Starting phenix.real_space_refine on Fri Mar 15 00:36:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/03_2024/6wbv_21599_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/03_2024/6wbv_21599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/03_2024/6wbv_21599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/03_2024/6wbv_21599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/03_2024/6wbv_21599_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/03_2024/6wbv_21599_updated.pdb" } resolution = 2.5 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= -0.013 sd= 0.959 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3344 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Co 2 6.85 5 P 2 5.49 5 S 47 5.16 5 C 4398 2.51 5 N 1114 2.21 5 O 1297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L ARG 112": "NH1" <-> "NH2" Residue "L ASP 188": "OD1" <-> "OD2" Residue "L GLU 191": "OE1" <-> "OE2" Residue "L PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6860 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3262 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 4, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1674 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1666 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 220, 1666 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1703 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' CO': 2, 'AGA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2181 SG CYS A 326 78.631 63.845 45.666 1.00 49.12 S Time building chain proxies: 5.32, per 1000 atoms: 0.78 Number of scatterers: 6860 At special positions: 0 Unit cell: (113.424, 110.088, 111.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Co 2 26.99 S 47 16.00 P 2 15.00 O 1297 8.00 N 1114 7.00 C 4398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 13 " distance=2.02 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 19 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " distance=2.04 Simple disulfide: pdb=" SG CYS L 218 " - pdb=" SG CYS H 133 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.04 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: 2.79 Conformation dependent library (CDL) restraints added in 1.6 seconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 11 sheets defined 43.8% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.876A pdb=" N THR A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 53 Processing helix chain 'A' and resid 59 through 84 removed outlier: 5.850A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 126 through 155 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 167 through 198 removed outlier: 3.956A pdb=" N ILE A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 201 through 229 removed outlier: 3.975A pdb=" N CYS A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.900A pdb=" N TYR A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 369 through 392 removed outlier: 3.540A pdb=" N LEU A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS A 387 " --> pdb=" O CYS A 383 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 483 removed outlier: 4.491A pdb=" N ILE A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 513 removed outlier: 5.157A pdb=" N GLY A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 492 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 505 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 506 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 511 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 513 " --> pdb=" O MET A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 545 removed outlier: 3.573A pdb=" N GLY A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 86 No H-bonds generated for 'chain 'L' and resid 84 through 86' Processing helix chain 'L' and resid 126 through 130 Processing helix chain 'L' and resid 187 through 192 removed outlier: 3.669A pdb=" N ARG L 192 " --> pdb=" O ASP L 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing sheet with id= A, first strand: chain 'B' and resid 7 through 11 Processing sheet with id= B, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= C, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.623A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU L 109 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLN L 41 " --> pdb=" O PRO L 50 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.815A pdb=" N TYR L 177 " --> pdb=" O ASN L 142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.240A pdb=" N TRP L 152 " --> pdb=" O ARG L 159 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.616A pdb=" N GLN H 66 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 112 through 114 removed outlier: 3.599A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU H 45 " --> pdb=" O PHE H 40 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 125 through 129 removed outlier: 5.573A pdb=" N TYR H 180 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 156 through 159 Processing sheet with id= J, first strand: chain 'H' and resid 174 through 176 Processing sheet with id= K, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.987A pdb=" N VAL H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1122 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: 1.96 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 1060 1.26 - 1.40: 1747 1.40 - 1.55: 4118 1.55 - 1.69: 12 1.69 - 1.83: 68 Bond restraints: 7005 Sorted by residual: bond pdb=" C SER L 32 " pdb=" O SER L 32 " ideal model delta sigma weight residual 1.243 1.122 0.121 9.50e-03 1.11e+04 1.63e+02 bond pdb=" C TYR L 34 " pdb=" O TYR L 34 " ideal model delta sigma weight residual 1.234 1.114 0.120 1.28e-02 6.10e+03 8.84e+01 bond pdb=" CA ALA L 31 " pdb=" C ALA L 31 " ideal model delta sigma weight residual 1.520 1.427 0.093 1.16e-02 7.43e+03 6.44e+01 bond pdb=" CA TYR L 34 " pdb=" C TYR L 34 " ideal model delta sigma weight residual 1.523 1.429 0.094 1.21e-02 6.83e+03 6.10e+01 bond pdb=" C ALA L 31 " pdb=" O ALA L 31 " ideal model delta sigma weight residual 1.235 1.175 0.059 1.13e-02 7.83e+03 2.77e+01 ... (remaining 7000 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.60: 215 106.60 - 113.46: 3970 113.46 - 120.31: 2600 120.31 - 127.16: 2674 127.16 - 134.02: 88 Bond angle restraints: 9547 Sorted by residual: angle pdb=" C ASN A 516 " pdb=" N PRO A 517 " pdb=" CA PRO A 517 " ideal model delta sigma weight residual 119.28 127.37 -8.09 1.10e+00 8.26e-01 5.41e+01 angle pdb=" C ALA L 55 " pdb=" CA ALA L 55 " pdb=" CB ALA L 55 " ideal model delta sigma weight residual 110.04 100.16 9.88 1.51e+00 4.39e-01 4.28e+01 angle pdb=" O5 AGA A 701 " pdb=" P1 AGA A 701 " pdb=" O6 AGA A 701 " ideal model delta sigma weight residual 93.68 110.17 -16.49 3.00e+00 1.11e-01 3.02e+01 angle pdb=" O5 AGA A 702 " pdb=" P1 AGA A 702 " pdb=" O6 AGA A 702 " ideal model delta sigma weight residual 93.68 109.83 -16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" N PRO A 515 " pdb=" CA PRO A 515 " pdb=" C PRO A 515 " ideal model delta sigma weight residual 112.47 121.47 -9.00 2.06e+00 2.36e-01 1.91e+01 ... (remaining 9542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 3720 17.21 - 34.42: 284 34.42 - 51.63: 96 51.63 - 68.84: 28 68.84 - 86.05: 14 Dihedral angle restraints: 4142 sinusoidal: 1565 harmonic: 2577 Sorted by residual: dihedral pdb=" C SER L 32 " pdb=" N SER L 32 " pdb=" CA SER L 32 " pdb=" CB SER L 32 " ideal model delta harmonic sigma weight residual -122.60 -135.46 12.86 0 2.50e+00 1.60e-01 2.65e+01 dihedral pdb=" C ALA L 55 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " pdb=" CB ALA L 55 " ideal model delta harmonic sigma weight residual -122.60 -110.94 -11.66 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" CA TYR H 50 " pdb=" C TYR H 50 " pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1086 0.111 - 0.221: 33 0.221 - 0.331: 2 0.331 - 0.442: 2 0.442 - 0.552: 1 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CA SER L 32 " pdb=" N SER L 32 " pdb=" C SER L 32 " pdb=" CB SER L 32 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA TRP H 103 " pdb=" N TRP H 103 " pdb=" C TRP H 103 " pdb=" CB TRP H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA PRO A 515 " pdb=" N PRO A 515 " pdb=" C PRO A 515 " pdb=" CB PRO A 515 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 1121 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 516 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C ASN A 516 " 0.052 2.00e-02 2.50e+03 pdb=" O ASN A 516 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO A 517 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 71 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C SER L 71 " 0.047 2.00e-02 2.50e+03 pdb=" O SER L 71 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY L 72 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 35 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C ASN H 35 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN H 35 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP H 36 " 0.016 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 25 2.42 - 3.04: 4172 3.04 - 3.66: 10406 3.66 - 4.28: 16114 4.28 - 4.90: 26538 Nonbonded interactions: 57255 Sorted by model distance: nonbonded pdb="CO CO A 704 " pdb=" O HOH A 806 " model vdw 1.797 2.220 nonbonded pdb=" O THR B 25 " pdb="CO CO A 704 " model vdw 1.798 2.220 nonbonded pdb=" ND2 ASN L 95 " pdb=" O TRP H 103 " model vdw 1.887 2.520 nonbonded pdb=" NE2 HIS A 507 " pdb="CO CO A 704 " model vdw 2.111 2.300 nonbonded pdb=" OG SER A 35 " pdb=" OE1 GLU A 219 " model vdw 2.113 2.440 ... (remaining 57250 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=0.50 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 6.480 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 25.450 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.121 7005 Z= 0.410 Angle : 0.935 16.494 9547 Z= 0.501 Chirality : 0.054 0.552 1124 Planarity : 0.007 0.067 1176 Dihedral : 15.749 86.050 2465 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.26 % Allowed : 9.05 % Favored : 86.68 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 18.