Starting phenix.real_space_refine on Wed Sep 25 23:42:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/09_2024/6vfi_21173.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/09_2024/6vfi_21173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/09_2024/6vfi_21173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/09_2024/6vfi_21173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/09_2024/6vfi_21173.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfi_21173/09_2024/6vfi_21173.cif" } resolution = 4.54 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= 0.001 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 37008 2.51 5 N 9768 2.21 5 O 11496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 288 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 58488 Number of models: 1 Model: "" Number of chains: 2 Chain: "0" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 959 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "1" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1478 Classifications: {'peptide': 197} Link IDs: {'TRANS': 196} Restraints were copied for chains: 3, 5, 7, 9, A, D, F, H, J, L, N, P, R, T, V, X, Z, b, d, f, h, j, l, 2, 4, 6, 8, C, B, E, G, I, K, M, O, Q, S, U, W, Y, a, c, e, g, i, k Time building chain proxies: 9.22, per 1000 atoms: 0.16 Number of scatterers: 58488 At special positions: 0 Unit cell: (188.49, 188.49, 188.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 216 16.00 O 11496 8.00 N 9768 7.00 C 37008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 55 " distance=2.04 Simple disulfide: pdb=" SG CYS A 103 " - pdb=" SG CYS A 155 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.29 Conformation dependent library (CDL) restraints added in 5.4 seconds 14928 Ramachandran restraints generated. 7464 Oldfield, 0 Emsley, 7464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14400 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'B' and resid 1 through 16 Processing helix chain 'B' and resid 18 through 33 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 71 through 84 Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 104 through 117 Processing helix chain 'A' and resid 2 through 21 Processing helix chain 'A' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 96 Processing helix chain 'A' and resid 101 through 120 Processing helix chain 'A' and resid 123 through 146 Processing helix chain 'A' and resid 148 through 170 Processing helix chain 'A' and resid 173 through 194 Processing helix chain 'C' and resid 1 through 16 Processing helix chain 'C' and resid 18 through 33 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 71 through 84 Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 104 through 117 Processing helix chain 'D' and resid 2 through 21 Processing helix chain 'D' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU D 44 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 96 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'D' and resid 123 through 146 Processing helix chain 'D' and resid 148 through 170 Processing helix chain 'D' and resid 173 through 194 Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 18 through 33 Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 52 through 67 Processing helix chain 'E' and resid 71 through 84 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'F' and resid 2 through 21 Processing helix chain 'F' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU F 44 " --> pdb=" O ARG F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 96 Processing helix chain 'F' and resid 101 through 120 Processing helix chain 'F' and resid 123 through 146 Processing helix chain 'F' and resid 148 through 170 Processing helix chain 'F' and resid 173 through 194 Processing helix chain 'G' and resid 1 through 16 Processing helix chain 'G' and resid 18 through 33 Processing helix chain 'G' and resid 36 through 50 Processing helix chain 'G' and resid 52 through 67 Processing helix chain 'G' and resid 71 through 84 Processing helix chain 'G' and resid 86 through 101 Processing helix chain 'G' and resid 104 through 117 Processing helix chain 'H' and resid 2 through 21 Processing helix chain 'H' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU H 54 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 96 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'H' and resid 123 through 146 Processing helix chain 'H' and resid 148 through 170 Processing helix chain 'H' and resid 173 through 194 Processing helix chain 'I' and resid 1 through 16 Processing helix chain 'I' and resid 18 through 33 Processing helix chain 'I' and resid 36 through 50 Processing helix chain 'I' and resid 52 through 67 Processing helix chain 'I' and resid 71 through 84 Processing helix chain 'I' and resid 86 through 101 Processing helix chain 'I' and resid 104 through 117 Processing helix chain 'J' and resid 2 through 21 Processing helix chain 'J' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU J 44 " --> pdb=" O ARG J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 96 Processing helix chain 'J' and resid 101 through 120 Processing helix chain 'J' and resid 123 through 146 Processing helix chain 'J' and resid 148 through 170 Processing helix chain 'J' and resid 173 through 194 Processing helix chain 'K' and resid 1 through 16 Processing helix chain 