Starting phenix.real_space_refine on Sat Mar 16 20:00:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9m_25762/03_2024/7t9m_25762_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9m_25762/03_2024/7t9m_25762.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/7t9m_25762/03_2024/7t9m_25762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9m_25762/03_2024/7t9m_25762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9m_25762/03_2024/7t9m_25762_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9m_25762/03_2024/7t9m_25762_neut_trim.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.023 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 S 50 5.16 5 C 5039 2.51 5 N 1255 2.21 5 O 1483 1.98 5 H 7719 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 184": "OE1" <-> "OE2" Residue "L PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "R ASP 36": "OD1" <-> "OD2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "R PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 219": "OD1" <-> "OD2" Residue "R PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 696": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15546 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 3219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 3219 Classifications: {'peptide': 217} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 205} Chain: "L" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3186 Classifications: {'peptide': 213} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "R" Number of atoms: 9071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 9071 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 27, 'TRANS': 537} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.03, per 1000 atoms: 0.45 Number of scatterers: 15546 At special positions: 0 Unit cell: (66.332, 131.376, 148.764, 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 50 16.00 O 1483 8.00 N 1255 7.00 C 5039 6.00 H 7719 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS L 213 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.03 Simple disulfide: pdb=" SG CYS R 29 " - pdb=" SG CYS R 41 " distance=2.03 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 408 " distance=2.03 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN R 198 " " NAG R 801 " - " ASN R 177 " " NAG R 802 " - " ASN R 77 " " NAG R 803 " - " ASN R 113 " Time building additional restraints: 13.38 Conformation dependent library (CDL) restraints added in 1.7 seconds 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1890 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 16 sheets defined 30.3% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.663A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 140 removed outlier: 3.761A pdb=" N THR H 139 " --> pdb=" O GLY H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 removed outlier: 3.879A pdb=" N SER H 168 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.997A pdb=" N ALA L 82 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 127 Processing helix chain 'L' and resid 181 through 188 removed outlier: 4.077A pdb=" N HIS L 188 " --> pdb=" O GLU L 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 269 removed outlier: 4.134A pdb=" N SER R 268 " --> pdb=" O PRO R 264 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 264 through 269' Processing helix chain 'R' and resid 279 through 288 removed outlier: 4.467A pdb=" N CYS R 283 " --> pdb=" O TYR R 279 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N CYS R 284 " --> pdb=" O PRO R 280 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA R 285 " --> pdb=" O SER R 281 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE R 286 " --> pdb=" O HIS R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 442 Processing helix chain 'R' and resid 447 through 477 Processing helix chain 'R' and resid 480 through 483 Processing helix chain 'R' and resid 484 through 491 Processing helix chain 'R' and resid 491 through 525 removed outlier: 3.684A pdb=" N ASN R 495 " --> pdb=" O GLY R 491 " (cutoff:3.500A) Processing helix chain 'R' and resid 534 through 555 removed outlier: 3.840A pdb=" N LEU R 555 " --> pdb=" O LEU R 551 " (cutoff:3.500A) Processing helix chain 'R' and resid 556 through 559 Processing helix chain 'R' and resid 576 through 610 Processing helix chain 'R' and resid 616 through 650 removed outlier: 3.974A pdb=" N ILE R 635 " --> pdb=" O PHE R 631 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N CYS R 636 " --> pdb=" O THR R 632 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET R 637 " --> pdb=" O ASP R 633 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA R 638 " --> pdb=" O PHE R 634 " (cutoff:3.500A) Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 655 through 682 removed outlier: 4.031A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) Proline residue: R 668 - end of helix removed outlier: 4.606A pdb=" N SER R 671 " --> pdb=" O TYR R 667 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N