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 879 helix: -0.19 (0.22), residues: 382 sheet: 0.01 (0.33), residues: 226 loop : -0.63 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP L 167 HIS 0.005 0.001 HIS L 38 PHE 0.023 0.002 PHE L 75 TYR 0.024 0.002 TYR H 78 ARG 0.009 0.001 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 0.720 Fit side-chains revert: symmetry clash REVERT: A 317 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8696 (mp) REVERT: A 341 ILE cc_start: 0.8536 (mp) cc_final: 0.8291 (mm) REVERT: A 364 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7896 (ttp-110) REVERT: A 366 LYS cc_start: 0.8414 (tppt) cc_final: 0.8202 (mptp) REVERT: A 516 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7554 (m-40) REVERT: L 49 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8009 (tptp) REVERT: H 16 GLN cc_start: 0.8131 (mt0) cc_final: 0.7927 (mt0) REVERT: H 216 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6492 (pm20) outliers start: 32 outliers final: 11 residues processed: 157 average time/residue: 0.9417 time to fit residues: 157.1709 Evaluate side-chains 125 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain L residue 218 CYS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.0000 chunk 50 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS A 86 ASN A 99 GLN A 141 ASN A 155 GLN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN L 141 ASN L 149 ASN L 194 ASN L 216 ASN H 3 GLN H 77 HIS H 83 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7005 Z= 0.235 Angle : 0.601 8.696 9547 Z= 0.314 Chirality : 0.043 0.196 1124 Planarity : 0.005 0.052 1176 Dihedral : 11.173 90.411 1036 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.33 % Allowed : 13.18 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.28), residues: 879 helix: 1.57 (0.25), residues: 389 sheet: 0.69 (0.34), residues: 223 loop : -0.20 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 34 HIS 0.003 0.001 HIS A 32 PHE 0.013 0.002 PHE L 213 TYR 0.026 0.002 TYR H 78 ARG 0.002 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8364 (mttt) REVERT: A 317 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8747 (mp) REVERT: A 341 ILE cc_start: 0.8559 (mp) cc_final: 0.8315 (mm) REVERT: A 378 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8099 (mp) REVERT: L 43 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8307 (mttt) REVERT: L 49 LYS cc_start: 0.8373 (ttmm) cc_final: 0.7950 (tptm) REVERT: H 16 GLN cc_start: 0.8232 (mt0) cc_final: 0.7957 (mt0) outliers start: 25 outliers final: 12 residues processed: 129 average time/residue: 1.0754 time to fit residues: 147.1131 Evaluate side-chains 118 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 103 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 65 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7005 Z= 0.328 Angle : 0.645 9.417 9547 Z= 0.336 Chirality : 0.045 0.226 1124 Planarity : 0.006 0.054 1176 Dihedral : 10.515 84.804 1019 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.99 % Allowed : 14.91 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.49 (0.28), residues: 879 helix: 1.87 (0.26), residues: 388 sheet: 1.07 (0.35), residues: 213 loop : -0.28 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 34 HIS 0.003 0.001 HIS A 535 PHE 0.014 0.002 PHE A 295 TYR 0.027 0.002 TYR H 78 ARG 0.005 0.001 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8654 (mmtp) cc_final: 0.8369 (mttt) REVERT: A 317 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8780 (mp) REVERT: A 341 ILE cc_start: 0.8496 (mp) cc_final: 0.8248 (mm) REVERT: L 49 LYS cc_start: 0.8457 (ttmm) cc_final: 0.8027 (tptm) REVERT: L 169 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7799 (m-30) REVERT: H 16 GLN cc_start: 0.8250 (mt0) cc_final: 0.7974 (mt0) outliers start: 30 outliers final: 17 residues processed: 129 average time/residue: 1.0857 time to fit residues: 147.9687 Evaluate side-chains 126 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7005 Z= 0.207 Angle : 0.563 9.116 9547 Z= 0.291 Chirality : 0.041 0.192 1124 Planarity : 0.005 0.052 1176 