'K' and resid 18 through 33 Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 67 Processing helix chain 'K' and resid 71 through 84 Processing helix chain 'K' and resid 86 through 101 Processing helix chain 'K' and resid 104 through 117 Processing helix chain 'L' and resid 2 through 21 Processing helix chain 'L' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU L 44 " --> pdb=" O ARG L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 96 Processing helix chain 'L' and resid 101 through 120 Processing helix chain 'L' and resid 123 through 146 Processing helix chain 'L' and resid 148 through 170 Processing helix chain 'L' and resid 173 through 194 Processing helix chain 'M' and resid 1 through 16 Processing helix chain 'M' and resid 18 through 33 Processing helix chain 'M' and resid 36 through 50 Processing helix chain 'M' and resid 52 through 67 Processing helix chain 'M' and resid 71 through 84 Processing helix chain 'M' and resid 86 through 101 Processing helix chain 'M' and resid 104 through 117 Processing helix chain 'N' and resid 2 through 21 Processing helix chain 'N' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU N 44 " --> pdb=" O ARG N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU N 54 " --> pdb=" O GLU N 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER N 70 " --> pdb=" O ALA N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 96 Processing helix chain 'N' and resid 101 through 120 Processing helix chain 'N' and resid 123 through 146 Processing helix chain 'N' and resid 148 through 170 Processing helix chain 'N' and resid 173 through 194 Processing helix chain 'O' and resid 1 through 16 Processing helix chain 'O' and resid 18 through 33 Processing helix chain 'O' and resid 36 through 50 Processing helix chain 'O' and resid 52 through 67 Processing helix chain 'O' and resid 71 through 84 Processing helix chain 'O' and resid 86 through 101 Processing helix chain 'O' and resid 104 through 117 Processing helix chain 'P' and resid 2 through 21 Processing helix chain 'P' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU P 44 " --> pdb=" O ARG P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU P 54 " --> pdb=" O GLU P 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER P 70 " --> pdb=" O ALA P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 96 Processing helix chain 'P' and resid 101 through 120 Processing helix chain 'P' and resid 123 through 146 Processing helix chain 'P' and resid 148 through 170 Processing helix chain 'P' and resid 173 through 194 Processing helix chain 'Q' and resid 1 through 16 Processing helix chain 'Q' and resid 18 through 33 Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 67 Processing helix chain 'Q' and resid 71 through 84 Processing helix chain 'Q' and resid 86 through 101 Processing helix chain 'Q' and resid 104 through 117 Processing helix chain 'R' and resid 2 through 21 Processing helix chain 'R' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU R 54 " --> pdb=" O GLU R 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 96 Processing helix chain 'R' and resid 101 through 120 Processing helix chain 'R' and resid 123 through 146 Processing helix chain 'R' and resid 148 through 170 Processing helix chain 'R' and resid 173 through 194 Processing helix chain 'S' and resid 1 through 16 Processing helix chain 'S' and resid 18 through 33 Processing helix chain 'S' and resid 36 through 50 Processing helix chain 'S' and resid 52 through 67 Processing helix chain 'S' and resid 71 through 84 Processing helix chain 'S' and resid 86 through 101 Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'T' and resid 2 through 21 Processing helix chain 'T' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU T 44 " --> pdb=" O ARG T 40 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU T 54 " --> pdb=" O GLU T 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER T 70 " --> pdb=" O ALA T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 96 Processing helix chain 'T' and resid 101 through 120 Processing helix chain 'T' and resid 123 through 146 Processing helix chain 'T' and resid 148 through 170 Processing helix chain 'T' and resid 173 through 194 Processing helix chain 'U' and resid 1 through 16 Processing helix chain 'U' and resid 18 through 33 Processing helix chain 'U' and resid 36 through 50 Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 71 through 84 Processing helix chain 'U' and resid 86 through 101 Processing helix chain 'U' and resid 104 through 117 Processing helix chain 'V' and resid 2 through 21 Processing helix chain 'V' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU V 44 " --> pdb=" O ARG V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU V 54 " --> pdb=" O GLU V 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER V 70 " --> pdb=" O ALA V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 74 through 96 Processing helix chain 'V' and resid 101 through 120 Processing helix chain 'V' and resid 123 through 146 Processing helix chain 'V' and resid 148 through 170 Processing helix chain 'V' and resid 173 through 194 Processing helix chain 'W' and resid 1 through 16 Processing helix chain 'W' and resid 18 through 33 Processing helix chain 'W' and resid 36 through 50 Processing helix chain 'W' and resid 52 through 67 Processing helix