CYS R 672 " --> pdb=" O PRO R 668 " (cutoff:3.500A) Proline residue: R 675 - end of helix removed outlier: 3.669A pdb=" N THR R 682 " --> pdb=" O TYR R 678 " (cutoff:3.500A) Processing helix chain 'R' and resid 682 through 693 removed outlier: 4.391A pdb=" N GLN R 686 " --> pdb=" O THR R 682 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.579A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.579A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.686A pdb=" N TYR H 32 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASN H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.698A pdb=" N VAL H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.628A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR H 182 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.628A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N TYR H 182 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 158 through 160 removed outlier: 3.667A pdb=" N LYS H 215 " --> pdb=" O CYS H 202 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL H 204 " --> pdb=" O VAL H 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.566A pdb=" N THR L 73 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB1, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.605A pdb=" N ASN L 52 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 115 through 117 removed outlier: 4.013A pdb=" N VAL L 132 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N TYR L 172 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 152 through 154 removed outlier: 3.631A pdb=" N ARG L 154 " --> pdb=" O TRP L 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP L 147 " --> pdb=" O ARG L 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 148 " --> pdb=" O THR L 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 56 through 58 removed outlier: 6.467A pdb=" N LEU R 57 " --> pdb=" O TYR R 82 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER R 84 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE R 81 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ARG R 109 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL R 83 " --> pdb=" O ARG R 109 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE R 106 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N PHE R 134 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE R 108 " --> pdb=" O PHE R 134 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE R 154 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LYS R 183 " --> pdb=" O PHE R 154 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU R 156 " --> pdb=" O LYS R 183 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LEU R 180 " --> pdb=" O LEU R 202 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA R 204 " --> pdb=" O LEU R 180 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N ASP R 232 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL R 205 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU R 231 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU R 252 " --> pdb=" O ASP R 276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 66 through 67 removed outlier: 3.677A pdb=" N ILE R 67 " --> pdb=" O GLN R 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 97 through 98 removed outlier: 6.188A pdb=" N PHE R 97 " --> pdb=" O LYS R 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'R' and resid 166 through 167 removed outlier: 3.620A pdb=" N ILE R 167 " --> pdb=" O SER R 191 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 933 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.95 Time building geometry restraints manager: 13.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7705 1.02 - 1.22: 34 1.22 - 1.42: 3324 1.42 - 1.62: 4608 1.62 - 1.82: 68 Bond restraints: 15739 Sorted by residual: bond pdb=" ND2 ASN R 135 " pdb="HD21 ASN R 135 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.65e+01 bond pdb=" ND2 ASN R 135 " pdb="HD22 ASN R 135 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN R 650 " pdb="HD22 ASN R 650 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN R 650 " pdb="HD21 ASN R 650 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" N THR R 399 " pdb=" CA THR R 399 " ideal model delta sigma weight residual 1.463 1.504 -0.041 6.90e-03 2.10e+04 3.56e+01 ... (remaining 15734 not shown) Histogram of bond angle deviations from ideal: 95.06 - 104.29: 146 104.29 - 113.51: 18910 113.51 - 122.73: 7286 122.73 - 131.95: 2051 131.95 - 141.18: 19 Bond angle restraints: 28412 Sorted by residual: angle pdb=" N THR R 399 " pdb=" CA THR R 399 " pdb=" C THR R 399 " ideal model delta sigma weight residual 112.17 125.36 -13.19 1.36e+00 5.41e-01 9.40e+01 angle pdb=" C CYS R 398 " pdb=" N THR R 399 " pdb=" CA THR R 399 " ideal model delta sigma weight residual 119.83 128.18 -8.35 1.11e+00 8.12e-01 5.66e+01 angle pdb=" C TYR L 139 " pdb=" N PRO L 140 " pdb=" CA PRO L 140 " ideal model delta sigma weight residual 119.98 111.67 8.31 1.16e+00 7.43e-01 