Starting phenix.real_space_refine on Thu Apr 11 09:16:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjv_34839/04_2024/8hjv_34839_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjv_34839/04_2024/8hjv_34839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjv_34839/04_2024/8hjv_34839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjv_34839/04_2024/8hjv_34839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjv_34839/04_2024/8hjv_34839_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hjv_34839/04_2024/8hjv_34839_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 3 5.49 5 Mg 48 5.21 5 S 71 5.16 5 C 15527 2.51 5 N 3231 2.21 5 O 3308 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 4": "NH1" <-> "NH2" Residue "3 ARG 40": "NH1" <-> "NH2" Residue "5 ARG 4": "NH1" <-> "NH2" Residue "5 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 40": "NH1" <-> "NH2" Residue "9 ARG 40": "NH1" <-> "NH2" Residue "A ARG 40": "NH1" <-> "NH2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "F ARG 4": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "H ARG 4": "NH1" <-> "NH2" Residue "H ARG 40": "NH1" <-> "NH2" Residue "J ARG 4": "NH1" <-> "NH2" Residue "J ARG 40": "NH1" <-> "NH2" Residue "L GLU 14": "OE1" <-> "OE2" Residue "L GLU 32": "OE1" <-> "OE2" Residue "L GLU 40": "OE1" <-> "OE2" Residue "L GLU 95": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 236": "OE1" <-> "OE2" Residue "M GLU 341": "OE1" <-> "OE2" Residue "M GLU 342": "OE1" <-> "OE2" Residue "M GLU 367": "OE1" <-> "OE2" Residue "M ARG 410": "NH1" <-> "NH2" Residue "M GLU 555": "OE1" <-> "OE2" Residue "M GLU 560": "OE1" <-> "OE2" Residue "M GLU 564": "OE1" <-> "OE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 40": "NH1" <-> "NH2" Residue "P ARG 4": "NH1" <-> "NH2" Residue "P ARG 40": "NH1" <-> "NH2" Residue "R ARG 4": "NH1" <-> "NH2" Residue "R ARG 40": "NH1" <-> "NH2" Residue "T PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 40": "NH1" <-> "NH2" Residue "V GLU 7": "OE1" <-> "OE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 221": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C ARG 280": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22193 Number of models: 1 Model: "" Number of chains: 68 Chain: "0" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "1" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 271 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "2" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "3" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "5" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "7" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "8" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "9" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "D" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "E" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "F" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "H" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "I" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "J" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "K" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "L" Number of atoms: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2337 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 16, 'TRANS': 277} Chain breaks: 1 Chain: "M" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2488 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 16, 'TRANS': 289} Chain: "N" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "P" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "Q" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "R" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "S" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "T" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "U" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "V" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 232 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "W" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Y" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 259 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "C" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2216 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 23, 'TRANS': 267} Chain: "Z" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 362 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "0" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "9" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'KGD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 329 Unusual residues: {'BCL': 1, 'BPH': 3, 'MQE': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 347 Unusual residues: {' FE': 1, 'BCL': 2, 'MQE': 2, 'PGV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 69 Planarities with less than four sites: {'MQE:plan-12': 1, 'MQE:plan-11': 1, 'MQE:plan-10': 1, 'PGV:plan-3': 1, 'MQE:plan-9': 1, 'MQE:plan-6': 1, 'MQE:plan-5': 1, 'MQE:plan-4': 1, 'MQE:plan-3': 1, 'MQE:plan-2': 1} Unresolved non-hydrogen planarities: 47 Chain: "N" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'KGD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 11.87, per 1000 atoms: 0.53 Number of scatterers: 22193 At special positions: 0 Unit cell: (131.271, 138.415, 132.164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 71 16.00 P 3 15.00 Mg 48 11.99 O 3308 8.00 N 3231 7.00 C 15527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=66, symmetry=0 Number of additional bonds: simple=66, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.84 Conformation dependent library (CDL) restraints added in 3.1 seconds 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4246 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 1 sheets defined 60.2% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain '0' and resid 21 through 50 removed outlier: 3.775A pdb=" N VAL 0 25 " --> pdb=" O ALA 0 21 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 33 Processing helix chain '2' and resid 20 through 50 removed outlier: 4.041A pdb=" N LEU 2 24 " --> pdb=" O ASN 2 20 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL 2 25 " --> pdb=" O ALA 2 21 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 33 Processing helix chain '4' and resid 21 through 50 removed outlier: 3.758A pdb=" N VAL 4 25 " --> pdb=" O ALA 4 21 " (cutoff:3.500A) Processing helix chain '5' and resid 8 through 33 Processing helix chain '6' and resid 21 through 50 removed outlier: 3.762A pdb=" N VAL 6 25 " --> pdb=" O ALA 6 21 " (cutoff:3.500A) Processing helix chain '7' and resid 8 through 33 Processing helix chain '8' and resid 12 through 14 No H-bonds generated for 'chain '8' and resid 12 through 14' Processing helix chain '8' and resid 21 through 50 removed outlier: 3.774A pdb=" N VAL 8 25 " --> pdb=" O ALA 8 21 " (cutoff:3.500A) Processing helix chain '9' and resid 8 through 33 Processing helix chain 'A' and resid 8 through 33 Processing helix chain 'B' and resid 21 through 50 removed outlier: 3.769A pdb=" N VAL B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 33 Processing helix chain 'E' and resid 21 through 50 removed outlier: 3.741A pdb=" N VAL E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP E 48 " --> pdb=" O HIS E 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 33 Processing helix chain 'G' and resid 21 through 50 removed outlier: 3.745A pdb=" N VAL G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 33 Processing helix chain 'I' and resid 21 through 50 removed outlier: 3.749A pdb=" N VAL I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 33 Processing helix chain 'K' and resid 21 through 50 removed outlier: 3.754A pdb=" N VAL K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 42 removed outlier: 3.578A pdb=" N GLU L 40 " --> pdb=" O PHE L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 55 removed outlier: 3.772A pdb=" N PHE L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 92 removed outlier: 3.510A pdb=" N ILE L 75 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLY L 91 " --> pdb=" O TYR L 87 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL L 92 " --> pdb=" O LEU L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 112 No H-bonds generated for 'chain 'L' and resid 110 through 112' Processing helix chain 'L' and resid 123 through 150 Processing helix chain 'L' and resid 155 through 171 removed outlier: 3.942A pdb=" N VAL L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 178 Processing helix chain 'L' and resid 192 through 202 Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'L' and resid 210 through 235 Processing helix chain 'L' and resid 245 through 252 Processing helix chain 'L' and resid 260 through 287 removed outlier: 4.327A pdb=" N HIS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG L 265 " --> pdb=" O ILE L 261 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL L 275 " --> pdb=" O GLY L 271 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU L 276 " --> pdb=" O ALA L 272 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR L 287 " --> pdb=" O PHE L 283 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 301 removed outlier: 3.943A pdb=" N PHE L 298 " --> pdb=" O PHE L 295 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP L 300 " --> pdb=" O GLY L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 305 No H-bonds generated for 'chain 'L' and resid 303 through 305' Processing helix chain 'M' and resid 339 through 341 No H-bonds generated for 'chain 'M' and resid 339 through 341' Processing helix chain 'M' and resid 360 through 365 Processing helix chain 'M' and resid 377 through 401 removed outlier: 3.646A pdb=" N ILE M 381 " --> pdb=" O LEU M 377 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER M 382 " --> pdb=" O TRP M 378 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY M 398 " --> pdb=" O LEU M 394 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 410 Processing helix chain 'M' and resid 412 through 414 No H-bonds generated for 'chain 'M' and resid 412 through 414' Processing helix chain 'M' and resid 436 through 463 removed outlier: 4.029A pdb=" N ALA M 440 " --> pdb=" O GLY M 436 " (cutoff:3.500A) Processing helix chain 'M' and resid 468 through 484 removed outlier: 3.929A pdb=" N LEU M 479 " --> pdb=" O SER M 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 494 through 496 No H-bonds generated for 'chain 'M' and resid 494 through 496' Processing helix chain 'M' and resid 502 through 516 removed outlier: 4.660A pdb=" N LEU M 506 " --> pdb=" O PHE M 502 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 521 No H-bonds generated for 'chain 'M' and resid 519 through 521' Processing helix chain 'M' and resid 523 through 548 Processing helix chain 'M' and resid 550 through 552 No H-bonds generated for 'chain 'M' and resid 550 through 552' Processing helix chain 'M' and resid 557 through 562 removed outlier: 3.951A pdb=" N MET M 562 " --> pdb=" O PHE M 558 " (cutoff:3.500A) Processing helix chain 'M' and resid 566 through 579 removed outlier: 3.661A pdb=" N TRP M 575 " --> pdb=" O ALA M 571 " (cutoff:3.500A) Processing helix chain 'M' and resid 587 through 608 removed outlier: 3.919A pdb=" N ALA M 600 " --> pdb=" O ALA M 596 " (cutoff:3.500A) Processing helix chain 'M' and resid 617 through 623 removed outlier: 3.721A pdb=" N THR M 623 " --> pdb=" O ALA M 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 635 through 637 No H-bonds generated for 'chain 'M' and resid 635 through 637' Processing helix chain 'N' and resid 8 through 33 Processing helix chain 'O' and resid 21 through 50 removed outlier: 3.766A pdb=" N VAL O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 33 Processing helix chain 'Q' and resid 21 through 49 removed outlier: 3.746A pdb=" N VAL Q 25 " --> pdb=" O ALA Q 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 8 through 33 Processing helix chain 'S' and resid 21 through 49 removed outlier: 3.740A pdb=" N VAL S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 33 Processing helix chain 'U' and resid 21 through 50 removed outlier: 3.774A pdb=" N VAL U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 31 Processing helix chain 'W' and resid 21 through 50 removed outlier: 3.773A pdb=" N VAL W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 29 Proline residue: Y 19 - end of helix Processing helix chain 'C' and resid 31 through 46 Processing helix chain 'C' and resid 72 through 84 removed outlier: 3.697A pdb=" N ALA C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 139 through 155 Processing helix chain 'C' and resid 219 through 235 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 256 through 273 removed outlier: 3.711A pdb=" N SER C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 297 No H-bonds generated for 'chain 'C' and resid 294 through 297' Processing helix chain 'Z' and resid 19 through 46 removed outlier: 3.840A pdb=" N VAL Z 25 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) Proline residue: Z 26 - end of helix removed outlier: 4.093A pdb=" N ILE Z 31 " --> pdb=" O LEU Z 27 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG Z 39 " --> pdb=" O ILE Z 35 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'L' and resid 7 through 9 1033 hydrogen bonds defined for protein. 3093 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: 5.86 Time building geometry restraints manager: 10.