chain 'W' and resid 71 through 84 Processing helix chain 'W' and resid 86 through 101 Processing helix chain 'W' and resid 104 through 117 Processing helix chain 'X' and resid 2 through 21 Processing helix chain 'X' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU X 44 " --> pdb=" O ARG X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU X 54 " --> pdb=" O GLU X 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER X 70 " --> pdb=" O ALA X 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 96 Processing helix chain 'X' and resid 101 through 120 Processing helix chain 'X' and resid 123 through 146 Processing helix chain 'X' and resid 148 through 170 Processing helix chain 'X' and resid 173 through 194 Processing helix chain 'Y' and resid 1 through 16 Processing helix chain 'Y' and resid 18 through 33 Processing helix chain 'Y' and resid 36 through 50 Processing helix chain 'Y' and resid 52 through 67 Processing helix chain 'Y' and resid 71 through 84 Processing helix chain 'Y' and resid 86 through 101 Processing helix chain 'Y' and resid 104 through 117 Processing helix chain 'Z' and resid 2 through 21 Processing helix chain 'Z' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU Z 44 " --> pdb=" O ARG Z 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU Z 54 " --> pdb=" O GLU Z 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER Z 70 " --> pdb=" O ALA Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 74 through 96 Processing helix chain 'Z' and resid 101 through 120 Processing helix chain 'Z' and resid 123 through 146 Processing helix chain 'Z' and resid 148 through 170 Processing helix chain 'Z' and resid 173 through 194 Processing helix chain '0' and resid 1 through 16 Processing helix chain '0' and resid 18 through 33 Processing helix chain '0' and resid 36 through 50 Processing helix chain '0' and resid 52 through 67 Processing helix chain '0' and resid 71 through 84 Processing helix chain '0' and resid 86 through 101 Processing helix chain '0' and resid 104 through 117 Processing helix chain '1' and resid 2 through 21 Processing helix chain '1' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU 1 44 " --> pdb=" O ARG 1 40 " (cutoff:3.500A) Processing helix chain '1' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU 1 54 " --> pdb=" O GLU 1 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER 1 70 " --> pdb=" O ALA 1 66 " (cutoff:3.500A) Processing helix chain '1' and resid 74 through 96 Processing helix chain '1' and resid 101 through 120 Processing helix chain '1' and resid 123 through 146 Processing helix chain '1' and resid 148 through 170 Processing helix chain '1' and resid 173 through 194 Processing helix chain '2' and resid 1 through 16 Processing helix chain '2' and resid 18 through 33 Processing helix chain '2' and resid 36 through 50 Processing helix chain '2' and resid 52 through 67 Processing helix chain '2' and resid 71 through 84 Processing helix chain '2' and resid 86 through 101 Processing helix chain '2' and resid 104 through 117 Processing helix chain '3' and resid 2 through 21 Processing helix chain '3' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU 3 44 " --> pdb=" O ARG 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU 3 54 " --> pdb=" O GLU 3 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER 3 70 " --> pdb=" O ALA 3 66 " (cutoff:3.500A) Processing helix chain '3' and resid 74 through 96 Processing helix chain '3' and resid 101 through 120 Processing helix chain '3' and resid 123 through 146 Processing helix chain '3' and resid 148 through 170 Processing helix chain '3' and resid 173 through 194 Processing helix chain '4' and resid 1 through 16 Processing helix chain '4' and resid 18 through 33 Processing helix chain '4' and resid 36 through 50 Processing helix chain '4' and resid 52 through 67 Processing helix chain '4' and resid 71 through 84 Processing helix chain '4' and resid 86 through 101 Processing helix chain '4' and resid 104 through 117 Processing helix chain '5' and resid 2 through 21 Processing helix chain '5' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU 5 44 " --> pdb=" O ARG 5 40 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU 5 54 " --> pdb=" O GLU 5 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER 5 70 " --> pdb=" O ALA 5 66 " (cutoff:3.500A) Processing helix chain '5' and resid 74 through 96 Processing helix chain '5' and resid 101 through 120 Processing helix chain '5' and resid 123 through 146 Processing helix chain '5' and resid 148 through 170 Processing helix chain '5' and resid 173 through 194 Processing helix chain '6' and resid 1 through 16 Processing helix chain '6' and resid 18 through 33 Processing helix chain '6' and resid 36 through 50 Processing helix chain '6' and resid 52 through 67 Processing helix chain '6' and resid 71 through 84 Processing helix chain '6' and resid 86 through 101 Processing helix chain '6' and resid 104 through 117 Processing helix chain '7' and resid 2 through 21 Processing helix chain '7' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU 7 44 " --> pdb=" O ARG 7 40 " (cutoff:3.500A) Processing helix chain '7' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU 7 54 " --> pdb=" O GLU 7 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER 7 70 " --> pdb=" O ALA 