Starting phenix.real_space_refine on Mon Mar 11 09:57:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/03_2024/7mhy_23836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/03_2024/7mhy_23836.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/03_2024/7mhy_23836_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/03_2024/7mhy_23836_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/03_2024/7mhy_23836_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/03_2024/7mhy_23836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/03_2024/7mhy_23836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/03_2024/7mhy_23836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhy_23836/03_2024/7mhy_23836_updated.pdb" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.402 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: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 P 6 5.49 5 S 48 5.16 5 C 5264 2.51 5 N 1177 2.21 5 O 1408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 30": "NH1" <-> "NH2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "M TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 122": "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: 7904 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 4003 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 474} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "M" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 887 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "N" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 812 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "O" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "P" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 683 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 88} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 714 Unusual residues: {'AJP': 14, 'HEM': 1, 'PKZ': 3} Classifications: {'undetermined': 18, 'water': 15} Link IDs: {None: 32} Unresolved non-hydrogen bonds: 796 Unresolved non-hydrogen angles: 1197 Unresolved non-hydrogen dihedrals: 1651 Unresolved non-hydrogen chiralities: 315 Planarities with less than four sites: {'PKZ:plan-3': 1, 'PKZ:plan-2': 1, 'PKZ:plan-1': 1, 'PKZ:plan-5': 1, 'PKZ:plan-4': 1} Unresolved non-hydrogen planarities: 26 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2668 SG CYS A 324 41.775 58.564 80.769 1.00 29.38 S Time building chain proxies: 4.93, per 1000 atoms: 0.62 Number of scatterers: 7904 At special positions: 0 Unit cell: (74.48, 90.972, 144.704, 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) Fe 1 26.01 S 48 16.00 P 6 15.00 O 1408 8.00 N 1177 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 115 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 112 " distance=2.05 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 115 " distance=2.03 Simple disulfide: pdb=" SG CYS P 42 " - pdb=" SG CYS P 112 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 42.1% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 4 through 28 Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 93 through 130 removed outlier: 8.291A pdb=" N THR A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 4.428A pdb=" N PHE A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.714A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.743A pdb=" N TRP A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 188 removed outlier: 4.176A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 237 through 264 removed outlier: 3.502A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 246 " --> pdb=" O CYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 282 through 314 Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 351 through 354 No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 361 through 378 Processing helix chain 'A' and resid 383 through 406 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 421 through 448 removed outlier: 3.775A pdb=" N CYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 468 through 489 removed outlier: 4.602A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 109 No H-bonds generated for 'chain 'M' and resid 107 through 109' Processing helix chain 'O' and resid 81 through 83 No H-bonds generated for 'chain 'O' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= B, first strand: chain 'M' and resid 22 through 25 Processing sheet with id= C, first strand: chain 'M' and resid 29 through 31 removed outlier: 3.789A pdb=" N GLY M 68 " --> pdb=" O TRP M 55 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS M 57 " --> pdb=" O TRP M 66 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TRP M 66 " --> pdb=" O LYS M 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 116 through 118 Processing sheet with id= E, first strand: chain 'N' and resid 23 through 26 Processing sheet with id= F, first strand: chain 'N' and resid 29 through 31 removed outlier: 6.465A pdb=" N LYS N 127 " --> pdb=" O LEU N 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'N' and resid 109 through 114 removed outlier: 6.176A pdb=" N LEU N 61 " --> pdb=" O LEU N 70 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU N 70 " --> pdb=" O LEU N 61 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'O' and resid 22 through 25 Processing sheet with id= I, first strand: chain 'O' and resid 77 through 79 removed outlier: 6.815A pdb=" N TRP O 55 " --> pdb=" O MET O 67 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP O 69 " --> pdb=" O MET O 53 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET O 53 " --> pdb=" O TRP O 69 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TYR O 127 " --> pdb=" O ARG O 117 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 23 through 26 removed outlier: 3.547A pdb=" N SER P 41 " --> pdb=" O THR P 26 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'P' and resid 109 through 114 removed outlier: 3.820A pdb=" N TRP P 59 " --> pdb=" O ILE P 72 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE P 72 " --> pdb=" O TRP P 59 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU P 61 " --> pdb=" O LEU P 70 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LEU P 70 " --> pdb=" O LEU P 61 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1020 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: 2.40 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 2811 1.37 - 1.54: 5170 1.54 - 1.71: 144 1.71 - 1.88: 74 1.88 - 2.04: 4 Bond restraints: 8203 Sorted by residual: bond pdb=" C1B PKZ A 503 " pdb=" O4B PKZ A 503 " ideal model delta sigma weight residual 1.642 1.402 0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C1B PKZ A 502 " pdb=" O4B PKZ A 502 " ideal model delta sigma weight residual 1.642 1.404 0.238 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C1B PKZ A 502 " pdb=" C2B PKZ A 502 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.07e+01 bond pdb=" C1B PKZ A 503 " pdb=" C2B PKZ A 503 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C9P PKZ A 502 " pdb=" N8P PKZ A 502 " ideal model delta sigma weight residual 1.477 1.325 0.152 2.00e-02 2.50e+03 5.80e+01 ... (remaining 8198 not shown) Histogram of bond angle deviations from ideal: 88.41 - 105.85: 287 105.85 - 123.29: 10594 123.29 - 140.73: 480 140.73 - 158.16: 0 158.16 - 175.60: 2 Bond angle restraints: 11363 Sorted by residual: angle pdb=" C9P PKZ A 503 " pdb=" CAP PKZ A 503 " pdb=" CBP PKZ A 503 " ideal model delta sigma weight residual 109.61 120.60 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" O3A PKZ A 503 " pdb=" P1A PKZ A 503 " pdb=" O5B PKZ A 503 " ideal model delta sigma weight residual 109.43 98.69 10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" N1A PKZ A 503 " pdb=" C6A PKZ A 503 " pdb=" N6A PKZ A 503 " ideal model delta sigma weight residual 108.45 118.89 -10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N1A PKZ A 502 " pdb=" C6A PKZ A 502 " pdb=" N6A PKZ A 502 " ideal model delta sigma weight residual 108.45 118.79 -10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C2A PKZ A 502 " pdb=" N3A PKZ A 502 " pdb=" C4A PKZ A 502 " ideal model delta sigma weight residual 120.05 110.24 9.81 3.00e+00 1.11e-01 1.07e+01 ... (remaining 11358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 4616 35.93 - 71.86: 395 71.86 - 107.79: 221 107.79 - 143.72: 415 143.72 - 179.65: 81 Dihedral angle restraints: 5728 sinusoidal: 3095 harmonic: 2633 Sorted by residual: dihedral pdb=" C VAL N 75 " pdb=" N VAL N 75 " pdb=" CA VAL N 75 " pdb=" CB VAL N 75 " ideal model delta harmonic sigma weight residual -122.00 -137.82 15.82 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" N VAL N 75 " pdb=" C VAL N 75 " pdb=" CA VAL N 75 " pdb=" CB VAL N 75 " ideal model delta harmonic sigma weight residual 123.40 137.15 -13.75 0 2.50e+00 1.60e-01 3.02e+01 dihedral pdb=" C22 AJP A 517 " pdb=" C20 AJP A 517 " pdb=" C21 AJP A 517 " pdb=" C80 AJP A 517 " ideal model delta sinusoidal sigma weight residual 65.75 -114.60 -179.65 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.206: 1175 1.206 - 2.411: 0 2.411 - 3.617: 0 3.617 - 4.823: 17 4.823 - 6.028: 139 Chirality restraints: 1331 Sorted by residual: chirality pdb=" C12 AJP A 511 " pdb=" C07 AJP A 511 " pdb=" C11 AJP A 511 " pdb=" C13 AJP A 511 " both_signs ideal model delta sigma weight residual False 3.01 -3.02 6.03 2.00e-01 2.50e+01 9.08e+02 chirality pdb=" C12 AJP A 516 " pdb=" C07 AJP A 516 " pdb=" C11 AJP A 516 " pdb=" C13 AJP A 516 " both_signs ideal model delta sigma weight residual False 3.01 -3.02 6.02 2.00e-01 2.50e+01 9.07e+02 chirality pdb=" C12 AJP A 506 " pdb=" C07 AJP A 506 " pdb=" C11 AJP A 506 " pdb=" C13 AJP A 506 " both_signs ideal model delta sigma weight residual False 3.01 -3.01 6.02 2.00e-01 2.50e+01 9.05e+02 ... (remaining 1328 not shown) Planarity restraints: 1243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3P PKZ A 502 " -0.086 2.00e-02 2.50e+03 7.10e-02 6.30e+01 pdb=" C5P PKZ A 502 " 0.024 2.00e-02 2.50e+03 pdb=" C6P PKZ A 502 " -0.065 2.00e-02 2.50e+03 pdb=" N4P PKZ A 502 " 0.113 2.00e-02 2.50e+03 pdb=" O5P PKZ A 502 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 271 " -0.033 2.00e-02 2.50e+03 2.82e-02 1.59e+01 pdb=" CG TYR A 271 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR A 271 