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.30: 2963 1.30 - 1.49: 10509 1.49 - 1.69: 9434 1.69 - 1.88: 119 1.88 - 2.08: 208 Bond restraints: 23233 Sorted by residual: bond pdb=" C HIS W 26 " pdb=" N ASP W 27 " ideal model delta sigma weight residual 1.334 1.221 0.113 1.27e-02 6.20e+03 7.91e+01 bond pdb=" C HIS U 44 " pdb=" N VAL U 45 " ideal model delta sigma weight residual 1.334 1.441 -0.107 1.26e-02 6.30e+03 7.20e+01 bond pdb=" C VAL 0 25 " pdb=" N HIS 0 26 " ideal model delta sigma weight residual 1.335 1.449 -0.115 1.36e-02 5.41e+03 7.10e+01 bond pdb=" C ILE 3 26 " pdb=" N HIS 3 27 " ideal model delta sigma weight residual 1.334 1.228 0.106 1.27e-02 6.20e+03 7.01e+01 bond pdb=" C HIS 1 27 " pdb=" N PHE 1 28 " ideal model delta sigma weight residual 1.334 1.442 -0.107 1.33e-02 5.65e+03 6.50e+01 ... (remaining 23228 not shown) Histogram of bond angle deviations from ideal: 81.28 - 99.68: 293 99.68 - 118.07: 18125 118.07 - 136.47: 13890 136.47 - 154.86: 100 154.86 - 173.26: 104 Bond angle restraints: 32512 Sorted by residual: angle pdb=" N TRP Q 48 " pdb=" CA TRP Q 48 " pdb=" C TRP Q 48 " ideal model delta sigma weight residual 112.12 100.96 11.16 1.34e+00 5.57e-01 6.94e+01 angle pdb=" N ALA C 51 " pdb=" CA ALA C 51 " pdb=" C ALA C 51 " ideal model delta sigma weight residual 109.72 119.92 -10.20 1.25e+00 6.40e-01 6.66e+01 angle pdb=" N TRP S 48 " pdb=" CA TRP S 48 " pdb=" C TRP S 48 " ideal model delta sigma weight residual 112.93 103.45 9.48 1.33e+00 5.65e-01 5.08e+01 angle pdb=" N TRP B 48 " pdb=" CA TRP B 48 " pdb=" C TRP B 48 " ideal model delta sigma weight residual 113.12 104.50 8.62 1.25e+00 6.40e-01 4.76e+01 angle pdb=" N ASP W 8 " pdb=" CA ASP W 8 " pdb=" C ASP W 8 " ideal model delta sigma weight residual 110.68 120.17 -9.49 1.39e+00 5.18e-01 4.66e+01 ... (remaining 32507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 11353 35.05 - 70.10: 724 70.10 - 105.15: 54 105.15 - 140.19: 7 140.19 - 175.24: 3 Dihedral angle restraints: 12141 sinusoidal: 5608 harmonic: 6533 Sorted by residual: dihedral pdb=" C1 BCL V 101 " pdb=" CGA BCL V 101 " pdb=" O2A BCL V 101 " pdb=" CBA BCL V 101 " ideal model delta sinusoidal sigma weight residual 180.00 51.14 128.86 1 6.00e+00 2.78e-02 4.34e+02 dihedral pdb=" C1 BCL L 401 " pdb=" CGA BCL L 401 " pdb=" O2A BCL L 401 " pdb=" CBA BCL L 401 " ideal model delta sinusoidal sigma weight residual -180.00 -65.07 -114.93 1 6.00e+00 2.78e-02 3.79e+02 dihedral pdb=" CBD BCL W 101 " pdb=" CGD BCL W 101 " pdb=" O2D BCL W 101 " pdb=" CED BCL W 101 " ideal model delta sinusoidal sigma weight residual -180.00 -94.58 -85.42 1 5.00e+00 4.00e-02 3.53e+02 ... (remaining 12138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.125: 3301 1.125 - 2.250: 0 2.250 - 3.374: 0 3.374 - 4.499: 0 4.499 - 5.624: 27 Chirality restraints: 3328 Sorted by residual: chirality pdb=" C18 BCL Q 101 " pdb=" C17 BCL Q 101 " pdb=" C19 BCL Q 101 " pdb=" C20 BCL Q 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.91 5.62 2.00e-01 2.50e+01 7.91e+02 chirality pdb=" C18 BCL E 101 " pdb=" C17 BCL E 101 " pdb=" C19 BCL E 101 " pdb=" C20 BCL E 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.91 5.62 2.00e-01 2.50e+01 7.90e+02 chirality pdb=" C18 BCL I 101 " pdb=" C17 BCL I 101 " pdb=" C19 BCL I 101 " pdb=" C20 BCL I 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.91 5.62 2.00e-01 2.50e+01 7.89e+02 ... (remaining 3325 not shown) Planarity restraints: 3826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 2 101 " -0.355 1.50e-02 4.44e+03 3.03e-01 2.04e+03 pdb=" C2 BCL 2 101 " 0.475 1.50e-02 4.44e+03 pdb=" C3 BCL 2 101 " 0.193 1.50e-02 4.44e+03 pdb=" C4 BCL 2 101 " -0.258 1.50e-02 4.44e+03 pdb=" C5 BCL 2 101 " -0.055 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL L 401 " 0.353 1.50e-02 4.44e+03 2.99e-01 1.98e+03 pdb=" C2 BCL L 401 " -0.446 1.50e-02 4.44e+03 pdb=" C3 BCL L 401 " -0.220 1.50e-02 4.44e+03 pdb=" C4 BCL L 401 " 0.043 1.50e-02 4.44e+03 pdb=" C5 BCL L 401 " 0.270 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C3D BCL V 101 " -0.051 5.00e-03 4.00e+04 9.42e-02 1.42e+03 pdb=" CAD BCL V 101 " 0.162 5.00e-03 4.00e+04 pdb=" CBD BCL V 101 " -0.044 5.00e-03 4.00e+04 pdb=" OBD BCL V 101 " -0.067 5.00e-03 4.00e+04 ... (remaining 3823 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 119 2.50 - 3.10: 15893 3.10 - 3.70: 32389 3.70 - 4.30: 47470 4.30 - 4.90: 77715 Nonbonded interactions: 173586 Sorted by model distance: nonbonded pdb=" NH1 ARG Z 39 " pdb=" CG LYS Z 43 " model vdw 1.901 3.520 nonbonded pdb=" OE2 GLU M 557 " pdb="FE FE M1004 " model vdw 1.961 2.260 nonbonded pdb=" OE1 GLU M 557 " pdb="FE FE M1004 " model vdw 2.016 2.260 nonbonded pdb=" ND2 ASN M 518 " pdb=" CE2 TYR M 521 " model vdw 2.053 3.420 nonbonded pdb=" NH2 ARG M 570 " pdb=" ND2 ASN Z 58 " model vdw 2.072 3.200 ... (remaining 173581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 'E' selection = chain 'G' selection = (chain 'I' and (resid 7 through 55 or resid 101 through 102)) selection = chain 'K' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = (chain '1' and resid 7 through 41) selection = (chain '3' and resid 7 through 41) selection = (chain '5' and resid 7 through 41) selection = (chain '7' and resid 7 through 41) selection = (chain '9' and resid 7 through 41) selection = (chain 'A' and resid 7 through 41) selection = (chain 'D' and resid 7 through 41) selection = (chain 'F' and resid 7 through 41) selection = (chain 'H' and resid 7 through 41) selection = (chain 'J' and resid 7 through 41) selection = (chain 'N' and resid 7 through 41) selection = (chain 'P' and resid 7 through 41) selection = (chain 'R' and resid 7 through 41) selection = (chain 'T' and resid 7 through 41) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.020 Extract box with map and model: 5.180 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 56.950 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.019 0.122 23233 Z= 0.996 Angle : 2.022 18.919 32512 Z= 0.872 Chirality : 0.517 5.624 3328 Planarity : 0.039 0.303 3826 Dihedral : 20.900 175.242 7895 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.99 % Allowed : 13.11 % Favored : 85.90 % Cbeta Deviations : 0.09 % 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: -0.85 (0.16), residues: 2193 helix: 0.51 (0.13), residues: 1327 sheet: None (None), residues: 0 loop : -2.33 (0.18), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 2 53 HIS 0.008 0.001 HIS L 192 PHE 0.022 0.002 PHE H 6 TYR 0.014 0.002 TYR M 408 ARG 0.004 0.000 ARG D 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 575 time to evaluate : 2.119 Fit side-chains revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.7862 (tppt) cc_final: 0.7295 (tptp) REVERT: 1 24 LEU cc_start: 0.8218 (mt) cc_final: 0.8000 (mp) REVERT: 2 52 PRO cc_start: 0.6655 (Cg_endo) cc_final: 0.6433 (Cg_exo) REVERT: 4 9 LEU cc_start: 0.7346 (mt) cc_final: 0.6973 (tp) REVERT: 5 27 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7946 (m90) REVERT: 6 28 ILE cc_start: 0.8113 (mt) cc_final: 0.7881 (mm) REVERT: A 27 HIS cc_start: 0.8413 (OUTLIER) cc_final: 0.7977 (m90) REVERT: A 40 ARG cc_start: 0.5896 (ttm-80) cc_final: 0.5677 (ttt90) REVERT: B 34 TYR cc_start: 0.7889 (m-10) cc_final: 0.7612 (m-10) REVERT: E 31 LYS cc_start: 0.7821 (mttt) cc_final: 0.7451 (mmmt) REVERT: E 46 LEU cc_start: 0.8081 (mt) cc_final: 0.7825 (mt) REVERT: H 7 GLU cc_start: 0.6269 (mt-10) cc_final: 0.5319 (mp0) REVERT: I 31 LYS cc_start: 0.7125 (mttt) cc_final: 0.6775 (mtpt) REVERT: J 6 PHE cc_start: 0.6033 (m-80) cc_final: 0.5729 (m-80) REVERT: K 8 ASP cc_start: 0.7899 (p0) cc_final: 0.7524 (p0) REVERT: K 13 GLN cc_start: 0.6634 (tt0) cc_final: 0.6399 (mp10) REVERT: K 24 LEU cc_start: 0.7343 (mt) cc_final: 0.6939 (mt) REVERT: K 51 THR cc_start: 0.7993 (p) cc_final: 0.7784 (m) REVERT: L 16 LEU cc_start: 0.5427 (tp) cc_final: 0.5224 (tp) REVERT: L 58 ASP cc_start: 0.6848 (t70) cc_final: 0.6049 (t70) REVERT: L 302 MET cc_start: 0.7224 (mmm) cc_final: 0.6992 (mmm) REVERT: M 503 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7384 (ttp-170) REVERT: M 632 ASN cc_start: 0.7674 (p0) cc_final: 0.7458 (p0) REVERT: P 27 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.7886 (m90) REVERT: R 27 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7656 (m90) REVERT: S 15 LYS cc_start: 0.7134 (ttmm) cc_final: 0.6803 (tptt) REVERT: W 31 LYS cc_start: 0.6744 (mttt) cc_final: 0.6317 (mmmt) REVERT: W 41 VAL cc_start: 0.7041 (t) cc_final: 0.6828 (m) REVERT: C 148 MET cc_start: 0.8797 (ttp) cc_final: 0.8553 (ttp) outliers start: 19 outliers final: 6 residues processed: 591 average time/residue: 0.3383 time to fit residues: 310.2289 Evaluate side-chains 340 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 329 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 27 HIS Chi-restraints excluded: chain 5 residue 27 HIS Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain D residue 27 HIS Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain M residue 503 ARG Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain R residue 27 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN A 37 ASN B 13 GLN G 7 ASN G 19 ASN H 37 ASN K 19 ASN L 306 ASN S 22 GLN T 37 ASN U 19 ASN V 27 HIS W 20 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 155 ASN C 168 GLN C 233 ASN Z 58 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 23233 Z= 0.316 Angle : 1.062 18.133 32512 Z= 0.384 Chirality : 0.044 0.215 3328 Planarity : 0.005 0.051 3826 Dihedral : 21.665 179.515 4025 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.92 % Allowed : 16.29 % Favored : 79.79 % 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: 1.18 (0.18), residues: 2193 helix: 2.32 (0.13), residues: 1337 sheet: None (None), residues: 0 loop : -1.89 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 38 HIS 0.012 0.002 HIS L 192 PHE 0.018 0.002 PHE M 519 TYR 0.020 0.002 TYR M 424 ARG 0.006 0.001 ARG 1 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 332 time to evaluate : 2.488 Fit side-chains REVERT: 0 15 LYS cc_start: 0.7899 (tppt) cc_final: 0.7321 (tptp) REVERT: 1 24 LEU cc_start: 0.8152 (mt) cc_final: 0.7921 (mp) REVERT: 2 52 PRO cc_start: 0.6639 (Cg_endo) cc_final: 0.6317 (Cg_exo) REVERT: 4 9 LEU cc_start: 0.7474 (mt) cc_final: 0.7089 (tp) REVERT: 6 28 ILE cc_start: 0.8098 (mt) cc_final: 0.7863 (mm) REVERT: B 34 TYR cc_start: 0.7979 (m-10) cc_final: 0.7719 (m-10) REVERT: E 31 LYS cc_start: 0.7761 (mttt) cc_final: 0.7497 (mmmt) REVERT: H 7 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5197 (mp0) REVERT: H 22 MET cc_start: 0.8427 (mmp) cc_final: 0.8125 (mmp) REVERT: I 31 LYS cc_start: 0.7239 (mttt) cc_final: 0.6834 (mtpt) REVERT: I 51 THR cc_start: 0.8436 (p) cc_final: 0.8218 (p) REVERT: K 13 GLN cc_start: 0.6753 (tt0) cc_final: 0.6349 (mp10) REVERT: K 24 LEU cc_start: 0.7308 (mt) cc_final: 0.6871 (mt) REVERT: K 51 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.7977 (m) REVERT: M 357 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6554 (t70) REVERT: M 387 PHE cc_start: 0.7153 (t80) cc_final: 0.6818 (t80) REVERT: P 24 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7793 (mp) REVERT: P 27 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8214 (m90) REVERT: R 27 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.8054 (m90) REVERT: S 15 LYS cc_start: 0.7195 (ttmm) cc_final: 0.6749 (tptt) REVERT: V 22 MET cc_start: 0.6828 (mmp) cc_final: 0.6403 (mmp) REVERT: W 30 VAL cc_start: 0.6671 (t) cc_final: 0.6299 (m) REVERT: W 31 LYS cc_start: 0.6757 (mttt) cc_final: 0.6280 (mmmt) REVERT: W 55 ARG cc_start: 0.6392 (ttp-170) cc_final: 0.6152 (ttm170) REVERT: Y 17 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7990 (t80) REVERT: C 63 THR cc_start: 0.8593 (t) cc_final: 0.8392 (m) REVERT: C 95 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7702 (mmtp) REVERT: C 122 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7261 (m-70) REVERT: C 145 MET cc_start: 0.8094 (mmt) cc_final: 0.7744 (mmt) REVERT: C 148 MET cc_start: 0.8956 (ttp) cc_final: 0.8684 (ttp) outliers start: 75 outliers final: 48 residues processed: 380 average time/residue: 0.3342 time to fit residues: 206.1863 Evaluate side-chains 352 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 297 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 27 HIS Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 7 residue 14 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 9 residue 15 SER Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain M residue 357 HIS Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain M residue 429 ASN Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain R residue 32 SER Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain V residue 27 HIS Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 25 VAL Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 HIS L 205 ASN P 37 ASN V 27 HIS W 19 ASN W 20 ASN C 87 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 269 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 23233 Z= 0.347 Angle : 1.061 19.661 32512 Z= 0.394 Chirality : 0.045 0.240 3328 Planarity : 0.005 0.044 3826 Dihedral : 20.412 179.671 4015 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.60 % Allowed : 15.67 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.28 (0.17), residues: 2193 helix: 2.56 (0.13), residues: 1348 sheet: None (None), residues: 0 loop : -2.20 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 38 HIS 0.021 0.002 HIS V 27 PHE 0.026 0.002 PHE M 519 TYR 0.023 0.002 TYR M 424 ARG 0.005 0.001 ARG 4 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 313 time to evaluate : 3.069 Fit side-chains revert: symmetry clash REVERT: 0 9 LEU cc_start: 0.7139 (tp) cc_final: 0.6842 (tt) REVERT: 0 15 LYS cc_start: 0.7990 (tppt) cc_final: 0.7346 (tptp) REVERT: 1 24 LEU cc_start: 