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 74 through 96 Processing helix chain '7' and resid 101 through 120 Processing helix chain '7' and resid 123 through 146 Processing helix chain '7' and resid 148 through 170 Processing helix chain '7' and resid 173 through 194 Processing helix chain '8' and resid 1 through 16 Processing helix chain '8' and resid 18 through 33 Processing helix chain '8' and resid 36 through 50 Processing helix chain '8' and resid 52 through 67 Processing helix chain '8' and resid 71 through 84 Processing helix chain '8' and resid 86 through 101 Processing helix chain '8' and resid 104 through 117 Processing helix chain '9' and resid 2 through 21 Processing helix chain '9' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU 9 44 " --> pdb=" O ARG 9 40 " (cutoff:3.500A) Processing helix chain '9' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU 9 54 " --> pdb=" O GLU 9 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER 9 70 " --> pdb=" O ALA 9 66 " (cutoff:3.500A) Processing helix chain '9' and resid 74 through 96 Processing helix chain '9' and resid 101 through 120 Processing helix chain '9' and resid 123 through 146 Processing helix chain '9' and resid 148 through 170 Processing helix chain '9' and resid 173 through 194 Processing helix chain 'a' and resid 1 through 16 Processing helix chain 'a' and resid 18 through 33 Processing helix chain 'a' and resid 36 through 50 Processing helix chain 'a' and resid 52 through 67 Processing helix chain 'a' and resid 71 through 84 Processing helix chain 'a' and resid 86 through 101 Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'b' and resid 2 through 21 Processing helix chain 'b' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU b 44 " --> pdb=" O ARG b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU b 54 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER b 70 " --> pdb=" O ALA b 66 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 96 Processing helix chain 'b' and resid 101 through 120 Processing helix chain 'b' and resid 123 through 146 Processing helix chain 'b' and resid 148 through 170 Processing helix chain 'b' and resid 173 through 194 Processing helix chain 'c' and resid 1 through 16 Processing helix chain 'c' and resid 18 through 33 Processing helix chain 'c' and resid 36 through 50 Processing helix chain 'c' and resid 52 through 67 Processing helix chain 'c' and resid 71 through 84 Processing helix chain 'c' and resid 86 through 101 Processing helix chain 'c' and resid 104 through 117 Processing helix chain 'd' and resid 2 through 21 Processing helix chain 'd' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU d 44 " --> pdb=" O ARG d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU d 54 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER d 70 " --> pdb=" O ALA d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 96 Processing helix chain 'd' and resid 101 through 120 Processing helix chain 'd' and resid 123 through 146 Processing helix chain 'd' and resid 148 through 170 Processing helix chain 'd' and resid 173 through 194 Processing helix chain 'e' and resid 1 through 16 Processing helix chain 'e' and resid 18 through 33 Processing helix chain 'e' and resid 36 through 50 Processing helix chain 'e' and resid 52 through 67 Processing helix chain 'e' and resid 71 through 84 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 104 through 117 Processing helix chain 'f' and resid 2 through 21 Processing helix chain 'f' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU f 44 " --> pdb=" O ARG f 40 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU f 54 " --> pdb=" O GLU f 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER f 70 " --> pdb=" O ALA f 66 " (cutoff:3.500A) Processing helix chain 'f' and resid 74 through 96 Processing helix chain 'f' and resid 101 through 120 Processing helix chain 'f' and resid 123 through 146 Processing helix chain 'f' and resid 148 through 170 Processing helix chain 'f' and resid 173 through 194 Processing helix chain 'g' and resid 1 through 16 Processing helix chain 'g' and resid 18 through 33 Processing helix chain 'g' and resid 36 through 50 Processing helix chain 'g' and resid 52 through 67 Processing helix chain 'g' and resid 71 through 84 Processing helix chain 'g' and resid 86 through 101 Processing helix chain 'g' and resid 104 through 117 Processing helix chain 'h' and resid 2 through 21 Processing helix chain 'h' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU h 44 " --> pdb=" O ARG h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU h 54 " --> pdb=" O GLU h 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER h 70 " --> pdb=" O ALA h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 74 through 96 Processing helix chain 'h' and resid 101 through 120 Processing helix chain 'h' and resid 123 through 146 Processing helix chain 'h' and resid 148 through 170 Processing helix chain 'h' and resid 173 through 194 Processing helix chain 'i' and resid 1 through 16 Processing helix chain 'i' and resid 18 through 33 Processing helix chain 'i' and resid 36 through 50 Processing helix chain 'i' and resid 52 through 67 Processing helix chain 'i' and resid 71 through 84 Processing helix chain 'i' and resid 86 through 101 Processing helix chain 'i' and resid 104 through 117 Processing helix chain 