Starting phenix.real_space_refine on Thu Dec 7 23:28:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e1m_27825/12_2023/8e1m_27825_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e1m_27825/12_2023/8e1m_27825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e1m_27825/12_2023/8e1m_27825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e1m_27825/12_2023/8e1m_27825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e1m_27825/12_2023/8e1m_27825_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e1m_27825/12_2023/8e1m_27825_updated.pdb" } resolution = 2.9 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= 0.003 sd= 0.027 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 3 5.49 5 S 29 5.16 5 C 3627 2.51 5 N 980 2.21 5 O 1052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "C TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C ASP 309": "OD1" <-> "OD2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 350": "OE1" <-> "OE2" Residue "C TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 117": "OE1" <-> "OE2" Residue "L GLU 129": "OE1" <-> "OE2" Residue "H ASP 121": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5691 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 955 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 958 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1921 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 104 Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 837 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 901 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.88, per 1000 atoms: 0.68 Number of scatterers: 5691 At special positions: 0 Unit cell: (93.45, 122.85, 79.8, 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 29 16.00 P 3 15.00 O 1052 8.00 N 980 7.00 C 3627 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 112 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 114 " distance=2.03 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: 2.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 8 sheets defined 48.2% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 removed outlier: 3.970A pdb=" N ILE A 14 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 83 removed outlier: 4.199A pdb=" N ARG A 46 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY A 47 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 48 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY A 49 " --> pdb=" O ARG A 46 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A 52 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS A 55 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA A 58 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.604A pdb=" N PHE A 65 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 67 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 69 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 71 " --> pdb=" O TRP A 68 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE A 72 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER A 73 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 75 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 80 " --> pdb=" O CYS A 77 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 101 Processing helix chain 'A' and resid 108 through 137 removed outlier: 3.608A pdb=" N ARG A 112 " --> pdb=" O TRP A 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 122 removed outlier: 3.538A pdb=" N GLN B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 168 Proline residue: B 146 - end of helix Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 196 through 219 removed outlier: 3.654A pdb=" N TYR B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 125 Processing helix chain 'C' and resid 127 through 151 Proline residue: C 149 - end of helix Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.525A pdb=" N LYS C 183 " --> pdb=" O GLN C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 297 through 307 Processing helix chain 'C' and resid 310 through 316 removed outlier: 3.870A pdb=" N LYS C 315 " --> pdb=" O LYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 335 removed outlier: 3.502A pdb=" N VAL C 324 " --> pdb=" O ALA C 320 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 108 No H-bonds generated for 'chain 'H' and resid 106 through 108' Processing helix chain 'H' and resid 119 through 121 No H-bonds generated for 'chain 'H' and resid 119 through 121' Processing sheet with id= A, first strand: chain 'C' and resid 337 through 339 removed outlier: 5.615A pdb=" N LYS C 379 " --> pdb=" O ILE C 385 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE C 385 " --> pdb=" O LYS C 379 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 342 through 347 removed outlier: 6.404A pdb=" N GLN C 372 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE C 346 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG C 370 " --> pdb=" O ILE C 346 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU C 421 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C 403 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE C 419 " --> pdb=" O THR C 403 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.611A pdb=" N VAL C 366 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA C 354 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 364 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 356 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE C 362 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.531A pdb=" N ASP L 94 " --> pdb=" O SER L 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER L 96 " --> pdb=" O SER L 89 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.162A pdb=" N LYS L 127 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL L 33 " --> pdb=" O LYS L 127 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLU L 129 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN L 61 " --> pdb=" O LEU L 70 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU L 70 " --> pdb=" O GLN L 61 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 22 through 27 Processing sheet with id= G, first strand: chain 'H' and resid 130 through 132 removed outlier: 4.112A pdb=" N GLY H 52 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N TRP H 66 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER H 59 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU H 64 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 115 through 117 removed outlier: 3.674A pdb=" N TYR H 125 " --> pdb=" O ARG H 116 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 918 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1826 1.34 - 1.46: 1421 1.46 - 1.59: 2506 1.59 - 1.71: 6 1.71 - 1.84: 46 Bond restraints: 5805 Sorted by residual: bond pdb=" CA7 CDL A 301 " pdb=" OA8 CDL A 301 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 bond pdb=" CB7 CDL A 301 " pdb=" OB8 CDL A 301 " ideal model delta sigma weight residual 1.334 1.446 -0.112 1.10e-02 8.26e+03 1.04e+02 bond pdb=" CB5 CDL A 301 " pdb=" OB6 CDL A 301 " ideal model delta sigma weight residual 1.342 1.450 -0.108 1.50e-02 4.44e+03 5.23e+01 bond pdb=" CA5 CDL A 301 " pdb=" OA6 CDL A 301 " ideal model delta sigma weight residual 1.342 1.449 -0.107 1.50e-02 4.44e+03 5.12e+01 bond pdb=" C8 PTY B 301 " pdb=" O7 PTY B 301 " ideal model delta sigma weight residual 1.331 1.454 -0.123 2.00e-02 2.50e+03 3.77e+01 ... (remaining 5800 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.32: 99 105.32 - 112.50: 3006 112.50 - 119.68: 1733 119.68 - 126.85: 2926 126.85 - 134.03: 76 Bond angle restraints: 7840 Sorted by residual: angle pdb=" C51 CDL A 301 " pdb=" CB5 CDL A 301 " pdb=" OB6 CDL A 301 " ideal model delta sigma weight residual 111.33 121.20 -9.87 1.32e+00 5.72e-01 5.58e+01 angle pdb=" C11 CDL A 301 " pdb=" CA5 CDL A 301 " pdb=" OA6 CDL A 301 " ideal model delta sigma weight residual 111.33 120.23 -8.90 1.32e+00 5.72e-01 4.53e+01 angle pdb=" C31 CDL A 301 " pdb=" CA7 CDL A 301 " pdb=" OA8 CDL A 301 " ideal model delta sigma weight residual 111.64 121.14 -9.50 1.65e+00 3.69e-01 3.33e+01 angle pdb=" OB6 CDL A 301 " pdb=" CB5 CDL A 301 " pdb=" OB7 CDL A 301 " ideal model delta sigma weight residual 123.92 118.41 5.51 1.00e+00 9.92e-01 3.01e+01 angle pdb=" C71 CDL A 301 " pdb=" CB7 CDL A 301 " pdb=" OB8 CDL A 301 " ideal model delta sigma weight residual 111.64 120.27 -8.63 1.65e+00 3.69e-01 2.75e+01 ... (remaining 7835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 3219 23.84 - 47.68: 188 47.68 - 71.52: 24 71.52 - 95.36: 5 95.36 - 119.20: 1 Dihedral angle restraints: 3437 sinusoidal: 1309 harmonic: 2128 Sorted by residual: dihedral pdb=" CB CYS A 10 " pdb=" SG CYS A 10 " pdb=" SG CYS A 77 " pdb=" CB CYS A 77 " ideal model delta sinusoidal sigma weight residual -86.00 -124.76 38.76 1 1.00e+01 1.00e-02 2.11e+01 dihedral pdb=" N1 PTY B 301 " pdb=" C2 PTY B 301 " pdb=" C3 PTY B 301 " pdb=" O11 PTY B 301 " ideal model delta sinusoidal sigma weight residual 65.33 -53.87 119.20 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" CA ILE B 166 " pdb=" C ILE B 166 " pdb=" N ASP B 167 " pdb=" CA ASP B 167 " ideal model delta harmonic sigma weight residual 180.00 160.55 19.45 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 3434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 508 0.031 - 0.063: 235 0.063 - 0.094: 68 0.094 - 0.125: 38 0.125 - 0.156: 7 Chirality restraints: 856 Sorted by residual: chirality pdb=" CA ILE L 72 " pdb=" N ILE L 72 " pdb=" C ILE L 72 " pdb=" CB ILE L 72 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA ILE C 362 " pdb=" N ILE C 362 " pdb=" C ILE C 362 " pdb=" CB ILE C 362 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CA ILE L 130 " pdb=" N ILE L 130 " pdb=" C ILE L 130 " pdb=" CB ILE L 130 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 853 not shown) Planarity restraints: 1003 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 146 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 8 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 9 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 67 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO L 68 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO L 68 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 68 " 0.021 5.00e-02 4.00e+02 ... (remaining 1000 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 272 2.72 - 3.27: 5752 3.27 - 3.81: 9387 3.81 - 4.36: 12185 4.36 - 4.90: 20863 Nonbonded interactions: 48459 Sorted by model distance: nonbonded pdb=" O LEU B 97 " pdb=" OG1 THR B 101 " model vdw 2.179 2.440 nonbonded pdb=" OD1 ASP L 50 " pdb=" OG SER L 55 " model vdw 2.181 2.440 nonbonded pdb=" OG SER L 48 " pdb=" OD2 ASP L 50 " model vdw 2.185 2.440 nonbonded pdb=" NZ LYS L 63 " pdb=" O ASP L 105 " model vdw 2.231 2.520 nonbonded pdb=" NZ LYS C 278 " pdb=" O PRO C 282 " model vdw 2.249 2.520 ... (remaining 48454 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.000 Extract box with map and model: 3.580 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.200 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 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 : 0.007 0.123 5805 Z= 0.436 Angle : 0.765 10.945 7840 Z= 0.411 Chirality : 0.043 0.156 856 Planarity : 0.004 0.049 1003 Dihedral : 14.841 119.204 2076 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: -0.83 (0.31), residues: 748 helix: -0.30 (0.26), residues: 370 sheet: -0.54 (0.45), residues: 142 loop : -0.63 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 66 HIS 0.003 0.001 HIS B 173 PHE 0.012 0.002 PHE A 96 TYR 0.016 0.002 TYR H 117 ARG 0.004 0.001 ARG L 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 111 average time/residue: 1.1400 time to fit residues: 132.5084 Evaluate side-chains 85 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.664 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.0908 time to fit residues: 1.0692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.0370 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN H 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5805 Z= 0.221 Angle : 0.572 8.216 7840 Z= 0.294 Chirality : 0.042 0.149 856 Planarity : 0.005 0.045 1003 Dihedral : 10.332 64.696 916 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.85 % Allowed : 10.89 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.41 (0.31), residues: 748 helix: 1.07 (0.26), residues: 369 sheet: -0.37 (0.46), residues: 135 loop : -0.41 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.003 0.001 HIS A 33 PHE 0.017 0.001 PHE A 96 TYR 0.012 0.001 TYR H 117 ARG 0.009 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 95 time to evaluate : 0.636 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 1.1020 time to fit residues: 111.1306 Evaluate side-chains 92 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 6 average time/residue: 0.3898 time to fit residues: 3.4775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5805 Z= 0.186 Angle : 0.520 9.231 7840 Z= 0.266 Chirality : 0.041 0.149 856 Planarity : 0.004 0.040 1003 Dihedral : 9.559 64.138 916 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.48 % Allowed : 14.76 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.98 (0.32), residues: 748 helix: 1.68 (0.27), residues: 370 sheet: -0.24 (0.45), residues: 135 loop : -0.32 (0.43), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 32 HIS 0.002 0.001 HIS A 33 PHE 0.014 0.001 PHE A 96 TYR 0.012 0.001 TYR H 117 ARG 0.007 0.000 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.662 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 97 average time/residue: 1.0443 time to fit residues: 106.7514 Evaluate side-chains 89 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.639 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 2 average time/residue: 0.1225 time to fit residues: 1.1887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5805 Z= 0.174 Angle : 0.509 8.800 7840 Z= 0.256 Chirality : 0.041 0.196 856 Planarity : 0.003 0.041 1003 Dihedral : 9.071 63.873 916 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.95 % Allowed : 14.94 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 (0.32), residues: 748 helix: 1.90 (0.27), residues: 372 sheet: 0.04 (0.46), residues: 135 loop : -0.23 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 32 HIS 0.003 0.001 HIS A 33 PHE 0.013 0.001 PHE A 96 TYR 0.015 0.001 TYR B 159 ARG 0.005 0.000 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.598 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 100 average time/residue: 1.0530 time to fit residues: 110.8532 Evaluate side-chains 91 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.700 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 1.0615 time to fit residues: 3.1294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 0 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5805 Z= 0.196 Angle : 0.533 9.128 7840 Z= 0.267 Chirality : 0.042 0.256 856 Planarity : 0.003 0.043 1003 Dihedral : 8.881 64.221 916 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.03 % Allowed : 15.13 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.47 (0.32), residues: 748 helix: 2.10 (0.27), residues: 368 sheet: 0.22 (0.46), residues: 135 loop : -0.26 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 32 HIS 0.003 0.001 HIS A 33 PHE 0.013 0.001 PHE A 96 TYR 0.020 0.001 TYR B 159 ARG 0.003 0.000 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.678 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 100 average time/residue: 1.0763 time to fit residues: 113.1530 Evaluate side-chains 91 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0532 time to fit residues: 0.9514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8284 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5805 Z= 0.174 Angle : 0.527 9.905 7840 Z= 0.263 Chirality : 0.041 0.182 856 Planarity : 0.003 0.041 1003 Dihedral : 8.631 64.504 916 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.21 % Allowed : 16.61 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.59 (0.32), residues: 748 helix: 2.18 (0.27), residues: 370 sheet: 0.33 (0.46), residues: 135 loop : -0.23 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 32 HIS 0.003 0.001 HIS A 33 PHE 0.012 0.001 PHE A 96 TYR 0.017 0.001 TYR B 159 ARG 0.001 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.677 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 102 average time/residue: 1.0663 time to fit residues: 114.4406 Evaluate side-chains 95 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.645 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0528 time to fit residues: 0.9349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 50.