0.8256 (mt) cc_final: 0.7971 (mt) REVERT: 2 52 PRO cc_start: 0.7411 (Cg_endo) cc_final: 0.7012 (Cg_exo) REVERT: 4 9 LEU cc_start: 0.7633 (mt) cc_final: 0.7184 (tp) REVERT: 6 28 ILE cc_start: 0.8193 (mt) cc_final: 0.7945 (mm) REVERT: 8 41 VAL cc_start: 0.8462 (t) cc_final: 0.8196 (p) REVERT: B 46 LEU cc_start: 0.7971 (mp) cc_final: 0.7771 (mp) REVERT: E 31 LYS cc_start: 0.7813 (mttt) cc_final: 0.7518 (mmmt) REVERT: H 7 GLU cc_start: 0.6255 (mt-10) cc_final: 0.5269 (mp0) REVERT: H 22 MET cc_start: 0.8516 (mmp) cc_final: 0.8252 (mmp) REVERT: I 15 LYS cc_start: 0.6603 (mtpt) cc_final: 0.6008 (tptm) REVERT: I 31 LYS cc_start: 0.7305 (mttt) cc_final: 0.6894 (mtpt) REVERT: K 13 GLN cc_start: 0.6657 (tt0) cc_final: 0.6450 (mp10) REVERT: M 387 PHE cc_start: 0.7112 (t80) cc_final: 0.6818 (t80) REVERT: M 429 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8424 (m-40) REVERT: M 630 TRP cc_start: 0.8425 (OUTLIER) cc_final: 0.7969 (t60) REVERT: Q 22 GLN cc_start: 0.7174 (mt0) cc_final: 0.6823 (mt0) REVERT: Q 55 ARG cc_start: 0.6700 (ttm110) cc_final: 0.6103 (ttp-170) REVERT: R 27 HIS cc_start: 0.8956 (OUTLIER) cc_final: 0.8225 (m90) REVERT: S 9 LEU cc_start: 0.7542 (mt) cc_final: 0.7132 (mm) REVERT: U 41 VAL cc_start: 0.8457 (t) cc_final: 0.8217 (p) REVERT: V 22 MET cc_start: 0.7001 (mmp) cc_final: 0.6797 (mmp) REVERT: W 30 VAL cc_start: 0.6883 (t) cc_final: 0.6564 (m) REVERT: W 41 VAL cc_start: 0.6907 (t) cc_final: 0.6672 (m) REVERT: W 55 ARG cc_start: 0.6472 (ttp-170) cc_final: 0.6192 (ttm170) REVERT: Y 17 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7840 (t80) REVERT: C 122 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7275 (m-70) outliers start: 88 outliers final: 63 residues processed: 377 average time/residue: 0.3211 time to fit residues: 195.8055 Evaluate side-chains 349 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 281 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 14 VAL Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 14 VAL Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 367 GLU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 429 ASN Chi-restraints excluded: chain M residue 433 ASP Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 562 MET Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain M residue 639 VAL Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain V residue 27 HIS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 293 CYS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 25 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 193 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 20 ASN 8 22 GLN B 13 GLN G 19 ASN ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 HIS C 87 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23233 Z= 0.206 Angle : 0.892 17.050 32512 Z= 0.320 Chirality : 0.040 0.220 3328 Planarity : 0.004 0.092 3826 Dihedral : 19.113 179.782 4011 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.60 % Allowed : 17.28 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.78 (0.18), residues: 2193 helix: 2.99 (0.13), residues: 1348 sheet: None (None), residues: 0 loop : -2.07 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 38 HIS 0.021 0.001 HIS V 27 PHE 0.014 0.001 PHE L 62 TYR 0.019 0.001 TYR C 81 ARG 0.004 0.000 ARG P 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 310 time to evaluate : 2.272 Fit side-chains revert: symmetry clash REVERT: 0 15 LYS cc_start: 0.7944 (tppt) cc_final: 0.7383 (tptp) REVERT: 4 9 LEU cc_start: 0.7647 (mt) cc_final: 0.7331 (tp) REVERT: 6 28 ILE cc_start: 0.8144 (mt) cc_final: 0.7883 (mm) REVERT: 8 41 VAL cc_start: 0.8319 (t) cc_final: 0.8099 (p) REVERT: B 46 LEU cc_start: 0.7881 (mp) cc_final: 0.7657 (mp) REVERT: E 31 LYS cc_start: 0.7821 (mttt) cc_final: 0.7541 (mmmt) REVERT: H 7 GLU cc_start: 0.6159 (mt-10) cc_final: 0.5358 (mp0) REVERT: I 18 PHE cc_start: 0.8165 (m-80) cc_final: 0.7852 (m-80) REVERT: I 31 LYS cc_start: 0.7284 (mttt) cc_final: 0.6894 (mtpt) REVERT: L 82 LEU cc_start: 0.8580 (mt) cc_final: 0.8274 (mt) REVERT: M 387 PHE cc_start: 0.7056 (t80) cc_final: 0.6780 (t80) REVERT: M 551 LYS cc_start: 0.6269 (mttm) cc_final: 0.5952 (tmtt) REVERT: M 630 TRP cc_start: 0.8379 (OUTLIER) cc_final: 0.7950 (t60) REVERT: P 27 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8438 (m90) REVERT: Q 55 ARG cc_start: 0.6732 (ttm110) cc_final: 0.6159 (ttp-170) REVERT: R 27 HIS cc_start: 0.8881 (OUTLIER) cc_final: 0.8167 (m90) REVERT: S 9 LEU cc_start: 0.7484 (mt) cc_final: 0.7164 (mm) REVERT: S 37 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7795 (mm) REVERT: V 22 MET cc_start: 0.6974 (mmp) cc_final: 0.6766 (mmp) REVERT: V 27 HIS cc_start: 0.6193 (OUTLIER) cc_final: 0.5038 (m90) REVERT: W 13 GLN cc_start: 0.6074 (OUTLIER) cc_final: 0.5705 (tm-30) REVERT: W 30 VAL cc_start: 0.6896 (t) cc_final: 0.6633 (m) REVERT: Y 17 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7937 (t80) REVERT: C 87 GLN cc_start: 0.7208 (mp10) cc_final: 0.6978 (mp-120) REVERT: C 122 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7181 (m-70) REVERT: C 145 MET cc_start: 0.8096 (mmt) cc_final: 0.7592 (mmt) REVERT: Z 56 LYS cc_start: 0.7006 (mttp) cc_final: 0.6788 (mmtt) outliers start: 69 outliers final: 43 residues processed: 361 average time/residue: 0.3081 time to fit residues: 180.9428 Evaluate side-chains 335 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 284 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 15 SER Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 451 THR Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 27 HIS Chi-restraints excluded: chain W residue 13 GLN Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 173 optimal weight: 0.0040 chunk 48 optimal weight: 10.0000 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 22 GLN B 13 GLN V 27 HIS ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23233 Z= 0.195 Angle : 0.860 15.863 32512 Z= 0.309 Chirality : 0.039 0.213 3328 Planarity : 0.004 0.101 3826 Dihedral : 18.457 179.750 4011 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.76 % Allowed : 17.60 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.95 (0.18), residues: 2193 helix: 3.11 (0.13), residues: 1354 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 38 HIS 0.015 0.001 HIS V 27 PHE 0.013 0.001 PHE L 185 TYR 0.017 0.001 TYR O 34 ARG 0.003 0.000 ARG 1 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 298 time to evaluate : 2.138 Fit side-chains REVERT: 4 9 LEU cc_start: 0.7581 (mt) cc_final: 0.7274 (tp) REVERT: 6 28 ILE cc_start: 0.8129 (mt) cc_final: 0.7877 (mm) REVERT: 8 41 VAL cc_start: 0.8335 (t) cc_final: 0.8120 (p) REVERT: B 46 LEU cc_start: 0.7882 (mp) cc_final: 0.7662 (mp) REVERT: E 31 LYS cc_start: 0.7814 (mttt) cc_final: 0.7559 (mmmt) REVERT: H 7 GLU cc_start: 0.6092 (mt-10) cc_final: 