'j' and resid 2 through 21 Processing helix chain 'j' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU j 44 " --> pdb=" O ARG j 40 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU j 54 " --> pdb=" O GLU j 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER j 70 " --> pdb=" O ALA j 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 74 through 96 Processing helix chain 'j' and resid 101 through 120 Processing helix chain 'j' and resid 123 through 146 Processing helix chain 'j' and resid 148 through 170 Processing helix chain 'j' and resid 173 through 194 Processing helix chain 'k' and resid 1 through 16 Processing helix chain 'k' and resid 18 through 33 Processing helix chain 'k' and resid 36 through 50 Processing helix chain 'k' and resid 52 through 67 Processing helix chain 'k' and resid 71 through 84 Processing helix chain 'k' and resid 86 through 101 Processing helix chain 'k' and resid 104 through 117 Processing helix chain 'l' and resid 2 through 21 Processing helix chain 'l' and resid 23 through 45 removed outlier: 4.007A pdb=" N LEU l 44 " --> pdb=" O ARG l 40 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 70 removed outlier: 4.178A pdb=" N GLU l 54 " --> pdb=" O GLU l 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER l 70 " --> pdb=" O ALA l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 74 through 96 Processing helix chain 'l' and resid 101 through 120 Processing helix chain 'l' and resid 123 through 146 Processing helix chain 'l' and resid 148 through 170 Processing helix chain 'l' and resid 173 through 194 5328 hydrogen bonds defined for protein. 15984 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: 18.46 Time building geometry restraints manager: 13.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 12192 1.32 - 1.45: 16056 1.45 - 1.57: 30264 1.57 - 1.70: 264 1.70 - 1.82: 288 Bond restraints: 59064 Sorted by residual: bond pdb=" CA ILE Z 102 " pdb=" C ILE Z 102 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.23e-02 6.61e+03 1.53e+01 bond pdb=" CA ILE J 102 " pdb=" C ILE J 102 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.23e-02 6.61e+03 1.53e+01 bond pdb=" CA ILE 5 102 " pdb=" C ILE 5 102 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.23e-02 6.61e+03 1.53e+01 bond pdb=" CA ILE H 102 " pdb=" C ILE H 102 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.23e-02 6.61e+03 1.53e+01 bond pdb=" CA ILE 1 102 " pdb=" C ILE 1 102 " ideal model delta sigma weight residual 1.524 1.476 0.048 1.23e-02 6.61e+03 1.53e+01 ... (remaining 59059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 70392 2.18 - 4.37: 8640 4.37 - 6.55: 744 6.55 - 8.73: 144 8.73 - 10.91: 24 Bond angle restraints: 79944 Sorted by residual: angle pdb=" N SER R 97 " pdb=" CA SER R 97 " pdb=" C SER R 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 angle pdb=" N SER j 97 " pdb=" CA SER j 97 " pdb=" C SER j 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 angle pdb=" N SER h 97 " pdb=" CA SER h 97 " pdb=" C SER h 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 angle pdb=" N SER 3 97 " pdb=" CA SER 3 97 " pdb=" C SER 3 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 angle pdb=" N SER D 97 " pdb=" CA SER D 97 " pdb=" C SER D 97 " ideal model delta sigma weight residual 110.53 121.44 -10.91 1.29e+00 6.01e-01 7.16e+01 ... (remaining 79939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 34827 15.84 - 31.69: 962 31.69 - 47.53: 385 47.53 - 63.38: 192 63.38 - 79.22: 24 Dihedral angle restraints: 36390 sinusoidal: 14046 harmonic: 22344 Sorted by residual: dihedral pdb=" CA ASP 8 86 " pdb=" CB ASP 8 86 " pdb=" CG ASP 8 86 " pdb=" OD1 ASP 8 86 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP e 86 " pdb=" CB ASP e 86 " pdb=" CG ASP e 86 " pdb=" OD1 ASP e 86 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP M 86 " pdb=" CB ASP M 86 " pdb=" CG ASP M 86 " pdb=" OD1 ASP M 86 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 36387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 5544 0.073 - 0.145: 3144 0.145 - 0.218: 840 0.218 - 0.291: 96 0.291 - 0.364: 24 Chirality restraints: 9648 Sorted by residual: chirality pdb=" CA ASN 0 76 " pdb=" N ASN 0 76 " pdb=" C ASN 0 76 " pdb=" CB ASN 0 76 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ASN O 76 " pdb=" N ASN O 76 " pdb=" C ASN O 76 " pdb=" CB ASN O 76 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ASN a 76 " pdb=" N ASN a 76 " pdb=" C ASN a 76 " pdb=" CB ASN a 76 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 ... (remaining 9645 not shown) Planarity restraints: 10128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR c 47 " 0.039 2.00e-02 2.50e+03 2.07e-02 8.58e+00 pdb=" CG TYR c 47 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR c 47 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR c 47 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR c 47 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR c 47 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR c 47 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR c 47 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 47 " -0.039 2.00e-02 2.50e+03 2.07e-02 8.58e+00 pdb=" CG TYR M 47 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR M 47 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR M 47 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR M 47 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR M 47 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR M 47 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR M 47 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR 8 47 " -0.039 2.00e-02 2.50e+03 2.07e-02 8.58e+00 pdb=" CG TYR 8 47 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR 8 47 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR 8 47 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR 8 47 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR 8 47 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR 8 47 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR 8 47 " -0.030 2.00e-02 2.50e+03 ... (remaining 10125 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 334 2.60 - 3.17: 57788 3.17 - 3.75: 97008 3.75 - 4.32: 133320 4.32 - 4.90: 207240 Nonbonded interactions: 495690 Sorted by model distance: nonbonded pdb=" SG CYS l 103 " pdb=" SG CYS l 155 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS X 103 " pdb=" SG CYS X 155 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS b 103 " pdb=" SG CYS b 155 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS 1 103 " pdb=" SG CYS 1 155 " model vdw 2.023 3.760 nonbonded pdb=" SG CYS H 103 " pdb=" SG CYS H 155 " model vdw 2.023 3.760 ... (remaining 495685 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 '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' } ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' selection = chain 'e' selection = chain 'g' selection = chain 'i' selection = chain 'k' } pdb_interpretation.ncs_group { reference = chain '1' selection = chain '3' selection = chain '5' selection = chain '7' selection = chain '9' selection = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'l' } Set refine NCS operators NCS operators will be refined. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.040 Extract box with map and model: 1.670 Check model and map are aligned: 0.330 Set scattering table: 0.400 Process input model: 78.120 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.030 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.018 0.078 59064 Z= 1.181 Angle : 1.468 10.913 79944 Z= 1.037 Chirality : 0.089 0.364 9648 Planarity : 0.008 0.029 10128 Dihedral : 10.928 79.219 21984 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 1.21 (0.08), residues: 7464 helix: 1.06 (0.05), residues: 6816 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.009 TRP S 40 PHE 0.008 0.004 PHE j 149 TYR 0.039 0.007 TYR M 47 ARG 0.005 0.001 ARG 4 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14928 Ramachandran restraints generated. 7464 Oldfield, 0 Emsley, 7464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14928 Ramachandran restraints generated. 7464 Oldfield, 0 Emsley, 7464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 12 LEU cc_start: 0.9600 (tp) cc_final: 0.9388 (tt) REVERT: 0 101 ASP cc_start: 0.8115 (t0) cc_final: 0.7864 (m-30) REVERT: 0 117 LEU cc_start: 0.8238 (mt) cc_final: 0.8032 (mp) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.1817 time to fit residues: 7.1023 Evaluate side-chains 21 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.080 Evaluate side-chains 87 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 91 THR cc_start: 0.8899 (m) cc_final: 0.8592 (p) REVERT: 1 129 LEU cc_start: 0.9087 (tp) cc_final: 0.8869 (mt) REVERT: 1 155 CYS cc_start: 0.8074 (m) cc_final: 0.7787 (t) REVERT: 1 162 GLU cc_start: 0.8299 (tp30) cc_final: 0.7956 (tt0) REVERT: 1 164 ILE cc_start: 0.8837 (mt) cc_final: 0.8615 (mt) REVERT: 1 167 LEU cc_start: 0.9349 (mt) cc_final: 0.9115 (mm) REVERT: 1 172 THR cc_start: 0.8188 (m) cc_final: 0.7719 (m) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1070 time to fit residues: 10.4047 Evaluate side-chains 33 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 0.7980 chunk 545 optimal weight: 4.9990 chunk 302 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 368 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 564 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 343 optimal weight: 20.0000 chunk 420 optimal weight: 10.0000 chunk 653 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 50 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 59064 Z= 0.245 Angle : 0.731 12.137 79944 Z= 0.374 Chirality : 0.043 0.326 9648 Planarity : 0.004 0.022 10128 Dihedral : 4.010 13.523 8424 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.39 % Allowed : 1.95 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.09), residues: 7464 helix: 1.77 (0.06), residues: 6648 sheet: None (None), residues: 0 loop : -1.14 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Y 40 PHE 0.004 0.002 PHE V 149 TYR 0.014 0.002 TYR e 19 ARG 0.004 0.000 ARG 2 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14696 Ramachandran restraints generated. 7348 Oldfield, 0 Emsley, 7348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14696 Ramachandran restraints generated. 