Starting phenix.real_space_refine on Fri Feb 16 14:05:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/02_2024/7k6q_22692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/02_2024/7k6q_22692.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/7k6q_22692/02_2024/7k6q_22692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/02_2024/7k6q_22692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/02_2024/7k6q_22692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/02_2024/7k6q_22692_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= 0.004 sd= 1.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 34 5.16 5 C 8919 2.51 5 N 2846 2.21 5 O 3487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G ASP 90": "OD1" <-> "OD2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "K PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 329": "OD1" <-> "OD2" Residue "K TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 412": "OE1" <-> "OE2" Residue "K GLU 437": "OE1" <-> "OE2" Residue "K PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15578 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 719 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ALY:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 715 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2, 'ALY:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3029 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 485 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 Time building chain proxies: 8.54, per 1000 atoms: 0.55 Number of scatterers: 15578 At special positions: 0 Unit cell: (110.745, 113.85, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 292 15.00 O 3487 8.00 N 2846 7.00 C 8919 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=0, symmetry=0 Time building additional restraints: 8.64 Conformation dependent library (CDL) restraints added in 1.7 seconds 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2318 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 4 sheets defined 53.6% alpha, 4.6% beta 142 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 8.69 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.950A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.914A pdb=" N TYR B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU B 52 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 53 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 66 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.463A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.681A pdb=" N THR D 122 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.881A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE F 66 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.533A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'K' and resid 196 through 201 Processing helix chain 'K' and resid 212 through 214 No H-bonds generated for 'chain 'K' and resid 212 through 214' Processing helix chain 'K' and resid 264 through 277 Processing helix chain 'K' and resid 284 through 302 removed outlier: 3.557A pdb=" N ILE K 292 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU K 293 " --> pdb=" O LYS K 289 " (cutoff:3.500A) Proline residue: K 294 - end of helix Processing helix chain 'K' and resid 305 through 320 Processing helix chain 'K' and resid 324 through 333 Processing helix chain 'K' and resid 339 through 353 removed outlier: 3.830A pdb=" N HIS K 343 " --> pdb=" O ARG K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 357 No H-bonds generated for 'chain 'K' and resid 355 through 357' Processing helix chain 'K' and resid 359 through 363 removed outlier: 3.501A pdb=" N HIS K 363 " --> pdb=" O LYS K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 386 Processing helix chain 'K' and resid 404 through 412 Processing helix chain 'K' and resid 425 through 445 Processing helix chain 'K' and resid 464 through 470 Processing helix chain 'K' and resid 485 through 497 removed outlier: 4.755A pdb=" N THR K 497 " --> pdb=" O LYS K 493 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 528 No H-bonds generated for 'chain 'K' and resid 526 through 528' Processing helix chain 'K' and resid 566 through 569 No H-bonds generated for 'chain 'K' and resid 566 through 569' Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 