0.5342 (mp0) REVERT: I 18 PHE cc_start: 0.8197 (m-80) cc_final: 0.7898 (m-80) REVERT: I 31 LYS cc_start: 0.7262 (mttt) cc_final: 0.6874 (mtpt) REVERT: L 82 LEU cc_start: 0.8517 (mt) cc_final: 0.8212 (mt) REVERT: M 387 PHE cc_start: 0.6972 (t80) cc_final: 0.6704 (t80) REVERT: M 551 LYS cc_start: 0.6358 (mttm) cc_final: 0.6142 (tptp) REVERT: M 630 TRP cc_start: 0.8386 (OUTLIER) cc_final: 0.7986 (t60) REVERT: P 27 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8520 (m90) REVERT: Q 55 ARG cc_start: 0.6821 (ttm110) cc_final: 0.6173 (ttp-170) REVERT: R 27 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.8140 (m90) REVERT: S 9 LEU cc_start: 0.7466 (mt) cc_final: 0.7152 (mm) REVERT: V 25 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5878 (mm) REVERT: W 30 VAL cc_start: 0.6915 (t) cc_final: 0.6668 (m) REVERT: Y 17 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7945 (t80) REVERT: C 122 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.6968 (m-70) REVERT: C 145 MET cc_start: 0.8171 (mmt) cc_final: 0.7693 (mmt) REVERT: Z 56 LYS cc_start: 0.7188 (mttp) cc_final: 0.6870 (mmtt) outliers start: 72 outliers final: 53 residues processed: 349 average time/residue: 0.3306 time to fit residues: 190.2879 Evaluate side-chains 333 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 274 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 15 SER Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 409 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 451 THR Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain M residue 630 TRP Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 27 HIS Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 22 GLN B 13 GLN K 7 ASN U 19 ASN V 27 HIS C 87 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23233 Z= 0.315 Angle : 0.949 18.411 32512 Z= 0.354 Chirality : 0.043 0.235 3328 Planarity : 0.005 0.083 3826 Dihedral : 18.471 179.633 4011 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.44 % Allowed : 17.18 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.63 (0.18), residues: 2193 helix: 2.78 (0.13), residues: 1355 sheet: None (None), residues: 0 loop : -2.01 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 38 HIS 0.010 0.002 HIS L 192 PHE 0.023 0.002 PHE M 519 TYR 0.022 0.002 TYR M 424 ARG 0.004 0.001 ARG 1 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 281 time to evaluate : 2.116 Fit side-chains REVERT: 2 37 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6892 (tt) REVERT: 4 9 LEU cc_start: 0.7579 (mt) cc_final: 0.7236 (tp) REVERT: 6 28 ILE cc_start: 0.8213 (mt) cc_final: 0.7946 (mm) REVERT: 8 41 VAL cc_start: 0.8471 (t) cc_final: 0.8205 (p) REVERT: E 31 LYS cc_start: 0.7844 (mttt) cc_final: 0.7561 (mmmt) REVERT: H 7 GLU cc_start: 0.5987 (mt-10) cc_final: 0.5400 (mp0) REVERT: I 18 PHE cc_start: 0.8145 (m-80) cc_final: 0.7879 (m-80) REVERT: I 31 LYS cc_start: 0.7368 (mttt) cc_final: 0.7006 (mtpt) REVERT: L 64 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8103 (tp) REVERT: M 387 PHE cc_start: 0.7057 (t80) cc_final: 0.6797 (t80) REVERT: P 27 HIS cc_start: 0.8850 (OUTLIER) cc_final: 0.8517 (m170) REVERT: Q 55 ARG cc_start: 0.6944 (ttm110) cc_final: 0.6457 (mtp180) REVERT: R 27 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8200 (m90) REVERT: S 9 LEU cc_start: 0.7527 (mt) cc_final: 0.7292 (mm) REVERT: S 37 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7737 (mm) REVERT: U 41 VAL cc_start: 0.8389 (t) cc_final: 0.8186 (p) REVERT: V 25 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5870 (mm) REVERT: V 27 HIS cc_start: 0.6302 (OUTLIER) cc_final: 0.5025 (m90) REVERT: W 30 VAL cc_start: 0.6964 (t) cc_final: 0.6680 (m) REVERT: W 38 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7325 (mp) REVERT: Y 17 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7773 (t80) REVERT: C 87 GLN cc_start: 0.7270 (mp10) cc_final: 0.7045 (mp-120) REVERT: C 122 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.6989 (m-70) REVERT: C 127 PHE cc_start: 0.3119 (OUTLIER) cc_final: 0.2788 (p90) REVERT: C 145 MET cc_start: 0.8208 (mmt) cc_final: 0.7849 (mmt) REVERT: C 182 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7968 (pp) REVERT: Z 56 LYS cc_start: 0.7367 (mttp) cc_final: 0.7116 (mttm) outliers start: 85 outliers final: 62 residues processed: 345 average time/residue: 0.3105 time to fit residues: 174.1258 Evaluate side-chains 347 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 273 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 19 ASN Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 409 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 451 THR Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain P residue 32 SER Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain S residue 37 LEU Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 27 HIS Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 162 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 7 ASN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 23233 Z= 0.282 Angle : 0.930 17.700 32512 Z= 0.350 Chirality : 0.042 0.234 3328 Planarity : 0.005 0.102 3826 Dihedral : 18.428 179.647 4011 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.91 % Allowed : 17.08 % Favored : 78.02 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.64 (0.18), residues: 2193 helix: 2.79 (0.13), residues: 1355 sheet: None (None), residues: 0 loop : -1.99 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 38 HIS 0.009 0.001 HIS L 192 PHE 0.019 0.001 PHE M 519 TYR 0.020 0.002 TYR M 424 ARG 0.004 0.000 ARG 1 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 282 time to evaluate : 2.180 Fit side-chains REVERT: 2 37 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6894 (tt) REVERT: 2 44 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.6927 (m90) REVERT: 4 9 LEU cc_start: 0.7580 (mt) cc_final: 0.7234 (tp) REVERT: 6 9 LEU cc_start: 0.6192 (mp) cc_final: 0.5785 (tp) REVERT: 6 28 ILE cc_start: 0.8223 (mt) cc_final: 0.7966 (mm) REVERT: 8 41 VAL cc_start: 0.8465 (t) cc_final: 0.8192 (p) REVERT: E 31 LYS cc_start: 0.7825 (mttt) cc_final: 0.7554 (mmmt) REVERT: G 34 TYR cc_start: 0.7566 (m-10) cc_final: 0.7010 (m-80) REVERT: H 7 GLU cc_start: 0.5995 (mt-10) cc_final: 0.5446 (mp0) REVERT: I 18 PHE cc_start: 0.8146 (m-80) cc_final: 0.7894 (m-80) REVERT: I 31 LYS cc_start: 0.7312 (mttt) cc_final: 0.6993 (mtpt) REVERT: L 64 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8158 (tp) REVERT: P 27 HIS cc_start: 0.8851 (OUTLIER) cc_final: 0.8532 (m90) REVERT: Q 55 ARG cc_start: 0.6905 (ttm110) cc_final: 0.6430 (mtp180) REVERT: R 27 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8127 (m90) REVERT: S 9 LEU cc_start: 0.7599 (mt) cc_final: 0.7297 (mm) REVERT: V 25 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5751 (mm) REVERT: V 27 HIS cc_start: 0.6181 (OUTLIER) cc_final: 0.5855 (m-70) REVERT: W 30 VAL cc_start: 0.6920 (t) cc_final: 0.6676 (m) REVERT: W 38 ILE cc_start: 0.7485 (OUTLIER) cc_final: 0.7274 (mp) REVERT: Y 17 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7814 (t80) REVERT: C 122 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6843 (m-70) REVERT: C 127 PHE cc_start: 0.3201 (OUTLIER) cc_final: 0.2873 (p90) REVERT: C 145 MET cc_start: 0.8149 (mmt) cc_final: 0.7911 (mmt) REVERT: C 182 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7973 (pp) REVERT: Z 56 LYS cc_start: 0.7376 (mttp) cc_final: 0.7036 (mmtt) outliers start: 94 outliers final: 68 residues processed: 351 average time/residue: 0.3022 time to fit residues: 173.6222 Evaluate side-chains 352 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 272 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 2 residue 44 HIS Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 409 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 451 THR Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 27 HIS Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 44 HIS Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 0.0020 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 175 optimal weight: 7.9990 overall best weight: 3.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 GLN K 7 ASN C 87 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23233 Z= 0.244 Angle : 0.886 16.433 32512 Z= 0.333 Chirality : 0.041 0.229 3328 Planarity : 0.005 0.103 3826 Dihedral : 18.020 179.669 4011 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.39 % Allowed : 17.55 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.74 (0.18), residues: 2193 helix: 2.87 (0.13), residues: 1356 sheet: None (None), residues: 0 loop : -1.96 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 38 HIS 0.009 0.001 HIS L 192 PHE 0.016 0.001 PHE M 519 TYR 0.017 0.002 TYR O 34 ARG 0.004 0.000 ARG 1 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 280 time to evaluate : 2.341 Fit side-chains revert: symmetry clash REVERT: 2 44 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.6881 (m90) REVERT: 4 9 LEU cc_start: 0.7715 (mt) cc_final: 0.7319 (tp) REVERT: 6 9 LEU cc_start: 0.6234 (mp) cc_final: 0.5877 (tp) REVERT: 6 28 ILE cc_start: 0.8212 (mt) cc_final: 0.7956 (mm) REVERT: 8 41 VAL cc_start: 0.8452 (t) cc_final: 0.8190 (p) REVERT: 9 16 THR cc_start: 0.8231 (m) cc_final: 0.8002 (m) REVERT: D 4 ARG cc_start: 0.4584 (ttm-80) cc_final: 0.4251 (ttm170) REVERT: E 31 LYS cc_start: 0.7841 (mttt) cc_final: 0.7574 (mmmt) REVERT: G 34 TYR cc_start: 0.7558 (m-10) cc_final: 0.7079 (m-80) REVERT: H 7 GLU cc_start: 0.5977 (mt-10) cc_final: 0.5448 (mp0) REVERT: I 18 PHE cc_start: 0.8153 (m-80) cc_final: 0.7654 (m-80) REVERT: I 31 LYS cc_start: 0.7292 (mttt) cc_final: 0.6985 (mtpt) REVERT: L 53 ARG cc_start: 0.7243 (mmm-85) cc_final: 0.6919 (mtm-85) REVERT: L 64 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8186 (tp) REVERT: M 519 PHE cc_start: 0.8996 (OUTLIER) cc_final: 0.8241 (t80) REVERT: P 27 HIS cc_start: 0.8850 (OUTLIER) cc_final: 0.8523 (m90) REVERT: Q 55 ARG cc_start: 0.6877 (ttm110) cc_final: 0.6405 (mtp180) REVERT: R 27 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8119 (m90) REVERT: S 9 LEU cc_start: 0.7582 (mt) cc_final: 0.7292 (mm) REVERT: V 25 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5698 (mm) REVERT: V 27 HIS cc_start: 0.5724 (OUTLIER) cc_final: 0.5459 (m-70) REVERT: W 30 VAL cc_start: 0.6899 (t) cc_final: 0.6681 (m) REVERT: W 38 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7275 (mp) REVERT: Y 17 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.7810 (t80) REVERT: C 127 PHE cc_start: 0.3168 (OUTLIER) cc_final: 0.2892 (p90) outliers start: 84 outliers final: 71 residues processed: 342 average time/residue: 0.3345 time to fit residues: 187.3339 Evaluate side-chains 352 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 271 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 2 residue 44 HIS Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain K residue 19 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 409 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 451 THR Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 27 HIS Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 44 HIS Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 7 ASN Q 13 GLN V 27 HIS C 87 GLN ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23233 Z= 0.251 Angle : 0.873 16.733 32512 Z= 0.333 Chirality : 0.041 0.228 3328 Planarity : 0.005 0.106 3826 Dihedral : 17.683 179.663 4011 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.60 % Allowed : 17.60 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.75 (0.18), residues: 2193 helix: 2.91 (0.13), residues: 1343 sheet: None (None), residues: 0 loop : -1.95 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 38 HIS 0.009 0.001 HIS L 192 PHE 0.017 0.001 PHE M 519 TYR 0.020 0.002 TYR C 133 ARG 0.004 0.000 ARG 1 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 274 time to evaluate : 2.122 Fit side-chains REVERT: 2 37 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6922 (tt) REVERT: 2 44 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.6956 (m90) REVERT: 4 9 LEU cc_start: 0.7708 (mt) cc_final: 0.7289 (tp) REVERT: 6 9 LEU cc_start: 0.6306 (mp) cc_final: 0.5881 (tp) REVERT: 6 28 ILE cc_start: 0.8247 (mt) cc_final: 0.7975 (mm) REVERT: 8 41 VAL cc_start: 0.8445 (t) cc_final: 0.8178 (p) REVERT: 9 16 THR cc_start: 0.8230 (m) cc_final: 0.8008 (m) REVERT: D 4 ARG cc_start: 0.4653 (ttm-80) cc_final: 0.4242 (ttm170) REVERT: D 18 LEU cc_start: 0.8736 (tp) cc_final: 0.8519 (tt) REVERT: E 31 LYS cc_start: 0.7859 (mttt) cc_final: 0.7586 (mmmt) REVERT: H 7 GLU cc_start: 0.5968 (mt-10) cc_final: 0.5485 (mp0) REVERT: I 18 PHE cc_start: 0.8111 (m-80) cc_final: 0.7597 (m-80) REVERT: I 31 LYS cc_start: 0.7295 (mttt) cc_final: 0.6968 (mtpt) REVERT: L 64 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8227 (tp) REVERT: M 519 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8243 (t80) REVERT: P 27 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8582 (m90) REVERT: Q 55 ARG cc_start: 0.6946 (ttm110) cc_final: 0.6491 (mtp180) REVERT: R 27 HIS cc_start: 0.8977 (OUTLIER) cc_final: 0.8153 (m90) REVERT: S 9 LEU cc_start: 0.7545 (mt) cc_final: 0.7306 (mm) REVERT: V 25 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5718 (mm) REVERT: W 38 ILE cc_start: 0.7409 (OUTLIER) cc_final: 0.7201 (mp) REVERT: Y 17 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7816 (t80) REVERT: C 122 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7057 (m-70) REVERT: C 127 PHE cc_start: 0.3176 (OUTLIER) cc_final: 0.2823 (p90) outliers start: 88 outliers final: 71 residues processed: 337 average time/residue: 0.3054 time to fit residues: 165.5993 Evaluate side-chains 342 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 260 time to evaluate : 2.