7348 Oldfield, 0 Emsley, 7348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: O 88 ASP cc_start: 0.8678 (p0) cc_final: 0.8280 (m-30) REVERT: O 95 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8021 (tm-30) REVERT: O 101 ASP cc_start: 0.8097 (t0) cc_final: 0.7610 (m-30) REVERT: O 110 ASN cc_start: 0.8000 (m-40) cc_final: 0.7666 (t0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1188 time to fit residues: 3.7788 Evaluate side-chains 17 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.080 Evaluate side-chains 49 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: l 26 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8257 (mm-30) REVERT: l 91 THR cc_start: 0.9048 (m) cc_final: 0.8804 (p) REVERT: l 93 LYS cc_start: 0.8651 (pptt) cc_final: 0.8292 (tptt) REVERT: l 161 LEU cc_start: 0.9469 (mt) cc_final: 0.9031 (mt) REVERT: l 172 THR cc_start: 0.8144 (m) cc_final: 0.7476 (m) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0878 time to fit residues: 4.9131 Evaluate side-chains 32 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 363 optimal weight: 0.0870 chunk 202 optimal weight: 7.9990 chunk 544 optimal weight: 0.9990 chunk 445 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 655 optimal weight: 20.0000 chunk 707 optimal weight: 1.9990 chunk 583 optimal weight: 0.5980 chunk 649 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 525 optimal weight: 6.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 59064 Z= 0.206 Angle : 0.658 7.068 79944 Z= 0.351 Chirality : 0.040 0.202 9648 Planarity : 0.004 0.026 10128 Dihedral : 3.985 14.780 8424 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: 1.50 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6672 sheet: None (None), residues: 0 loop : -1.64 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP 4 40 PHE 0.001 0.000 PHE j 149 TYR 0.025 0.002 TYR 2 19 ARG 0.006 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14074 Ramachandran restraints generated. 7037 Oldfield, 0 Emsley, 7037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14074 Ramachandran restraints generated. 7037 Oldfield, 0 Emsley, 7037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 88 ASP cc_start: 0.8502 (p0) cc_final: 0.8209 (m-30) REVERT: 0 95 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8585 (tm-30) REVERT: 0 101 ASP cc_start: 0.8076 (t0) cc_final: 0.7671 (m-30) REVERT: 0 104 ASN cc_start: 0.7893 (t0) cc_final: 0.7563 (t0) REVERT: 0 110 ASN cc_start: 0.8109 (m-40) cc_final: 0.7747 (t0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.1234 time to fit residues: 3.2578 Evaluate side-chains 17 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.081 Evaluate side-chains 41 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.131 Fit side-chains REVERT: P 26 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8232 (tp30) REVERT: P 91 THR cc_start: 0.9042 (m) cc_final: 0.8774 (p) REVERT: P 93 LYS cc_start: 0.8679 (pptt) cc_final: 0.8381 (tptt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0604 time to fit residues: 3.1119 Evaluate side-chains 26 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 647 optimal weight: 5.9990 chunk 492 optimal weight: 0.7980 chunk 339 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 312 optimal weight: 4.9990 chunk 439 optimal weight: 3.9990 chunk 657 optimal weight: 4.9990 chunk 695 optimal weight: 0.0020 chunk 343 optimal weight: 6.9990 chunk 623 optimal weight: 0.0870 chunk 187 optimal weight: 2.9990 overall best weight: 0.9770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 59064 Z= 0.206 Angle : 0.658 7.068 79944 Z= 0.351 Chirality : 0.040 0.202 9648 Planarity : 0.004 0.026 10128 Dihedral : 3.985 14.780 8424 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.50 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6672 sheet: None (None), residues: 0 loop : -1.64 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP Y 40 PHE 0.001 0.000 PHE j 149 TYR 0.025 0.002 TYR 4 19 ARG 0.006 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13452 Ramachandran restraints generated. 6726 Oldfield, 0 Emsley, 6726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13452 Ramachandran restraints generated. 6726 Oldfield, 0 Emsley, 6726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 88 ASP cc_start: 0.8505 (p0) cc_final: 0.8209 (m-30) REVERT: K 95 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8588 (tm-30) REVERT: K 101 ASP cc_start: 0.8094 (t0) cc_final: 0.7691 (m-30) REVERT: K 104 ASN cc_start: 0.7900 (t0) cc_final: 0.7574 (t0) REVERT: K 110 ASN cc_start: 0.8103 (m-40) cc_final: 0.7735 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0995 time to fit residues: 2.5852 Evaluate side-chains 17 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.080 Evaluate side-chains 39 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.131 Fit side-chains REVERT: 7 26 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8227 (tp30) REVERT: 7 91 THR cc_start: 0.9030 (m) cc_final: 0.8776 (p) REVERT: 7 93 LYS cc_start: 0.8607 (pptt) cc_final: 0.8398 (tptt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0818 time to fit residues: 3.8507 Evaluate side-chains 28 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 579 optimal weight: 0.7980 chunk 395 optimal weight: 40.0000 chunk 10 optimal weight: 50.0000 chunk 518 optimal weight: 8.9990 chunk 287 optimal weight: 8.9990 chunk 593 optimal weight: 10.0000 chunk 481 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 355 optimal weight: 0.0070 chunk 624 optimal weight: 6.9990 chunk 175 optimal weight: 0.2980 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 59064 Z= 0.206 Angle : 0.658 7.068 79944 Z= 0.351 Chirality : 0.040 0.202 9648 Planarity : 0.004 0.026 10128 Dihedral : 3.985 14.780 8424 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.50 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6672 sheet: None (None), residues: 0 loop : -1.64 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP 4 40 PHE 0.001 0.000 PHE d 149 TYR 0.025 0.002 TYR G 19 ARG 0.006 0.000 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13452 Ramachandran restraints generated. 