Dihedral : 10.263 79.735 1019 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.33 % Allowed : 16.78 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.81 (0.29), residues: 879 helix: 2.21 (0.26), residues: 389 sheet: 1.17 (0.35), residues: 213 loop : -0.22 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 34 HIS 0.004 0.001 HIS A 32 PHE 0.011 0.002 PHE L 213 TYR 0.025 0.002 TYR H 78 ARG 0.002 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 0.804 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8641 (mmtp) cc_final: 0.8391 (mttt) REVERT: A 319 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.7932 (tmm) REVERT: A 341 ILE cc_start: 0.8500 (mp) cc_final: 0.8252 (mm) REVERT: L 18 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7274 (ptm160) REVERT: L 49 LYS cc_start: 0.8374 (ttmm) cc_final: 0.7933 (tptm) REVERT: H 16 GLN cc_start: 0.8168 (mt0) cc_final: 0.7868 (mt0) outliers start: 25 outliers final: 15 residues processed: 125 average time/residue: 1.1642 time to fit residues: 153.3777 Evaluate side-chains 119 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 10.0000 chunk 1 optimal weight: 0.0050 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 58 optimal weight: 0.0370 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 overall best weight: 0.2272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 7005 Z= 0.116 Angle : 0.484 9.793 9547 Z= 0.246 Chirality : 0.038 0.162 1124 Planarity : 0.004 0.049 1176 Dihedral : 9.392 68.759 1017 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.40 % Allowed : 17.98 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.34 (0.29), residues: 879 helix: 2.75 (0.27), residues: 387 sheet: 1.41 (0.35), residues: 214 loop : -0.07 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 167 HIS 0.003 0.000 HIS A 32 PHE 0.010 0.001 PHE A 295 TYR 0.018 0.001 TYR H 78 ARG 0.001 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 119 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8582 (mmtp) cc_final: 0.8375 (mttt) REVERT: A 341 ILE cc_start: 0.8355 (mp) cc_final: 0.8103 (mm) REVERT: L 49 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7734 (tptm) REVERT: L 182 THR cc_start: 0.8033 (m) cc_final: 0.7584 (t) REVERT: H 16 GLN cc_start: 0.8096 (mt0) cc_final: 0.7825 (mt0) outliers start: 18 outliers final: 7 residues processed: 131 average time/residue: 1.0601 time to fit residues: 146.7497 Evaluate side-chains 111 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN H 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7005 Z= 0.273 Angle : 0.600 9.873 9547 Z= 0.308 Chirality : 0.043 0.229 1124 Planarity : 0.005 0.049 1176 Dihedral : 9.106 67.338 1010 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.46 % Allowed : 18.38 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.08 (0.29), residues: 879 helix: 2.37 (0.26), residues: 388 sheet: 1.36 (0.35), residues: 213 loop : -0.02 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 34 HIS 0.004 0.001 HIS L 94 PHE 0.013 0.002 PHE A 295 TYR 0.027 0.002 TYR H 78 ARG 0.003 0.001 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8650 (mmtp) cc_final: 0.8408 (mttt) REVERT: A 317 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8859 (mp) REVERT: A 341 ILE cc_start: 0.8552 (mp) cc_final: 0.8285 (mm) REVERT: L 18 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7223 (ptm160) REVERT: L 49 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7957 (tptm) REVERT: H 16 GLN cc_start: 0.8175 (mt0) cc_final: 0.7873 (mt0) outliers start: 26 outliers final: 18 residues processed: 124 average time/residue: 1.1948 time to fit residues: 156.1467 Evaluate side-chains 126 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 102 ASN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7005 Z= 0.199 Angle : 0.559 9.587 9547 Z= 0.286 Chirality : 0.041 0.200 1124 Planarity : 0.005 0.047 1176 Dihedral : 8.781 60.602 1010 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.93 % Allowed : 18.91 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.17 (0.29), residues: 879 helix: 2.42 (0.26), residues: 388 sheet: 1.42 (0.35), residues: 213 loop : 0.08 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 34 HIS 0.004 0.001 HIS A 32 PHE 0.011 0.001 PHE A 295 TYR 0.024 0.001 TYR H 78 ARG 0.002 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 105 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8634 (mmtp) cc_final: 0.8385 (mttt) REVERT: A 341 ILE cc_start: 0.8514 (mp) cc_final: 0.8259 (mm) REVERT: L 18 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7259 (ptm160) REVERT: L 49 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7922 (tptm) REVERT: L 182 THR cc_start: 0.8093 (m) cc_final: 0.7648 (t) REVERT: H 16 GLN cc_start: 