56 through 59 No H-bonds generated for 'chain 'L' and resid 56 through 59' Processing sheet with id= A, first strand: chain 'K' and resid 186 through 188 Processing sheet with id= B, first strand: chain 'K' and resid 237 through 240 Processing sheet with id= C, first strand: chain 'K' and resid 529 through 536 removed outlier: 4.178A pdb=" N GLY K 548 " --> pdb=" O LEU K 536 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU K 417 " --> pdb=" O PHE K 395 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ASP K 397 " --> pdb=" O LEU K 417 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE K 419 " --> pdb=" O ASP K 397 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 12 through 15 removed outlier: 6.135A pdb=" N SER L 65 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LYS L 6 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU L 67 " --> pdb=" O LYS L 6 " (cutoff:3.500A) 477 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 7.47 Time building geometry restraints manager: 9.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2978 1.33 - 1.45: 5034 1.45 - 1.57: 7807 1.57 - 1.69: 580 1.69 - 1.81: 55 Bond restraints: 16454 Sorted by residual: bond pdb=" O3' DA I 91 " pdb=" P DC I 92 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.50e-02 4.44e+03 1.48e+01 bond pdb=" N ASP D 51 " pdb=" CA ASP D 51 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" O3' DA I 90 " pdb=" P DA I 91 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.04e+01 bond pdb=" O3' DA I 131 " pdb=" P DG I 132 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.50e-02 4.44e+03 7.53e+00 bond pdb=" N ASP C 90 " pdb=" CA ASP C 90 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.23e-02 6.61e+03 7.24e+00 ... (remaining 16449 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.04: 1862 106.04 - 113.00: 8721 113.00 - 119.95: 5857 119.95 - 126.91: 6296 126.91 - 133.86: 785 Bond angle restraints: 23521 Sorted by residual: angle pdb=" C4' DA I 91 " pdb=" C3' DA I 91 " pdb=" O3' DA I 91 " ideal model delta sigma weight residual 110.00 103.65 6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" O3' DT J 15 " pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 111.50 117.75 -6.25 1.50e+00 4.44e-01 1.74e+01 angle pdb=" O3' DA I 90 " pdb=" C3' DA I 90 " pdb=" C2' DA I 90 " ideal model delta sigma weight residual 111.50 105.33 6.17 1.50e+00 4.44e-01 1.69e+01 angle pdb=" O3' DT I 89 " pdb=" C3' DT I 89 " pdb=" C2' DT I 89 " ideal model delta sigma weight residual 111.50 106.14 5.36 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " ideal model delta sigma weight residual 110.00 104.64 5.36 1.50e+00 4.44e-01 1.28e+01 ... (remaining 23516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.40: 7471 29.40 - 58.81: 1574 58.81 - 88.21: 93 88.21 - 117.62: 1 117.62 - 147.02: 3 Dihedral angle restraints: 9142 sinusoidal: 5555 harmonic: 3587 Sorted by residual: dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 72.98 147.02 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 73.40 146.60 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 86.16 133.84 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 9139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2363 0.064 - 0.128: 319 0.128 - 0.192: 19 0.192 - 0.256: 3 0.256 - 0.320: 1 Chirality restraints: 2705 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C2' SAM K 601 " pdb=" C1' SAM K 601 " pdb=" C3' SAM K 601 " pdb=" O2' SAM K 601 " both_signs ideal model delta sigma weight residual False -2.76 -2.53 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' DT I 89 " pdb=" C4' DT I 89 " pdb=" O3' DT I 89 " pdb=" C2' DT I 89 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2702 not shown) Planarity restraints: 1971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 86 " -0.219 9.50e-02 1.11e+02 9.83e-02 6.51e+00 pdb=" NE ARG H 86 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG H 86 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 86 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 86 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 42 " -0.203 9.50e-02 1.11e+02 9.15e-02 6.12e+00 pdb=" NE ARG E 42 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG E 42 