46) hydrogen bonds : angle 5.32444 ( 138) *********************** 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: 18 poor density : 61 time to evaluate : 0.278 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: 0.5841 (OUTLIER) cc_final: 0.5540 (t) REVERT: B 20 CYS cc_start: 0.6989 (p) cc_final: 0.6665 (t) outliers start: 18 outliers final: 13 residues processed: 71 average time/residue: 0.0747 time to fit residues: 8.6990 Evaluate side-chains 69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain m residue 10 HIS 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 20 CYS Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain G residue 20 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain E residue 20 CYS 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 22 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.365477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.5921 r_free = 0.5921 target = 0.302023 restraints weight = 15786.963| |-----------------------------------------------------------------------------| r_work (start): 0.5340 rms_B_bonded: 1.14 r_work: 0.5992 rms_B_bonded: 0.44 restraints_weight: 0.5000 r_work: 0.5932 rms_B_bonded: 0.77 restraints_weight: 0.2500 r_work: 0.5637 rms_B_bonded: 2.76 restraints_weight: 0.1250 r_work (final): 0.5637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.4710 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= 0.177 Angle : 0.634 6.327 6280 Z= 0.335 Chirality : 0.045 0.123 736 Planarity : 0.002 0.011 760 Dihedral : 6.100 45.189 618 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.19 % Favored : 84.81 % Rotamer: Outliers : 2.99 % Allowed : 29.10 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.25 (0.23), 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 ARG 0.002 0.000 ARG e 22 TYR 0.009 0.002 TYR L 14 PHE 0.005 0.001 PHE c 24 HIS 0.002 0.000 HIS o 10 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 4656) covalent geometry : angle 0.63398 ( 6280) hydrogen bonds : bond 0.01439 ( 46) hydrogen bonds : angle 5.38549 ( 138) *********************** 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 74 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 CYS cc_start: 0.6936 (p) cc_final: 0.6670 (t) outliers start: 16 outliers final: 14 residues processed: 65 average time/residue: 0.0768 time to fit residues: 8.2488 Evaluate side-chains 70 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 17 LEU 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 20 CYS Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain G residue 20 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain E residue 20 CYS 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 29 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.5386 r_free = 0.5386 target = 0.363685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.5933 r_free = 0.5933 target = 0.297153 restraints weight = 15940.753| |-----------------------------------------------------------------------------| r_work (start): 0.5322 rms_B_bonded: 0.87 r_work: 0.6021 rms_B_bonded: 0.36 restraints_weight: 0.5000 r_work: 0.5955 rms_B_bonded: 0.65 restraints_weight: 0.2500 r_work: 0.5673 rms_B_bonded: 2.29 restraints_weight: 0.1250 r_work (final): 0.5673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 4656 Z= 0.209 Angle : 0.667 6.696 6280 Z= 0.352 Chirality : 0.047 0.121 736 Planarity : 0.002 0.010 760 Dihedral : 6.015 29.171 617 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.35 % Favored : 83.65 % Rotamer: Outliers : 2.61 % Allowed : 29.85 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.27 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.01 (0.18), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG k 22 TYR 0.011 0.002 TYR J 14 PHE 0.006 0.002 PHE m 24 HIS 0.003 0.001 HIS n 10 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 4656) covalent geometry : angle 0.66683 ( 6280) hydrogen bonds : bond 0.01510 ( 46) hydrogen bonds : angle 5.57316 ( 138) ********************** 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 69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 CYS cc_start: 0.6922 (p) cc_final: 0.6705 (t) outliers start: 14 outliers final: 14 residues processed: 60 average time/residue: 0.0789 time to fit residues: 7.6930 Evaluate side-chains 66 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 17 LEU 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 20 CYS Chi-restraints excluded: chain I residue 20 CYS Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain G residue 20 CYS Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain E residue 20 CYS 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 3 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.5419 r_free = 0.5419 target = 0.368645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.5958 r_free = 0.5958 target = 0.304031 restraints weight = 15805.705| |-----------------------------------------------------------------------------| r_work (start): 0.5353 rms_B_bonded: 1.14 r_work: 0.6008 rms_B_bonded: 0.45 restraints_weight: 0.5000 r_work: 0.5957 rms_B_bonded: 0.78 restraints_weight: 0.2500 r_work: 0.5738 rms_B_bonded: 2.50 restraints_weight: 0.1250 r_work (final): 0.5738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.4891 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= 0.162 Angle : 0.629 5.958 6280 Z= 0.332 Chirality : 0.045 0.126 736 Planarity : 0.002 0.010 760 Dihedral : 5.780 28.719 617 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 2.99 % Allowed : 29.48 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.24 (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 ARG 0.002 0.000 ARG e 22 TYR 0.008 0.001 TYR L 14 PHE 0.005 0.001 PHE e 24 HIS 0.002 0.001 HIS o 10 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4656) covalent geometry : angle 0.62892 ( 6280) hydrogen bonds : bond 0.01450 ( 46) hydrogen bonds : angle 5.35864 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2732.44 seconds wall clock time: 48 minutes 12.24 seconds (2892.24 seconds total)