6726 Oldfield, 0 Emsley, 6726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13452 Ramachandran restraints generated. 6726 Oldfield, 0 Emsley, 6726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 88 ASP cc_start: 0.8505 (p0) cc_final: 0.8209 (m-30) REVERT: K 95 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8588 (tm-30) REVERT: K 101 ASP cc_start: 0.8094 (t0) cc_final: 0.7691 (m-30) REVERT: K 104 ASN cc_start: 0.7900 (t0) cc_final: 0.7574 (t0) REVERT: K 110 ASN cc_start: 0.8103 (m-40) cc_final: 0.7735 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0990 time to fit residues: 2.5841 Evaluate side-chains 17 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.081 Evaluate side-chains 38 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.134 Fit side-chains REVERT: 7 26 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8227 (tp30) REVERT: 7 91 THR cc_start: 0.9049 (m) cc_final: 0.8776 (p) REVERT: 7 93 LYS cc_start: 0.8604 (pptt) cc_final: 0.8398 (tptt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0632 time to fit residues: 2.9999 Evaluate side-chains 28 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 30.0000 chunk 626 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 408 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 696 optimal weight: 0.8980 chunk 578 optimal weight: 7.9990 chunk 322 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 365 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 59064 Z= 0.206 Angle : 0.658 7.068 79944 Z= 0.351 Chirality : 0.040 0.202 9648 Planarity : 0.004 0.026 10128 Dihedral : 3.985 14.780 8424 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.50 (0.09), residues: 7464 helix: 1.34 (0.06), residues: 6672 sheet: None (None), residues: 0 loop : -1.64 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP 0 40 PHE 0.001 0.000 PHE D 149 TYR 0.025 0.002 TYR 6 19 ARG 0.006 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13452 Ramachandran restraints generated. 6726 Oldfield, 0 Emsley, 6726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13452 Ramachandran restraints generated. 6726 Oldfield, 0 Emsley, 6726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 88 ASP cc_start: 0.8505 (p0) cc_final: 0.8209 (m-30) REVERT: K 95 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8588 (tm-30) REVERT: K 101 ASP cc_start: 0.8094 (t0) cc_final: 0.7691 (m-30) REVERT: K 104 ASN cc_start: 0.7900 (t0) cc_final: 0.7574 (t0) REVERT: K 110 ASN cc_start: 0.8103 (m-40) cc_final: 0.7735 (t0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.1000 time to fit residues: 2.5961 Evaluate side-chains 17 residues out of total 91 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.081 Evaluate side-chains 38 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.133 Fit side-chains REVERT: 7 26 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8227 (tp30) REVERT: 7 91 THR cc_start: 0.9049 (m) cc_final: 0.8776 (p) REVERT: 7 93 LYS cc_start: 0.8604 (pptt) cc_final: 0.8398 (tptt) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0648 time to fit residues: 3.0818 Evaluate side-chains 28 residues out of total 166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.4121 > 50: distance: 5 - 6: 53.776 distance: 6 - 7: 70.115 distance: 6 - 9: 4.399 distance: 7 - 8: 56.831 distance: 7 - 14: 39.808 distance: 9 - 10: 7.079 distance: 10 - 11: 39.762 distance: 11 - 12: 62.544 distance: 12 - 13: 57.574 distance: 14 - 15: 22.430 distance: 15 - 16: 25.857 distance: 15 - 18: 43.638 distance: 16 - 17: 43.932 distance: 16 - 22: 45.653 distance: 18 - 19: 55.130 distance: 19 - 20: 59.860 distance: 19 - 21: 57.664 distance: 22 - 23: 40.400 distance: 23 - 24: 56.807 distance: 23 - 26: 62.675 distance: 24 - 25: 53.353 distance: 24 - 28: 34.413 distance: 26 - 27: 48.892 distance: 28 - 29: 68.073 distance: 29 - 30: 52.762 distance: 30 - 31: 45.973 distance: 30 - 32: 33.100 distance: 32 - 33: 49.191 distance: 33 - 34: 54.146 distance: 33 - 36: 40.053 distance: 34 - 35: 51.916 distance: 34 - 38: 8.596 distance: 36 - 37: 34.679 distance: 38 - 39: 39.433 distance: 39 - 40: 42.234 distance: 39 - 42: 26.696 distance: 40 - 41: 20.626 distance: 40 - 44: 66.249 distance: 42 - 43: 48.107 distance: 44 - 45: 70.238 distance: 45 - 46: 39.052 distance: 45 - 48: 57.826 distance: 46 - 56: 61.466 distance: 48 - 49: 69.065 distance: 49 - 50: 68.443 distance: 49 - 51: 63.611 distance: 50 - 52: 69.261 distance: 51 - 53: 6.676 distance: 52 - 54: 56.563 distance: 53 - 54: 41.470 distance: 54 - 55: 39.426 distance: 56 - 57: 15.327 distance: 57 - 58: 34.487 distance: 57 - 60: 25.257 distance: 58 - 59: 48.777 distance: 58 - 65: 40.099 distance: 60 - 61: 44.230 distance: 61 - 62: 41.159 distance: 62 - 63: 61.568 distance: 62 - 64: 46.168 distance: 65 - 66: 33.458 distance: 66 - 67: 17.300 distance: 66 - 69: 43.759 distance: 67 - 68: 37.805 distance: 69 - 70: 28.323 distance: 69 - 71: 23.679