5.13e+01 angle pdb=" N TYR L 93 " pdb=" CA TYR L 93 " pdb=" C TYR L 93 " ideal model delta sigma weight residual 109.81 125.01 -15.20 2.21e+00 2.05e-01 4.73e+01 angle pdb=" N ASN L 137 " pdb=" CA ASN L 137 " pdb=" C ASN L 137 " ideal model delta sigma weight residual 111.24 120.27 -9.03 1.38e+00 5.25e-01 4.28e+01 ... (remaining 28407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 6830 17.71 - 35.43: 599 35.43 - 53.14: 144 53.14 - 70.86: 34 70.86 - 88.57: 12 Dihedral angle restraints: 7619 sinusoidal: 4094 harmonic: 3525 Sorted by residual: dihedral pdb=" N TYR L 93 " pdb=" C TYR L 93 " pdb=" CA TYR L 93 " pdb=" CB TYR L 93 " ideal model delta harmonic sigma weight residual 122.80 150.70 -27.90 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" C TYR L 93 " pdb=" N TYR L 93 " pdb=" CA TYR L 93 " pdb=" CB TYR L 93 " ideal model delta harmonic sigma weight residual -122.60 -150.02 27.42 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" CB CYS R 494 " pdb=" SG CYS R 494 " pdb=" SG CYS R 569 " pdb=" CB CYS R 569 " ideal model delta sinusoidal sigma weight residual -86.00 -132.37 46.37 1 1.00e+01 1.00e-02 2.98e+01 ... (remaining 7616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.256: 1282 0.256 - 0.513: 2 0.513 - 0.769: 2 0.769 - 1.025: 0 1.025 - 1.282: 1 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CA TYR L 93 " pdb=" N TYR L 93 " pdb=" C TYR L 93 " pdb=" CB TYR L 93 " both_signs ideal model delta sigma weight residual False 2.51 1.23 1.28 2.00e-01 2.50e+01 4.11e+01 chirality pdb=" CA TYR L 139 " pdb=" N TYR L 139 " pdb=" C TYR L 139 " pdb=" CB TYR L 139 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" CA THR R 399 " pdb=" N THR R 399 " pdb=" C THR R 399 " pdb=" CB THR R 399 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.58 2.00e-01 2.50e+01 8.36e+00 ... (remaining 1284 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 137 " -0.297 2.00e-02 2.50e+03 4.19e-01 2.64e+03 pdb=" CG ASN L 137 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN L 137 " 0.317 2.00e-02 2.50e+03 pdb=" ND2 ASN L 137 " -0.017 2.00e-02 2.50e+03 pdb="HD21 ASN L 137 " -0.677 2.00e-02 2.50e+03 pdb="HD22 ASN L 137 " 0.638 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 135 " -0.270 2.00e-02 2.50e+03 2.85e-01 1.22e+03 pdb=" CG ASN R 135 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN R 135 " 0.257 2.00e-02 2.50e+03 pdb=" ND2 ASN R 135 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN R 135 " 0.410 2.00e-02 2.50e+03 pdb="HD22 ASN R 135 " -0.423 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 650 " -0.087 2.00e-02 2.50e+03 8.51e-02 1.09e+02 pdb=" CG ASN R 650 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN R 650 " 0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN R 650 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN R 650 " 0.119 2.00e-02 2.50e+03 pdb="HD22 ASN R 650 " -0.122 2.00e-02 2.50e+03 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1372 2.23 - 2.82: 33260 2.82 - 3.41: 39682 3.41 - 4.01: 53816 4.01 - 4.60: 82035 Nonbonded interactions: 210165 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" H GLY L 100 " model vdw 1.637 1.850 nonbonded pdb=" OE1 GLU L 184 " pdb="HH12 ARG L 187 " model vdw 1.682 1.850 nonbonded pdb=" HG3 PRO L 8 " pdb=" HE2 MET L 11 " model vdw 1.696 2.440 nonbonded pdb=" OD1 ASP R 232 " pdb=" HG SER R 234 " model vdw 1.729 1.850 nonbonded pdb=" HE2 HIS H 35 " pdb=" OE1 GLU H 99 " model vdw 1.729 1.850 ... (remaining 210160 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.230 Extract box with map and model: 18.650 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 52.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.005 0.066 8020 Z= 0.355 Angle : 0.878 15.204 10924 Z= 0.485 Chirality : 0.065 1.282 1287 Planarity : 0.005 0.065 1350 Dihedral : 12.803 88.199 2935 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.91 % Allowed : 0.79 % Favored : 98.30 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 987 helix: 1.73 (0.31), residues: 258 sheet: -0.33 (0.35), residues: 253 loop : -0.51 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 546 HIS 0.002 0.001 HIS R 537 PHE 0.022 0.001 PHE R 434 TYR 0.044 0.002 TYR L 93 ARG 0.003 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 89 average time/residue: 0.3873 time to fit residues: 48.5739 Evaluate side-chains 64 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 171 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8020 Z= 0.220 Angle : 0.562 9.468 10924 Z= 0.297 Chirality : 0.042 0.297 1287 Planarity : 0.004 0.057 1350 Dihedral : 5.790 55.614 1176 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.57 % Allowed : 5.33 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 987 helix: 2.08 (0.32), residues: 257 sheet: -0.23 (0.34), residues: 261 loop : -0.31 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 546 HIS 0.003 0.001 HIS L 91 PHE 0.014 0.001 PHE R 434 TYR 0.039 0.001 TYR L 93 ARG 0.004 0.000 ARG L 