0.8151 (mt0) cc_final: 0.7836 (mt0) outliers start: 22 outliers final: 15 residues processed: 118 average time/residue: 1.1091 time to fit residues: 138.2827 Evaluate side-chains 119 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7005 Z= 0.137 Angle : 0.510 9.608 9547 Z= 0.258 Chirality : 0.039 0.164 1124 Planarity : 0.004 0.046 1176 Dihedral : 7.911 53.958 1010 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.26 % Allowed : 19.71 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.45 (0.29), residues: 879 helix: 2.65 (0.26), residues: 388 sheet: 1.60 (0.35), residues: 214 loop : 0.17 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 34 HIS 0.004 0.001 HIS A 32 PHE 0.010 0.001 PHE A 295 TYR 0.021 0.001 TYR H 78 ARG 0.002 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8612 (mmtp) cc_final: 0.8354 (tttt) REVERT: A 341 ILE cc_start: 0.8395 (mp) cc_final: 0.8113 (mm) REVERT: L 49 LYS cc_start: 0.8262 (ttmm) cc_final: 0.7798 (tptm) REVERT: L 182 THR cc_start: 0.8069 (m) cc_final: 0.7601 (t) REVERT: H 16 GLN cc_start: 0.8115 (mt0) cc_final: 0.7850 (mt0) outliers start: 17 outliers final: 12 residues processed: 116 average time/residue: 1.1617 time to fit residues: 141.9831 Evaluate side-chains 113 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN H 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7005 Z= 0.185 Angle : 0.549 9.664 9547 Z= 0.281 Chirality : 0.041 0.178 1124 Planarity : 0.004 0.046 1176 Dihedral : 7.877 58.149 1010 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.26 % Allowed : 19.71 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.33 (0.29), residues: 879 helix: 2.52 (0.26), residues: 388 sheet: 1.55 (0.35), residues: 213 loop : 0.15 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 34 HIS 0.003 0.001 HIS L 94 PHE 0.011 0.001 PHE A 295 TYR 0.023 0.001 TYR H 78 ARG 0.001 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8373 (tttt) REVERT: A 341 ILE cc_start: 0.8492 (mp) cc_final: 0.8225 (mm) REVERT: L 49 LYS cc_start: 0.8345 (ttmm) cc_final: 0.7904 (tptm) REVERT: L 182 THR cc_start: 0.8072 (m) cc_final: 0.7609 (t) REVERT: H 16 GLN cc_start: 0.8140 (mt0) cc_final: 0.7838 (mt0) outliers start: 17 outliers final: 16 residues processed: 115 average time/residue: 1.1591 time to fit residues: 140.6643 Evaluate side-chains 115 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 69 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 73 optimal weight: 0.0670 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN L 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7005 Z= 0.132 Angle : 0.512 9.520 9547 Z= 0.259 Chirality : 0.039 0.151 1124 Planarity : 0.004 0.045 1176 Dihedral : 7.371 59.258 1010 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.46 % Allowed : 20.24 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.53 (0.29), residues: 879 helix: 2.68 (0.26), residues: 388 sheet: 1.70 (0.35), residues: 214 loop : 0.19 (0.39), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 34 HIS 0.004 0.001 HIS A 32 PHE 0.010 0.001 PHE A 295 TYR 0.020 0.001 TYR H 78 ARG 0.001 0.000 ARG A 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: B 24 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8398 (mttt) REVERT: A 341 ILE cc_start: 0.8380 (mp) cc_final: 0.8103 (mm) REVERT: L 49 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7782 (tptm) REVERT: L 182 THR cc_start: 0.8037 (m) cc_final: 0.7581 (t) REVERT: H 16 GLN cc_start: 0.8136 (mt0) cc_final: 0.7836 (mt0) outliers start: 11 outliers final: 10 residues processed: 106 average time/residue: 1.2731 time to fit residues: 142.1115 Evaluate side-chains 107 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 203 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 219 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 79 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.159914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108959 restraints weight = 12973.797| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.13 r_work: 0.3341 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7005 Z= 0.311 Angle : 0.627 9.845 9547 Z= 0.323 Chirality : 0.044 0.203 1124 Planarity : 0.005 0.046 1176 Dihedral : 7.921 55.953 1010 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.80 % Allowed : 19.31 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.16 (0.29), residues: 879 helix: 2.29 (0.26), residues: 388 sheet: 1.40 (0.35), residues: 223 loop : 0.22 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 34 HIS 0.004 0.001 HIS L 94 PHE 0.014 0.002 PHE A 295 TYR 0.026 0.002 TYR H 78 ARG 0.003 0.001 ARG H 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3274.74 seconds wall clock time: 58 minutes 15.31 seconds (3495.31 seconds total)