Starting phenix.real_space_refine on Tue Sep 24 16:07:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/09_2024/8sbd_40305.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/09_2024/8sbd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/09_2024/8sbd_40305.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/09_2024/8sbd_40305.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/09_2024/8sbd_40305.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sbd_40305/09_2024/8sbd_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-5461/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: 2.87, per 1000 atoms: 0.32 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: 2.19 Conformation dependent library (CDL) restraints added in 716.1 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: 0.85 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: 2.86 Time building geometry restraints manager: 2.60 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: 0.00 Found NCS groups: 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' } 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: 0.450 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: 0.160 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 20.400 Find NCS groups from input model: 0.240 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4656 Z= 0.206 Angle : 0.725 4.629 6280 Z= 0.437 Chirality : 0.043 0.139 736 Planarity : 0.002 0.006 760 Dihedral : 12.978 52.500 1576 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.97 % Allowed : 8.96 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.24), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.19), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS b 10 PHE 0.007 0.002 PHE m 24 TYR 0.007 0.001 TYR i 16 ARG 0.001 0.000 ARG o 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 0.738 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: 0.1648 time to fit residues: 28.1276 Evaluate side-chains 78 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 63 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 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= 0.263 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 *********************** 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 fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 0.852 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: 0.5387 (OUTLIER) cc_final: 0.4666 (m) REVERT: l 7 CYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6884 (m) REVERT: J 12 SER cc_start: 0.8413 (m) cc_final: 0.8077 (m) REVERT: G 8 THR cc_start: 0.8712 (t) cc_final: 0.8445 (m) outliers start: 33 outliers final: 17 residues processed: 108 average time/residue: 0.1804 time to fit residues: 30.4046 Evaluate side-chains 80 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 36 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 4656 Z= 0.199 Angle : 0.596 4.819 6280 Z= 0.320 Chirality : 0.045 0.126 736 Planarity : 0.002 0.014 760 Dihedral : 6.984 45.310 626 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 5.04 % Allowed : 16.04 % Favored : 78.92 % 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: -4.49 (0.25), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.19), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS l 10 PHE 0.004 0.001 PHE e 24 TYR 0.010 0.001 TYR n 16 ARG 0.001 0.000 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 68 time to evaluate : 0.769 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: 0.5330 (OUTLIER) cc_final: 0.5003 (m) outliers start: 27 outliers final: 19 residues processed: 87 average time/residue: 0.1681 time to fit residues: 22.8123 Evaluate side-chains 73 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 53 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 7 CYS Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain N residue 18 ASN 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 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 D residue 18 ASN Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain A residue 20 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3238 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= 0.333 Angle : 0.681 6.590 6280 Z= 0.362 Chirality : 0.047 0.129 736 Planarity : 0.003 0.014 760 Dihedral : 7.241 45.982 622 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.85 % Favored : 86.15 % Rotamer: Outliers : 5.41 % Allowed : 19.59 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.89 (0.24), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.18), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS l 10 PHE 0.010 0.002 PHE m 24 TYR 0.014 0.002 TYR J 14 ARG 0.002 0.000 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 65 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 86 average time/residue: 0.1631 time to fit residues: 22.1034 Evaluate side-chains 77 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 54 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 17 LEU 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 N residue 18 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 7 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 Chi-restraints excluded: chain A residue 20 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 18 ASN M 5 GLN K 5 GLN E 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3960 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= 0.410 Angle : 0.734 7.619 6280 Z= 0.388 Chirality : 0.049 0.128 736 Planarity : 0.003 0.016 760 Dihedral : 7.280 42.620 620 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 29.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.12 % Favored : 82.88 % Rotamer: Outliers : 5.78 % Allowed : 22.57 % Favored : 71.64 % 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: -5.08 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (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 i 16 ARG 0.003 0.000 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 57 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 THR cc_start: 0.8714 (t) cc_final: 0.8388 (m) REVERT: B 20 CYS cc_start: 0.6179 (p) cc_final: 0.5874 (t) outliers start: 31 outliers final: 26 residues processed: 82 average time/residue: 0.1651 time to fit residues: 21.4082 Evaluate side-chains 75 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 49 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain c residue 26 TYR Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 20 CYS Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain N residue 18 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 7 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 4656 Z= 0.404 Angle : 0.730 7.392 6280 Z= 0.390 Chirality : 0.049 0.134 736 Planarity : 0.003 0.024 760 Dihedral : 7.112 41.837 619 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 29.