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG E 42 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 42 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO H 103 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.031 5.00e-02 4.00e+02 ... (remaining 1968 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 448 2.67 - 3.23: 13672 3.23 - 3.78: 29199 3.78 - 4.34: 37907 4.34 - 4.90: 55691 Nonbonded interactions: 136917 Sorted by model distance: nonbonded pdb=" OE2 GLU K 422 " pdb=" O2' SAM K 601 " model vdw 2.108 2.440 nonbonded pdb=" OG1 THR H 32 " pdb=" OP1 DC J 104 " model vdw 2.114 2.440 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.166 2.440 nonbonded pdb=" OH TYR K 274 " pdb=" OD2 ASP K 344 " model vdw 2.183 2.440 nonbonded pdb=" NH2 ARG A 40 " pdb=" O2 DT J 83 " model vdw 2.214 2.520 ... (remaining 136912 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 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 16 or (resid 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 through 19 or (resid 20 and (name N or name CA or nam \ e C or name O or name CB )) or resid 21 through 22 or (resid 23 and (name N or n \ ame CA or name C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and (resid 16 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } 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=0.25 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.280 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 53.300 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:3.190 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 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 : 0.006 0.061 16454 Z= 0.308 Angle : 0.777 8.745 23521 Z= 0.457 Chirality : 0.042 0.320 2705 Planarity : 0.006 0.098 1971 Dihedral : 24.803 147.020 6824 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.37 (0.24), residues: 1201 helix: 1.64 (0.19), residues: 717 sheet: -0.22 (0.56), residues: 85 loop : -0.07 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 543 HIS 0.010 0.001 HIS K 355 PHE 0.014 0.001 PHE G 25 TYR 0.011 0.001 TYR D 40 ARG 0.018 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.438 Fit side-chains REVERT: B 20 LYS cc_start: 0.8441 (tttm) cc_final: 0.7988 (ttmt) REVERT: B 25 ASN cc_start: 0.8207 (m-40) cc_final: 0.7936 (m-40) REVERT: D 119 THR cc_start: 0.8678 (m) cc_final: 0.8443 (p) REVERT: E 42 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7326 (mtt180) REVERT: E 59 GLU cc_start: 0.8132 (pm20) cc_final: 0.7785 (pm20) REVERT: E 74 ILE cc_start: 0.9059 (mm) cc_final: 0.8830 (mt) REVERT: F 77 LYS cc_start: 0.8813 (mttt) cc_final: 0.8419 (mtmt) REVERT: F 84 MET cc_start: 0.8239 (mmm) cc_final: 0.8010 (mmm) REVERT: H 51 ASP cc_start: 0.7563 (p0) cc_final: 0.7319 (p0) REVERT: K 493 LYS cc_start: 0.8665 (tttt) cc_final: 0.8426 (ttmm) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3658 time to fit residues: 87.2987 Evaluate side-chains 135 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 114 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS B 93 GLN G 31 HIS ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 521 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16454 Z= 0.284 Angle : 0.563 5.978 23521 Z= 0.332 Chirality : 0.037 0.143 2705 Planarity : 0.005 0.049 1971 Dihedral : 28.958 140.000 4590 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.21 % Allowed : 5.65 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.29 (0.24), residues: 1201 helix: 1.43 (0.19), residues: 718 sheet: 0.31 (0.59), residues: 81 loop : 0.06 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 543 HIS 0.006 0.001 HIS K 347 PHE 0.020 0.002 PHE G 25 TYR 0.013 0.001 TYR C 57 ARG 0.012 0.001 ARG L 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 1.416 Fit side-chains REVERT: B 20 LYS cc_start: 0.8422 (tttm) cc_final: 0.8028 (ttmt) REVERT: E 42 ARG cc_start: 0.7584 (mtm110) cc_final: 0.7349 (mtt180) REVERT: E 59 GLU cc_start: 0.8112 (pm20) cc_final: 0.7636 (pm20) REVERT: F 77 LYS cc_start: 0.8902 (mttt) cc_final: 0.8616 (mttp) REVERT: F 92 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7799 (ttp80) REVERT: H 51 ASP cc_start: 0.7663 (p0) cc_final: 0.7434 (p0) REVERT: H 59 MET cc_start: 0.8468 (tpp) cc_final: 0.8226 (tpp) REVERT: K 202 HIS cc_start: 0.7687 (m90) cc_final: 0.7485 (m170) REVERT: K 493 LYS cc_start: 0.8663 (tttt) cc_final: 0.8436 (ttmm) outliers start: 12 outliers final: 11 residues processed: 152 average time/residue: 0.3633 time to fit residues: 77.1932 Evaluate side-chains 143 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 404 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 0.0040 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 84 ASN K 316 ASN ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16454 Z= 0.230 Angle : 0.525 5.760 23521 Z= 0.312 Chirality : 0.035 0.145 2705 Planarity : 0.005 0.044 1971 Dihedral : 28.940 140.872 4590 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.41 % Allowed : 6.96 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.23 (0.24), residues: 1201 helix: 1.32 (0.19), residues: 716 sheet: 0.45 (0.60), residues: 81 loop : 0.15 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 543 HIS 0.003 0.001 HIS K 347 PHE 0.014 0.001 PHE G 25 TYR 0.011 0.001 TYR C 57 ARG 0.005 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 1.315 Fit side-chains REVERT: B 20 LYS cc_start: 0.8452 (tttm) cc_final: 0.8017 (ttmt) REVERT: D 42 TYR cc_start: 0.7543 (t80) cc_final: 0.7323 (t80) REVERT: E 59 GLU cc_start: 0.8074 (pm20) cc_final: 0.7580 (pm20) REVERT: F 77 LYS cc_start: 0.8917 (mttt) cc_final: 0.8509 (mttp) REVERT: F 92 ARG cc_start: 0.8250 (ttp80) cc_final: 0.7851 (ttp80) REVERT: H 42 TYR cc_start: 0.7569 (t80) cc_final: 0.7268 (t80) REVERT: H 59 MET cc_start: 0.8464 (tpp) cc_final: 0.8146 (tpp) REVERT: H 80 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8253 (mp) REVERT: K 493 LYS cc_start: 0.8667 (tttt) cc_final: 0.8440 (ttmm) REVERT: L 72 ARG cc_start: 0.6640 (tmm-80) cc_final: 0.6307 (tmm-80) outliers start: 14 outliers final: 9 residues processed: 144 average time/residue: 0.3305 time to fit residues: 66.6272 Evaluate side-chains 140 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 404 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.0470 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 141 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 25 ASN K 355 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16454 Z= 0.177 Angle : 0.502 6.477 23521 Z= 0.301 Chirality : 0.034 0.144 2705 Planarity : 0.004 0.039 1971 Dihedral : 28.739 140.120 4590 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.31 % Allowed : 8.48 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.35 (0.24), residues: 1201 helix: 1.41 (0.19), residues: 714 sheet: 0.52 (0.59), residues: 81 loop : 0.20 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 543 HIS 0.003 0.000 HIS F 75 PHE 0.009 0.001 PHE G 25 TYR 0.010 0.001 TYR C 57 ARG 0.007 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 1.387 Fit side-chains REVERT: A 59 GLU cc_start: 0.7597 (pm20) cc_final: 0.7320 (pm20) REVERT: B 20 LYS cc_start: 0.8455 (tttm) cc_final: 0.8018 (ttmt) REVERT: B 88 TYR cc_start: 0.8196 (m-10) cc_final: 0.7824 (m-10) REVERT: D 42 TYR cc_start: 0.7415 (t80) cc_final: 0.7190 (t80) REVERT: E 59 GLU cc_start: 0.8030 (pm20) cc_final: 0.7522 (pm20) REVERT: F 77 LYS cc_start: 0.8892 (mttt) cc_final: 0.8471 (mttp) REVERT: L 72 ARG cc_start: 0.6672 (tmm-80) cc_final: 0.6354 (tmm-80) outliers start: 13 outliers final: 9 residues processed: 144 average time/residue: 0.3474 time to fit residues: 69.8900 Evaluate side-chains 138 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 72 optimal weight: 0.3980 chunk 126 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN L 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16454 Z= 0.167 Angle : 0.494 7.035 23521 Z= 0.297 Chirality : 0.034 0.143 2705 Planarity : 0.004 0.039 1971 Dihedral : 28.663 139.344 4590 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.31 % Allowed : 8.98 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.41 (0.24), residues: 1201 helix: 1.48 (0.19), residues: 713 sheet: 0.56 (0.59), residues: 81 loop : 0.20 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 543 HIS 0.009 0.001 HIS K 202 PHE 0.009 0.001 PHE G 25 TYR 0.010 0.001 TYR C 57 ARG 0.007 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.462 Fit side-chains REVERT: B 20 LYS cc_start: 0.8458 (tttm) cc_final: 0.8024 (ttmt) REVERT: C 94 ASN cc_start: 0.9028 (t0) cc_final: 0.8682 (t0) REVERT: D 42 TYR cc_start: 0.7381 (t80) cc_final: 0.7154 (t80) REVERT: E 59 GLU cc_start: 0.7964 (pm20) cc_final: 0.7457 (pm20) REVERT: H 42 TYR cc_start: 0.7554 (t80) cc_final: 0.7233 (t80) REVERT: L 72 ARG cc_start: 0.6542 (tmm-80) cc_final: 0.6276 (tmm-80) outliers start: 13 outliers final: 9 residues processed: 142 average time/residue: 0.3259 time to fit residues: 65.4650 Evaluate side-chains 139 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 404 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.6980 chunk 127 optimal weight: 0.0870 chunk 27 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 46 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16454 Z= 0.165 Angle : 0.496 8.002 23521 Z= 0.296 Chirality : 0.033 0.145 2705 Planarity : 0.004 0.039 1971 Dihedral : 28.632 138.985 4590 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.72 % Allowed : 9.18 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1201 helix: 1.52 (0.19), residues: 712 sheet: 0.60 (0.60), residues: 81 loop : 0.20 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 543 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE G 25 TYR 0.010 0.001 TYR C 57 ARG 0.008 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 1.481 Fit side-chains REVERT: B 20 LYS cc_start: 0.8458 (tttm) cc_final: 0.8037 (ttmt) REVERT: C 94 ASN cc_start: 0.9026 (t0) cc_final: 0.8682 (t0) REVERT: D 42 TYR cc_start: 0.7357 (t80) cc_final: 0.7087 (t80) REVERT: E 59 GLU cc_start: 0.7917 (pm20) cc_final: 0.7420 (pm20) REVERT: F 77 LYS cc_start: 0.8869 (mttt) cc_final: 0.8496 (mtmt) REVERT: K 556 MET cc_start: 0.7445 (mmm) cc_final: 0.7113 (mmm) REVERT: L 72 ARG cc_start: 0.6632 (tmm-80) cc_final: 0.6378 (tmm-80) outliers start: 17 outliers final: 13 residues processed: 144 average time/residue: 0.3205 time to fit residues: 65.2593 Evaluate side-chains 143 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 404 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 0.0030 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 16454 Z= 0.441 Angle : 0.616 8.876 23521 Z= 0.353 Chirality : 0.041 0.161 2705 Planarity : 0.005 0.042 1971 Dihedral : 29.544 139.255 4590 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.41 % Allowed : 9.79 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.92 (0.24), residues: 1201 helix: 1.08 (0.19), residues: 716 sheet: 0.46 (0.59), residues: 81 loop : -0.03 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 543 HIS 0.008 0.002 HIS K 347 PHE 0.020 0.002 PHE E 78 TYR 0.015 0.002 TYR K 534 ARG 0.007 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.342 Fit side-chains REVERT: D 42 TYR cc_start: 0.7753 (t80) cc_final: 0.7423 (t80) REVERT: D 108 LYS cc_start: 0.8478 (mtmt) cc_final: 0.8275 (mtmt) REVERT: E 59 GLU cc_start: 0.8061 (pm20) cc_final: 0.7681 (pm20) REVERT: H 42 TYR cc_start: 0.7633 (t80) cc_final: 0.7319 (t80) REVERT: K 318 MET cc_start: 0.8388 (ppp) cc_final: 0.8154 (ppp) REVERT: K 445 TYR cc_start: 0.8017 (m-10) cc_final: 0.7262 (m-10) REVERT: L 72 ARG cc_start: 0.6737 (tmm-80) cc_final: 0.6511 (tmm-80) outliers start: 14 outliers final: 12 residues processed: 137 average time/residue: 0.3471 time to fit residues: 66.2234 Evaluate side-chains 136 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 404 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 128 optimal weight: 0.0470 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16454 Z= 0.196 Angle : 0.521 8.664 23521 Z= 0.307 Chirality : 0.035 0.152 2705 Planarity : 0.004 0.041 1971 Dihedral : 28.999 138.220 4590 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.41 % Allowed : 10.39 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.19 (0.24), residues: 1201 helix: 1.30 (0.19), residues: 713 sheet: 0.66 (0.59), residues: 80 loop : 0.06 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 182 HIS 0.004 0.001 HIS K 347 PHE 0.009 0.001 PHE G 25 TYR 0.018 0.001 TYR B 88 ARG 0.007 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.469 Fit side-chains REVERT: B 20 LYS cc_start: 0.8491 (tttm) cc_final: 0.8081 (ttmt) REVERT: B 84 MET cc_start: 0.7897 (mmm) cc_final: 0.7682 (mmm) REVERT: D 42 TYR cc_start: 0.7560 (t80) cc_final: 0.7257 (t80) REVERT: D 79 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7649 (mtm-85) REVERT: E 59 GLU cc_start: 0.8045 (pm20) cc_final: 0.7531 (pm20) REVERT: F 77 LYS cc_start: 0.8926 (mttt) cc_final: 0.8555 (mtmt) REVERT: H 42 TYR cc_start: 0.7549 (t80) cc_final: 0.7189 (t80) REVERT: K 318 MET cc_start: 0.8323 (ppp) cc_final: 0.8118 (ppp) REVERT: L 72 ARG cc_start: 0.6695 (tmm-80) cc_final: 0.6489 (tmm-80) outliers start: 14 outliers final: 11 residues processed: 143 average time/residue: 0.3777 time to fit residues: 76.7287 Evaluate side-chains 143 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 132 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 404 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.0030 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16454 Z= 0.210 Angle : 0.521 8.969 23521 Z= 0.307 Chirality : 0.035 0.148 2705 Planarity : 0.004 0.040 1971 Dihedral : 29.003 138.262 4590 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.41 % Allowed : 10.29 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.24 (0.24), residues: 1201 helix: 1.34 (0.19), residues: 715 sheet: 0.65 (0.60), residues: 80 loop : 0.08 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 543 HIS 0.004 0.001 HIS K 347 PHE 0.011 0.001 PHE G 25 TYR 0.016 0.001 TYR D 83 ARG 0.008 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 138 time to evaluate : 1.389 Fit side-chains REVERT: B 20 LYS cc_start: 0.8495 (tttm) cc_final: 0.8081 (ttmt) REVERT: D 42 TYR cc_start: 0.7584 (t80) cc_final: 0.7239 (t80) REVERT: E 59 GLU cc_start: 0.8037 (pm20) cc_final: 0.7516 (pm20) REVERT: F 77 LYS cc_start: 0.8935 (mttt) cc_final: 0.8554 (mtmt) REVERT: H 42 TYR cc_start: 0.7521 (t80) cc_final: 0.7154 (t80) REVERT: K 318 MET cc_start: 0.8320 (ppp) cc_final: 0.8113 (ppp) outliers start: 14 outliers final: 12 residues processed: 145 average time/residue: 0.3404 time to fit residues: 70.2285 Evaluate side-chains 148 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 404 ASN Chi-restraints excluded: chain K residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16454 Z= 0.243 Angle : 0.533 9.308 23521 Z= 0.311 Chirality : 0.035 0.150 2705 Planarity : 0.004 0.041 1971 Dihedral : 29.063 138.081 4590 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.21 % Allowed : 10.60 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.17 (0.24), residues: 1201 helix: 1.31 (0.19), residues: 714 sheet: 0.56 (0.59), residues: 80 loop : 0.01 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 543 HIS 0.005 0.001 HIS K 347 PHE 0.012 0.001 PHE G 25 TYR 0.015 0.001 TYR F 88 ARG 0.008 0.000 ARG E 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.363 Fit side-chains REVERT: B 20 LYS cc_start: 0.8498 (tttm) cc_final: 0.8083 (ttmt) REVERT: B 84 MET cc_start: 0.8238 (tpp) cc_final: 0.8011 (mmm) REVERT: D 42 TYR cc_start: 0.7599 (t80) cc_final: 0.7209 (t80) REVERT: E 59 GLU cc_start: 0.8073 (pm20) cc_final: 0.7532 (pm20) REVERT: F 77 LYS cc_start: 0.8939 (mttt) cc_final: 0.8561 (mtmt) REVERT: H 42 TYR cc_start: 0.7537 (t80) cc_final: 0.7153 (t80) REVERT: K 318 MET cc_start: 0.8352 (ppp) cc_final: 0.8146 (ppp) outliers start: 12 outliers final: 12 residues processed: 143 average time/residue: 0.3405 time to fit residues: 68.3774 Evaluate side-chains 149 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 404 ASN Chi-restraints excluded: chain K residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.111559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.079085 restraints weight = 27031.540| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.04 r_work: 0.3028 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16454 Z= 0.191 Angle : 0.519 9.208 23521 Z= 0.305 Chirality : 0.034 0.146 2705 Planarity : 0.004 0.040 1971 Dihedral : 28.946 138.485 4590 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.11 % Allowed : 10.90 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.28 (0.24), residues: 1201 helix: 1.41 (0.19), residues: 711 sheet: 0.61 (0.60), residues: 80 loop : 0.05 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 543 HIS 0.003 0.001 HIS K 347 PHE 0.008 0.001 PHE D 65 TYR 0.016 0.001 TYR F 88 ARG 0.008 0.000 ARG E 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.49 seconds wall clock time: 53 minutes 49.82 seconds (3229.82 seconds total)