Starting phenix.real_space_refine on Sat Jan 18 04:53:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vfi_21173/01_2025/6vfi_21173.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vfi_21173/01_2025/6vfi_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/cci-nas-00/data/ceres_data/6vfi_21173/01_2025/6vfi_21173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vfi_21173/01_2025/6vfi_21173.map" model { file = "/net/cci-nas-00/data/ceres_data/6vfi_21173/01_2025/6vfi_21173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vfi_21173/01_2025/6vfi_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): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 9.76, per 1000 atoms: 0.17 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: 13.22 Conformation dependent library (CDL) restraints added in 5.9 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: 3.71 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: 20.91 Time building geometry restraints manager: 15.28 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: 0.42 Found NCS groups: 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' } ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'C' selection = chain 'B' 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' } Set up NCS constraints Number of NCS constrained groups: 2 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' } pdb_interpretation.ncs_group { reference = chain '0' selection = chain '2' selection = chain '4' selection = chain '6' selection = chain '8' selection = chain 'C' selection = chain 'B' 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' } 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.820 Check model and map are aligned: 0.380 Set scattering table: 0.440 Process input model: 85.070 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.560 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: 0.010 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.890 ------------------------------------------------------------------------------- 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 87 residues out of total 166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.137 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: 0.1121 time to fit residues: 10.8312 Evaluate side-chains 33 residues out of total 166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.136 Evaluate side-chains 37 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.084 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: 0.1701 time to fit residues: 6.6722 Evaluate side-chains 21 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.084 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle 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 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.072637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.062116 restraints weight = 5726.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.064150 restraints weight = 3499.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065649 restraints weight = 2405.655| |-----------------------------------------------------------------------------| r_work (final): 0.3191 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.051611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.044654 restraints weight = 5501.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046069 restraints weight = 3583.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047097 restraints weight = 2558.329| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 2 40 PHE 0.004 0.002 PHE T 149 TYR 0.014 0.002 TYR Q 19 ARG 0.004 0.000 ARG Q 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 49 residues out of total 166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: l 26 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8177 (mm-30) REVERT: l 91 THR cc_start: 0.9114 (m) cc_final: 0.8836 (p) REVERT: l 93 LYS cc_start: 0.8590 (pptt) cc_final: 0.8279 (tptt) REVERT: l 161 LEU cc_start: 0.9489 (mt) cc_final: 0.8999 (mt) REVERT: l 172 THR cc_start: 0.7758 (m) cc_final: 0.7041 (m) outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.0923 time to fit residues: 5.1388 Evaluate side-chains 32 residues out of total 166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.138 Evaluate side-chains 29 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: O 88 ASP cc_start: 0.8755 (p0) cc_final: 0.8368 (m-30) REVERT: O 95 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8045 (tm-30) REVERT: O 101 ASP cc_start: 0.8222 (t0) cc_final: 0.7728 (m-30) REVERT: O 110 ASN cc_start: 0.7974 (m-40) cc_final: 0.7591 (t0) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1197 time to fit residues: 3.7950 Evaluate side-chains 17 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 522 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 476 optimal weight: 3.9990 chunk 379 optimal weight: 10.0000 chunk 597 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.068872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.057762 restraints weight = 6687.