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.31 % Favored : 82.69 % Rotamer: Outliers : 5.41 % Allowed : 24.44 % 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: -5.17 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.94 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS h 10 PHE 0.009 0.002 PHE c 24 TYR 0.015 0.003 TYR i 16 ARG 0.002 0.001 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 51 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 THR cc_start: 0.8718 (t) cc_final: 0.8403 (m) REVERT: B 20 CYS cc_start: 0.6597 (p) cc_final: 0.6309 (t) outliers start: 29 outliers final: 27 residues processed: 71 average time/residue: 0.1679 time to fit residues: 19.0613 Evaluate side-chains 74 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 47 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain m residue 11 LEU Chi-restraints excluded: chain k residue 17 LEU Chi-restraints excluded: chain d residue 10 HIS Chi-restraints excluded: chain a residue 17 LEU Chi-restraints excluded: chain P residue 6 CYS Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 20 CYS Chi-restraints excluded: chain N residue 6 CYS Chi-restraints excluded: chain N residue 18 ASN Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 7 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 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 20 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.4437 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= 0.284 Angle : 0.658 6.384 6280 Z= 0.353 Chirality : 0.047 0.129 736 Planarity : 0.002 0.023 760 Dihedral : 6.699 40.961 619 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 25.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 5.04 % Allowed : 25.75 % 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: -5.22 (0.22), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.98 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS l 10 PHE 0.005 0.001 PHE g 24 TYR 0.009 0.002 TYR i 16 ARG 0.002 0.001 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 55 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 8 THR cc_start: 0.8689 (t) cc_final: 0.8363 (m) REVERT: B 20 CYS cc_start: 0.6640 (p) cc_final: 0.6381 (t) outliers start: 27 outliers final: 24 residues processed: 73 average time/residue: 0.1854 time to fit residues: 22.5146 Evaluate side-chains 74 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 50 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 11 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 N residue 6 CYS Chi-restraints excluded: chain L residue 6 CYS Chi-restraints excluded: chain L residue 7 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 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 Chi-restraints excluded: chain A residue 20 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4580 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= 0.270 Angle : 0.646 6.296 6280 Z= 0.346 Chirality : 0.047 0.142 736 Planarity : 0.002 0.015 760 Dihedral : 6.469 41.549 619 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer: Outliers : 4.66 % Allowed : 26.68 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.32 (0.22), 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 0.002 0.000 HIS l 10 PHE 0.005 0.001 PHE e 24 TYR 0.009 0.002 TYR i 16 ARG 0.002 0.001 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 58 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 CYS cc_start: 0.6535 (p) cc_final: 0.6324 (t) outliers start: 25 outliers final: 21 residues processed: 74 average time/residue: 0.1651 time to fit residues: 19.4318 Evaluate side-chains 77 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 11 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 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 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4687 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= 0.269 Angle : 0.641 6.341 6280 Z= 0.343 Chirality : 0.047 0.133 736 Planarity : 0.002 0.014 760 Dihedral : 6.397 41.973 618 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.81 % Favored : 85.19 % Rotamer: Outliers : 4.29 % Allowed : 26.68 % Favored : 69.03 % 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: -5.33 (0.22), 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 0.002 0.001 HIS o 10 PHE 0.005 0.001 PHE e 24 TYR 0.009 0.002 TYR i 16 ARG 0.002 0.000 ARG e 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 22 residues processed: 73 average time/residue: 0.1655 time to fit residues: 19.3628 Evaluate side-chains 79 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 11 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 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 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR 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 33 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 4656 Z= 0.318 Angle : 0.671 6.738 6280 Z= 0.360 Chirality : 0.047 0.141 736 Planarity : 0.002 0.012 760 Dihedral : 6.525 38.172 618 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 26.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.31 % Favored : 82.69 % Rotamer: Outliers : 4.29 % Allowed : 27.05 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.10 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS h 10 PHE 0.006 0.002 PHE m 24 TYR 0.012 0.002 TYR i 16 ARG 0.002 0.000 ARG e 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 21 residues processed: 70 average time/residue: 0.1659 time to fit residues: 18.6464 Evaluate side-chains 77 residues out of total 536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 56 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 11 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 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 6 CYS Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain B residue 6 CYS Chi-restraints excluded: chain B residue 8 THR 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 22 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.5382 r_free = 0.5382 target = 0.362660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.5958 r_free = 0.5958 target = 0.299648 restraints weight = 15822.153| |-----------------------------------------------------------------------------| r_work (start): 0.5330 rms_B_bonded: 1.11 r_work: 0.5937 rms_B_bonded: 0.47 restraints_weight: 0.5000 r_work: 0.5897 rms_B_bonded: 0.77 restraints_weight: 0.2500 r_work: 0.5631 rms_B_bonded: 2.62 restraints_weight: 0.1250 r_work (final): 0.5631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 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 : 0.003 0.076 4656 Z= 0.222 Angle : 0.620 5.715 6280 Z= 0.334 Chirality : 0.046 0.132 736 Planarity : 0.002 0.014 760 Dihedral : 6.163 33.745 618 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.69 % Favored : 87.31 % Rotamer: Outliers : 3.92 % Allowed : 27.24 % 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 (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: -5.30 (0.23), residues: 520 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.17), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS j 5 PHE 0.005 0.001 PHE g 25 TYR 0.006 0.001 TYR B 14 ARG 0.002 0.000 ARG e 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2852.46 seconds wall clock time: 51 minutes 13.95 seconds (3073.95 seconds total)