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5805 Z= 0.176 Angle : 0.542 10.305 7840 Z= 0.267 Chirality : 0.041 0.161 856 Planarity : 0.003 0.040 1003 Dihedral : 8.455 64.379 916 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.40 % Allowed : 16.79 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.67 (0.32), residues: 748 helix: 2.25 (0.27), residues: 369 sheet: 0.37 (0.45), residues: 135 loop : -0.19 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 32 HIS 0.003 0.001 HIS A 33 PHE 0.012 0.001 PHE A 96 TYR 0.016 0.001 TYR B 159 ARG 0.001 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.664 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 99 average time/residue: 1.0515 time to fit residues: 109.6125 Evaluate side-chains 97 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.608 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.8579 time to fit residues: 2.5907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN L 62 GLN H 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5805 Z= 0.261 Angle : 0.582 10.069 7840 Z= 0.289 Chirality : 0.042 0.167 856 Planarity : 0.003 0.041 1003 Dihedral : 8.683 64.441 916 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.66 % Allowed : 17.71 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.71 (0.32), residues: 748 helix: 2.22 (0.27), residues: 371 sheet: 0.42 (0.46), residues: 135 loop : -0.10 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.004 0.001 HIS A 33 PHE 0.012 0.001 PHE A 96 TYR 0.016 0.001 TYR B 159 ARG 0.002 0.000 ARG L 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.650 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 97 average time/residue: 1.0577 time to fit residues: 107.9832 Evaluate side-chains 94 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.8683 time to fit residues: 2.6836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN C 408 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5805 Z= 0.174 Angle : 0.565 11.220 7840 Z= 0.277 Chirality : 0.041 0.145 856 Planarity : 0.003 0.042 1003 Dihedral : 8.329 65.078 916 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.11 % Allowed : 18.63 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.80 (0.32), residues: 748 helix: 2.29 (0.27), residues: 371 sheet: 0.47 (0.45), residues: 135 loop : -0.05 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 32 HIS 0.002 0.001 HIS A 33 PHE 0.012 0.001 PHE A 96 TYR 0.020 0.001 TYR B 159 ARG 0.002 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.681 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 98 average time/residue: 1.0172 time to fit residues: 105.4274 Evaluate side-chains 93 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.666 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.8690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.0470 chunk 48 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 0.4980 chunk 58 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5805 Z= 0.149 Angle : 0.576 11.809 7840 Z= 0.284 Chirality : 0.040 0.138 856 Planarity : 0.004 0.042 1003 Dihedral : 8.016 64.725 916 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.11 % Allowed : 19.00 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.83 (0.31), residues: 748 helix: 2.32 (0.27), residues: 370 sheet: 0.56 (0.45), residues: 135 loop : -0.07 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 32 HIS 0.002 0.001 HIS A 33 PHE 0.012 0.001 PHE A 96 TYR 0.016 0.001 TYR B 159 ARG 0.002 0.000 ARG C 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.692 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 1.1439 time to fit residues: 117.6417 Evaluate side-chains 92 residues out of total 613 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 1.7258 time to fit residues: 2.6370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 0.0000 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.0270 chunk 60 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 408 GLN L 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.084072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.062757 restraints weight = 12583.795| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.55 r_work: 0.2827 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5805 Z= 0.189 Angle : 0.597 11.538 7840 Z= 0.298 Chirality : 0.041 0.150 856 Planarity : 0.004 0.041 1003 Dihedral : 7.997 64.631 916 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.74 % Allowed : 19.93 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 1.88 (0.31), residues: 748 helix: 2.37 (0.27), residues: 370 sheet: 0.58 (0.45), residues: 135 loop : -0.07 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.003 0.001 HIS A 33 PHE 0.013 0.001 PHE A 96 TYR 0.014 0.001 TYR B 159 ARG 0.002 0.000 ARG A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.62 seconds wall clock time: 44 minutes 11.65 seconds (2651.65 seconds total)