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 2 residue 44 HIS Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 6 residue 54 ILE Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain K residue 19 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 409 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 451 THR Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain W residue 10 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 44 HIS Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain Z residue 58 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.0060 chunk 90 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 199 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 169 optimal weight: 0.7980 overall best weight: 2.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 7 ASN C 87 GLN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23233 Z= 0.203 Angle : 0.819 16.530 32512 Z= 0.313 Chirality : 0.039 0.218 3328 Planarity : 0.004 0.107 3826 Dihedral : 17.450 179.703 4011 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.13 % Allowed : 18.38 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.91 (0.18), residues: 2193 helix: 3.04 (0.13), residues: 1348 sheet: None (None), residues: 0 loop : -1.92 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 38 HIS 0.008 0.001 HIS L 192 PHE 0.014 0.001 PHE L 185 TYR 0.017 0.001 TYR O 34 ARG 0.004 0.000 ARG 1 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4386 Ramachandran restraints generated. 2193 Oldfield, 0 Emsley, 2193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 267 time to evaluate : 3.091 Fit side-chains revert: symmetry clash REVERT: 2 44 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.6768 (m90) REVERT: 4 9 LEU cc_start: 0.7704 (mt) cc_final: 0.7312 (tp) REVERT: 6 9 LEU cc_start: 0.6258 (mp) cc_final: 0.5991 (tp) REVERT: 6 18 PHE cc_start: 0.6696 (m-80) cc_final: 0.6423 (m-80) REVERT: 6 28 ILE cc_start: 0.8182 (mt) cc_final: 0.7924 (mm) REVERT: 9 16 THR cc_start: 0.8217 (m) cc_final: 0.7991 (m) REVERT: D 4 ARG cc_start: 0.4685 (ttm-80) cc_final: 0.4280 (ttm170) REVERT: E 31 LYS cc_start: 0.7861 (mttt) cc_final: 0.7583 (mmmt) REVERT: H 7 GLU cc_start: 0.5942 (mt-10) cc_final: 0.5442 (mp0) REVERT: I 18 PHE cc_start: 0.8104 (m-80) cc_final: 0.7598 (m-80) REVERT: I 31 LYS cc_start: 0.7256 (mttt) cc_final: 0.6985 (mtpt) REVERT: L 64 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8198 (tp) REVERT: L 82 LEU cc_start: 0.8433 (mt) cc_final: 0.8106 (mt) REVERT: M 519 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8190 (t80) REVERT: P 27 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8564 (m90) REVERT: Q 55 ARG cc_start: 0.6780 (ttm110) cc_final: 0.6350 (mtp180) REVERT: R 27 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8125 (m90) REVERT: S 9 LEU cc_start: 0.7418 (mt) cc_final: 0.7204 (mm) REVERT: U 46 LEU cc_start: 0.7929 (tt) cc_final: 0.7035 (mt) REVERT: W 38 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7238 (mp) REVERT: Y 17 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7850 (t80) REVERT: C 122 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.6974 (m-70) REVERT: C 127 PHE cc_start: 0.3207 (OUTLIER) cc_final: 0.2813 (p90) outliers start: 79 outliers final: 64 residues processed: 326 average time/residue: 0.3286 time to fit residues: 174.0754 Evaluate side-chains 337 residues out of total 1915 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 264 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 10 VAL Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 2 residue 44 HIS Chi-restraints excluded: chain 3 residue 38 TRP Chi-restraints excluded: chain 4 residue 42 ILE Chi-restraints excluded: chain 5 residue 24 LEU Chi-restraints excluded: chain 7 residue 17 LEU Chi-restraints excluded: chain 7 residue 33 SER Chi-restraints excluded: chain 8 residue 10 VAL Chi-restraints excluded: chain 9 residue 18 LEU Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain F residue 27 HIS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 27 HIS Chi-restraints excluded: chain K residue 19 ASN Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 181 TRP Chi-restraints excluded: chain L residue 206 PHE Chi-restraints excluded: chain L residue 240 ASN Chi-restraints excluded: chain L residue 304 ILE Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain M residue 347 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain M residue 409 LEU Chi-restraints excluded: chain M residue 449 VAL Chi-restraints excluded: chain M residue 451 THR Chi-restraints excluded: chain M residue 493 ASN Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 519 PHE Chi-restraints excluded: chain M residue 613 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 47 CYS Chi-restraints excluded: chain O residue 55 ARG Chi-restraints excluded: chain P residue 24 LEU Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 27 HIS Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 17 LEU Chi-restraints excluded: chain R residue 27 HIS Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 32 THR Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 44 HIS Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 17 PHE Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 122 HIS Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 157 THR Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 244 HIS Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 9.9990 chunk 146 optimal weight: 0.0770 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 overall best weight: 3.1144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 13 GLN G 7 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.115993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.096576 restraints weight = 40224.785| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.25 r_work: 0.3073 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23233 Z= 0.235 Angle : 0.841 16.650 32512 Z= 0.323 Chirality : 0.041 0.226 3328 Planarity : 0.005 0.107 3826 Dihedral : 17.405 179.696 4011 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.02 % Allowed : 18.64 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.84 % 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: 1.84 (0.18), residues: 2193 helix: 2.98 (0.13), residues: 1348 sheet: None (None), residues: 0 loop : -1.93 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 38 HIS 0.009 0.001 HIS L 192 PHE 0.016 0.001 PHE L 185 TYR 0.019 0.002 TYR C 133 ARG 0.003 0.000 ARG 1 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4838.40 seconds wall clock time: 88 minutes 56.20 seconds (5336.20 seconds total)