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 64 average time/residue: 0.3432 time to fit residues: 33.0331 Evaluate side-chains 62 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 626 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.2980 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8020 Z= 0.275 Angle : 0.538 9.445 10924 Z= 0.278 Chirality : 0.041 0.245 1287 Planarity : 0.003 0.036 1350 Dihedral : 5.281 55.046 1174 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.79 % Allowed : 5.90 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.28), residues: 987 helix: 2.23 (0.31), residues: 262 sheet: -0.27 (0.35), residues: 249 loop : -0.32 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 546 HIS 0.002 0.001 HIS L 91 PHE 0.014 0.001 PHE R 434 TYR 0.022 0.001 TYR L 93 ARG 0.002 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 93 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6957 (t80) outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.3307 time to fit residues: 31.5337 Evaluate side-chains 62 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 93 TYR Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 543 VAL Chi-restraints excluded: chain R residue 599 CYS Chi-restraints excluded: chain R residue 626 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 25 optimal weight: 0.0870 chunk 78 optimal weight: 9.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8020 Z= 0.198 Angle : 0.494 6.223 10924 Z= 0.256 Chirality : 0.041 0.202 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.877 53.370 1174 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.57 % Allowed : 7.03 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 987 helix: 2.33 (0.31), residues: 262 sheet: -0.29 (0.34), residues: 260 loop : -0.20 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 161 HIS 0.002 0.000 HIS L 91 PHE 0.021 0.001 PHE R 416 TYR 0.020 0.001 TYR L 93 ARG 0.003 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.3418 time to fit residues: 31.2352 Evaluate side-chains 59 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 599 CYS Chi-restraints excluded: chain R residue 626 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8020 Z= 0.355 Angle : 0.555 8.505 10924 Z= 0.287 Chirality : 0.041 0.196 1287 Planarity : 0.003 0.035 1350 Dihedral : 5.135 48.605 1174 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.13 % Allowed : 6.92 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.28), residues: 987 helix: 2.40 (0.32), residues: 257 sheet: -0.43 (0.34), residues: 250 loop : -0.46 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.003 0.001 HIS L 91 PHE 0.011 0.001 PHE R 434 TYR 0.038 0.001 TYR L 93 ARG 0.003 0.000 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 453 MET cc_start: 0.8008 (tpt) cc_final: 0.7769 (tmm) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.3424 time to fit residues: 32.0663 Evaluate side-chains 62 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 136 ASN Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 543 VAL Chi-restraints excluded: chain R residue 599 CYS Chi-restraints excluded: chain R residue 626 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8020 Z= 0.247 Angle : 0.506 7.168 10924 Z= 0.262 Chirality : 0.041 0.181 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.835 46.759 1174 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.91 % Allowed : 8.50 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.28), residues: 987 helix: 2.45 (0.31), residues: 257 sheet: -0.37 (0.34), residues: 248 loop : -0.41 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.004 0.001 HIS R 32 PHE 0.012 0.001 PHE R 434 TYR 0.029 0.001 TYR L 93 ARG 0.003 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 61 average time/residue: 0.2901 time to fit residues: 27.9192 Evaluate side-chains 61 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 543 VAL Chi-restraints excluded: chain R residue 599 CYS Chi-restraints excluded: chain R residue 626 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8020 Z= 0.164 Angle : 0.485 7.698 10924 Z= 0.248 Chirality : 0.041 0.147 1287 Planarity : 0.003 0.037 1350 Dihedral : 4.552 44.890 1174 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.57 % Allowed : 9.18 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.28), residues: 987 helix: 2.54 (0.31), residues: 257 sheet: -0.33 (0.33), residues: 261 loop : -0.28 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.002 0.000 HIS L 91 PHE 0.009 0.001 PHE R 434 TYR 0.012 0.001 TYR L 139 ARG 0.002 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 89 GLU cc_start: 0.6613 (tp30) cc_final: 0.6332 (tp30) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 0.2712 time to fit residues: 25.7648 Evaluate side-chains 60 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 136 ASN Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 626 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8020 Z= 0.340 Angle : 0.535 8.042 10924 Z= 