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.059511 restraints weight = 4379.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.060890 restraints weight = 3169.874| |-----------------------------------------------------------------------------| r_work (final): 0.3059 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.047241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.041461 restraints weight = 5671.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.042731 restraints weight = 3683.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.043633 restraints weight = 2607.886| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 59064 Z= 0.254 Angle : 0.648 5.615 79944 Z= 0.359 Chirality : 0.040 0.211 9648 Planarity : 0.004 0.026 10128 Dihedral : 3.905 14.022 8424 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.39 % Allowed : 2.33 % 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: 1.46 (0.09), residues: 7464 helix: 1.35 (0.06), residues: 6696 sheet: None (None), residues: 0 loop : -2.12 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP Y 40 PHE 0.005 0.002 PHE F 149 TYR 0.025 0.003 TYR A 49 ARG 0.005 0.001 ARG J 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 38 residues out of total 166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.168 Fit side-chains REVERT: 7 26 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8149 (tp30) REVERT: 7 91 THR cc_start: 0.9209 (m) cc_final: 0.8898 (p) REVERT: 7 93 LYS cc_start: 0.8722 (pptt) cc_final: 0.8327 (tptt) REVERT: 7 131 VAL cc_start: 0.9620 (m) cc_final: 0.9404 (p) REVERT: 7 182 MET cc_start: 0.8687 (tmm) cc_final: 0.8485 (tmm) outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.0764 time to fit residues: 3.6339 Evaluate side-chains 24 residues out of total 166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.141 Evaluate side-chains 21 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 88 ASP cc_start: 0.8784 (p0) cc_final: 0.8423 (m-30) REVERT: 2 95 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8593 (tm-30) REVERT: 2 101 ASP cc_start: 0.8272 (t0) cc_final: 0.7909 (m-30) REVERT: 2 110 ASN cc_start: 0.7973 (m-40) cc_final: 0.7724 (t0) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1037 time to fit residues: 2.4494 Evaluate side-chains 17 residues out of total 91 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.391 > 50: distance: 0 - 38: 27.354 distance: 1 - 2: 23.258 distance: 1 - 3: 6.550 distance: 2 - 4: 37.611 distance: 5 - 6: 40.325 distance: 6 - 7: 29.304 distance: 6 - 9: 29.515 distance: 7 - 8: 12.705 distance: 7 - 14: 14.576 distance: 8 - 47: 32.430 distance: 9 - 10: 41.731 distance: 10 - 11: 31.503 distance: 11 - 12: 20.565 distance: 11 - 13: 17.814 distance: 14 - 15: 18.361 distance: 15 - 16: 20.328 distance: 15 - 18: 27.748 distance: 16 - 17: 35.841 distance: 16 - 26: 28.840 distance: 17 - 56: 22.316 distance: 18 - 19: 9.983 distance: 19 - 20: 25.429 distance: 19 - 21: 22.875 distance: 20 - 22: 23.632 distance: 21 - 23: 25.612 distance: 22 - 24: 27.920 distance: 23 - 24: 23.940 distance: 24 - 25: 21.223 distance: 26 - 27: 5.118 distance: 27 - 28: 22.865 distance: 27 - 30: 23.172 distance: 28 - 29: 53.720 distance: 28 - 38: 16.050 distance: 29 - 61: 22.705 distance: 30 - 31: 22.661 distance: 31 - 32: 29.889 distance: 31 - 33: 29.271 distance: 32 - 34: 13.100 distance: 33 - 35: 4.385 distance: 34 - 36: 25.066 distance: 35 - 36: 21.797 distance: 38 - 39: 21.257 distance: 39 - 40: 10.159 distance: 39 - 42: 40.509 distance: 40 - 41: 29.902 distance: 40 - 47: 27.794 distance: 41 - 69: 33.007 distance: 42 - 43: 41.138 distance: 43 - 44: 19.355 distance: 44 - 45: 30.780 distance: 44 - 46: 30.966 distance: 47 - 48: 29.227 distance: 48 - 51: 19.928 distance: 49 - 50: 6.669 distance: 49 - 56: 30.610 distance: 51 - 52: 24.864 distance: 52 - 53: 26.922 distance: 53 - 54: 24.190 distance: 54 - 55: 13.036 distance: 56 - 57: 32.092 distance: 57 - 58: 33.646 distance: 57 - 60: 32.019 distance: 58 - 59: 42.275 distance: 58 - 61: 40.008 distance: 61 - 62: 8.786 distance: 62 - 63: 24.129 distance: 62 - 65: 33.658 distance: 63 - 64: 25.448 distance: 63 - 69: 22.442 distance: 65 - 66: 17.581 distance: 66 - 67: 11.697 distance: 66 - 68: 7.667 distance: 69 - 70: 8.345 distance: 70 - 71: 4.905 distance: 70 - 73: 7.132 distance: 71 - 72: 9.657 distance: 73 - 74: 3.635