Starting phenix.real_space_refine (version: dev) on Tue Feb 21 19:24:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/02_2023/7k6q_22692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/02_2023/7k6q_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_2023/7k6q_22692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/02_2023/7k6q_22692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/02_2023/7k6q_22692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k6q_22692/02_2023/7k6q_22692_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 9.09, per 1000 atoms: 0.58 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: 8.15 Conformation dependent library (CDL) restraints added in 1.5 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: 6.82 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: 6.88 Time building geometry restraints manager: 8.55 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: 7224 29.40 - 58.81: 1525 58.81 - 88.21: 93 88.21 - 117.62: 1 117.62 - 147.02: 3 Dihedral angle restraints: 8846 sinusoidal: 5259 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 8843 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 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. 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: 1.130 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: 0.010 Extract box with map and model: 7.490 Check model and map are aligned: 0.220 Process input model: 50.050 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.160 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 24.922 147.020 6528 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 % 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 *********************** 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 : 1.393 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.3829 time to fit residues: 91.2007 Evaluate side-chains 133 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7216 ------------------------------------------------------------------------------- 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: 2.9990 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: 1.9186 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 16454 Z= 0.339 Angle : 0.585 6.063 23521 Z= 0.342 Chirality : 0.039 0.151 2705 Planarity : 0.005 0.048 1971 Dihedral : 29.678 140.213 4294 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.11 % 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: 1.22 (0.24), residues: 1201 helix: 1.40 (0.19), residues: 717 sheet: 0.28 (0.59), residues: 81 loop : 0.01 (0.29), residues: 403 *********************** 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 152 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 1.443 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 147 average time/residue: 0.3562 time to fit residues: 72.4695 Evaluate side-chains 138 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.339 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1409 time to fit residues: 4.3207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 143 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1587 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= 0.226 Angle : 0.529 6.578 23521 Z= 0.314 Chirality : 0.035 0.146 2705 Planarity : 0.005 0.043 1971 Dihedral : 29.572 140.164 4294 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.71 % 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: 1.19 (0.24), residues: 1201 helix: 1.31 (0.19), residues: 715 sheet: 0.45 (0.59), residues: 81 loop : 0.08 (0.29), residues: 405 *********************** 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 142 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 1.434 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 140 average time/residue: 0.3426 time to fit residues: 67.2156 Evaluate side-chains 129 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3183 time to fit residues: 2.5641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** H 84 ASN K 316 ASN ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1782 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= 0.215 Angle : 0.517 6.655 23521 Z= 0.308 Chirality : 0.035 0.148 2705 Planarity : 0.005 0.041 1971 Dihedral : 29.540 140.149 4294 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 1.01 % 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: 0.57 (0.60), residues: 81 loop : 0.12 (0.29), residues: 404 *********************** 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 142 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.444 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 0.3497 time to fit residues: 67.4320 Evaluate side-chains 132 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 1.381 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1451 time to fit residues: 3.3905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 120 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 126 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1913 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= 0.222 Angle : 0.519 7.344 23521 Z= 0.308 Chirality : 0.035 0.149 2705 Planarity : 0.004 0.041 1971 Dihedral : 29.579 139.104 4294 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.30 % 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: 1.21 (0.24), residues: 1201 helix: 1.32 (0.19), residues: 716 sheet: 0.61 (0.60), residues: 81 loop : 0.07 (0.29), residues: 404 *********************** 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 134 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.386 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 133 average time/residue: 0.3516 time to fit residues: 65.2100 Evaluate side-chains 128 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1359 time to fit residues: 1.8888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.7980 chunk 127 optimal weight: 0.0040 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.7204 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16454 Z= 0.186 Angle : 0.505 7.455 23521 Z= 0.300 Chirality : 0.034 0.147 2705 Planarity : 0.004 0.040 1971 Dihedral : 29.452 139.130 4294 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.81 % 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: 1.34 (0.24), residues: 1201 helix: 1.46 (0.20), residues: 709 sheet: 0.65 (0.60), residues: 81 loop : 0.08 (0.29), residues: 411 *********************** 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 141 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 1.420 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 138 average time/residue: 0.3432 time to fit residues: 67.3828 Evaluate side-chains 133 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1423 time to fit residues: 2.5573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 4.9990 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: 5.9990 chunk 88 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN K 211 GLN ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.010 0.070 16454 Z= 0.611 Angle : 0.702 8.975 23521 Z= 0.395 Chirality : 0.045 0.170 2705 Planarity : 0.006 0.046 1971 Dihedral : 30.561 139.698 4294 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.81 % 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: 0.54 (0.24), residues: 1201 helix: 0.83 (0.19), residues: 717 sheet: 0.11 (0.59), residues: 83 loop : -0.27 (0.30), residues: 401 *********************** 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 142 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.438 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 138 average time/residue: 0.3609 time to fit residues: 69.4401 Evaluate side-chains 136 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 1.326 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1332 time to fit residues: 3.1238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 128 optimal weight: 0.0030 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN K 211 GLN ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 16454 Z= 0.203 Angle : 0.532 7.821 23521 Z= 0.313 Chirality : 0.035 0.150 2705 Planarity : 0.004 0.043 1971 Dihedral : 29.896 138.500 4294 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.10 % 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: 1.01 (0.24), residues: 1201 helix: 1.20 (0.19), residues: 710 sheet: 0.53 (0.59), residues: 80 loop : -0.09 (0.29), residues: 411 *********************** 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 137 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.478 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.3369 time to fit residues: 64.5349 Evaluate side-chains 132 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1325 time to fit residues: 1.7947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2318 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= 0.209 Angle : 0.533 9.188 23521 Z= 0.312 Chirality : 0.035 0.150 2705 Planarity : 0.004 0.042 1971 Dihedral : 29.778 138.979 4294 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.40 % 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: 1.34 (0.20), residues: 709 sheet: 0.57 (0.59), residues: 80 loop : -0.02 (0.29), residues: 412 *********************** 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 140 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 1.528 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 138 average time/residue: 0.3605 time to fit residues: 70.4767 Evaluate side-chains 136 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 135 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1461 time to fit residues: 2.0558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 0.0170 chunk 92 optimal weight: 4.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16454 Z= 0.197 Angle : 0.530 9.356 23521 Z= 0.309 Chirality : 0.034 0.148 2705 Planarity : 0.004 0.042 1971 Dihedral : 29.676 139.276 4294 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 0.20 % 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: 1.22 (0.24), residues: 1201 helix: 1.38 (0.20), residues: 710 sheet: 0.54 (0.59), residues: 80 loop : -0.00 (0.29), residues: 411 ********************** 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 142 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 1.311 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 141 average time/residue: 0.3406 time to fit residues: 67.8028 Evaluate side-chains 138 residues out of total 1058 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1320 time to fit residues: 1.8789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 106 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 101 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.112300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079685 restraints weight = 27261.643| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.08 r_work: 0.3026 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3750 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3750 r_free = 0.3750 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3747 r_free = 0.3747 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16454 Z= 0.185 Angle : 0.524 8.991 23521 Z= 0.307 Chirality : 0.034 0.147 2705 Planarity : 0.004 0.041 1971 Dihedral : 29.608 139.316 4294 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.00 % 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: 1.44 (0.20), residues: 710 sheet: 0.57 (0.59), residues: 80 loop : -0.02 (0.29), residues: 411 =============================================================================== Job complete usr+sys time: 2606.08 seconds wall clock time: 48 minutes 9.73 seconds (2889.73 seconds total)