0.277 Chirality : 0.041 0.176 1287 Planarity : 0.003 0.036 1350 Dihedral : 4.824 44.162 1174 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.91 % Allowed : 9.18 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.28), residues: 987 helix: 2.47 (0.31), residues: 260 sheet: -0.49 (0.32), residues: 263 loop : -0.36 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 36 HIS 0.003 0.001 HIS L 91 PHE 0.011 0.001 PHE R 666 TYR 0.020 0.001 TYR L 93 ARG 0.002 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 8 residues processed: 61 average time/residue: 0.2938 time to fit residues: 28.3518 Evaluate side-chains 62 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 136 ASN Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 626 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8020 Z= 0.349 Angle : 0.548 7.928 10924 Z= 0.285 Chirality : 0.041 0.176 1287 Planarity : 0.004 0.040 1350 Dihedral : 5.041 43.905 1174 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.02 % Allowed : 8.73 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.27), residues: 987 helix: 2.33 (0.31), residues: 260 sheet: -0.67 (0.32), residues: 263 loop : -0.55 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 546 HIS 0.005 0.001 HIS L 91 PHE 0.020 0.001 PHE R 666 TYR 0.018 0.001 TYR L 139 ARG 0.004 0.000 ARG L 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 401 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 62 average time/residue: 0.3140 time to fit residues: 30.2365 Evaluate side-chains 63 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain L residue 46 TRP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 136 ASN Chi-restraints excluded: chain L residue 171 THR Chi-restraints excluded: chain R residue 239 THR Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 626 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.2352 > 50: distance: 241 - 251: 4.191 distance: 251 - 252: 6.557 distance: 251 - 260: 3.276 distance: 252 - 253: 6.083 distance: 252 - 255: 7.471 distance: 252 - 261: 9.664 distance: 253 - 254: 11.647 distance: 253 - 273: 3.146 distance: 255 - 256: 5.879 distance: 255 - 262: 15.017 distance: 255 - 263: 13.774 distance: 256 - 257: 5.675 distance: 256 - 264: 4.370 distance: 256 - 265: 7.848 distance: 257 - 258: 5.730 distance: 257 - 266: 6.025 distance: 257 - 267: 6.779 distance: 258 - 259: 3.681 distance: 258 - 268: 5.472 distance: 259 - 271: 3.736 distance: 259 - 272: 4.895 distance: 273 - 274: 4.220 distance: 273 - 281: 7.701 distance: 274 - 275: 3.803 distance: 274 - 277: 16.327 distance: 275 - 285: 4.266 distance: 277 - 278: 13.776 distance: 277 - 284: 7.896 distance: 278 - 279: 11.455 distance: 278 - 280: 8.656 distance: 285 - 286: 9.343 distance: 285 - 290: 16.735 distance: 286 - 287: 3.490 distance: 286 - 289: 13.172 distance: 286 - 291: 7.799 distance: 287 - 288: 4.961 distance: 287 - 295: 5.102 distance: 289 - 292: 16.491 distance: 289 - 293: 15.096 distance: 289 - 294: 6.188 distance: 295 - 306: 7.304 distance: 296 - 299: 3.678 distance: 296 - 307: 5.886 distance: 297 - 298: 4.885 distance: 297 - 315: 11.847 distance: 299 - 308: 4.548 distance: 299 - 309: 4.029 distance: 300 - 302: 5.050 distance: 301 - 310: 4.567 distance: 303 - 305: 3.385 distance: 303 - 312: 3.819 distance: 304 - 305: 3.088 distance: 305 - 314: 3.319 distance: 315 - 316: 4.376 distance: 316 - 317: 6.629 distance: 316 - 320: 8.418 distance: 316 - 321: 14.858 distance: 317 - 318: 4.379 distance: 317 - 322: 7.648 distance: 322 - 323: 5.627 distance: 322 - 326: 6.635 distance: 323 - 324: 8.734 distance: 323 - 327: 10.382 distance: 323 - 328: 14.599 distance: 324 - 325: 7.044 distance: 324 - 329: 4.308 distance: 329 - 336: 8.927 distance: 330 - 331: 3.289 distance: 330 - 337: 6.897 distance: 331 - 332: 5.794 distance: 331 - 345: 5.297 distance: 333 - 334: 3.054 distance: 333 - 335: 3.946 distance: 333 - 338: 4.970 distance: 334 - 339: 3.163 distance: 334 - 340: 15.004 distance: 334 - 341: 6.484 distance: 335 - 342: 11.254 distance: 335 - 344: 10.162 distance: 345 - 346: 6.745 distance: 345 - 357: 9.905 distance: 346 - 347: 6.324 distance: 346 - 349: 3.381 distance: 346 - 358: 6.530 distance: 347 - 348: 22.035 distance: 347 - 366: 17.330 distance: 349 - 350: 4.102 distance: 349 - 360: 4.476 distance: 350 - 351: 5.002 distance: 350 - 352: 3.038 distance: 352 - 354: 4.562 distance: 352 - 362: 3.090 distance: 353 - 355: 7.385 distance: 353 - 363: 4.841 distance: 354 - 355: 4.678 distance: 354 - 364: 3.224 distance: 355 - 356: 6.113 distance: 356 - 365: 14.290 distance: 366 - 367: 16.314 distance: 366 - 372: 20.849 distance: 367 - 368: 6.553 distance: 367 - 370: 13.874 distance: 367 - 373: 11.509 distance: 368 - 369: 3.273 distance: 368 - 377: 6.113 distance: 370 - 371: 12.733 distance: 370 - 374: 8.540 distance: 370 - 375: 10.292 distance: 371 - 376: 37.860 distance: 377 - 378: 8.405 distance: 377 - 381: 9.134 distance: 378 - 379: 5.934 distance: 378 - 382: 11.155 distance: 378 - 383: 9.378