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 271 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 271 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 271 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A 271 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 271 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P PKZ A 502 " 0.033 2.00e-02 2.50e+03 2.71e-02 9.15e+00 pdb=" C9P PKZ A 502 " -0.010 2.00e-02 2.50e+03 pdb=" CAP PKZ A 502 " 0.025 2.00e-02 2.50e+03 pdb=" N8P PKZ A 502 " -0.043 2.00e-02 2.50e+03 pdb=" O9P PKZ A 502 " -0.005 2.00e-02 2.50e+03 ... (remaining 1240 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 290 2.71 - 3.26: 7463 3.26 - 3.80: 12819 3.80 - 4.35: 16387 4.35 - 4.90: 27579 Nonbonded interactions: 64538 Sorted by model distance: nonbonded pdb=" OH TYR A 210 " pdb=" OD2 ASP A 314 " model vdw 2.160 2.440 nonbonded pdb=" O MET A 328 " pdb=" OH TYR A 479 " model vdw 2.265 2.440 nonbonded pdb=" O2B PKZ A 502 " pdb=" O7A PKZ A 502 " model vdw 2.278 2.440 nonbonded pdb=" O LEU A 143 " pdb=" OG1 THR A 146 " model vdw 2.327 2.440 nonbonded pdb=" O SER N 116 " pdb=" OG SER N 116 " model vdw 2.336 2.440 ... (remaining 64533 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: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.390 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.310 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 0.012 0.240 8203 Z= 0.786 Angle : 1.072 10.990 11363 Z= 0.475 Chirality : 1.792 6.028 1331 Planarity : 0.005 0.071 1243 Dihedral : 53.384 179.652 4040 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.54 % Allowed : 0.67 % Favored : 98.79 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.28), residues: 888 helix: 1.92 (0.26), residues: 385 sheet: 0.61 (0.37), residues: 198 loop : -0.92 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 465 HIS 0.012 0.002 HIS A 428 PHE 0.030 0.003 PHE A 58 TYR 0.069 0.003 TYR A 271 ARG 0.003 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 152 time to evaluate : 0.859 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. outliers start: 4 outliers final: 3 residues processed: 155 average time/residue: 1.1398 time to fit residues: 187.9316 Evaluate side-chains 147 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain N residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 0.0040 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 488 GLN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8203 Z= 0.209 Angle : 2.782 36.725 11363 Z= 0.950 Chirality : 0.259 1.878 1331 Planarity : 0.004 0.034 1243 Dihedral : 42.542 179.612 2552 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.75 % Allowed : 9.85 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.30 (0.28), residues: 888 helix: 2.32 (0.26), residues: 381 sheet: 0.68 (0.36), residues: 201 loop : -0.92 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 388 HIS 0.005 0.001 HIS A 428 PHE 0.033 0.002 PHE A 17 TYR 0.025 0.002 TYR A 271 ARG 0.003 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 0.766 Fit side-chains TARDY: cannot create tardy model for: "SER A 29 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 148 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7909 (ptp-170) REVERT: P 58 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7143 (mp0) outliers start: 13 outliers final: 7 residues processed: 147 average time/residue: 1.0520 time to fit residues: 164.9591 Evaluate side-chains 139 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 0.0670 chunk 22 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN A 450 ASN N 54 ASN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8203 Z= 0.186 Angle : 2.722 34.661 11363 Z= 0.927 Chirality : 0.259 1.902 1331 Planarity : 0.004 0.030 1243 Dihedral : 41.567 179.949 2549 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.02 % Allowed : 12.82 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.44 (0.28), residues: 888 helix: 2.40 (0.26), residues: 388 sheet: 0.76 (0.36), residues: 202 loop : -0.90 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 467 HIS 0.004 0.001 HIS A 428 PHE 0.022 0.001 PHE A 17 TYR 0.023 0.001 TYR A 180 ARG 0.003 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 0.811 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: P 58 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7137 (mp0) outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 1.0132 time to fit residues: 156.3661 Evaluate side-chains 140 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.0050 chunk 81 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN A 450 ASN N 54 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8203 Z= 0.189 Angle : 2.710 34.304 11363 Z= 0.923 Chirality : 0.260 1.864 1331 Planarity : 0.004 0.031 1243 Dihedral : 41.530 179.959 2548 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.24 % Allowed : 14.17 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 888 helix: 2.45 (0.26), residues: 388 sheet: 0.75 (0.37), residues: 202 loop : -0.88 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 467 HIS 0.004 0.001 HIS A 428 PHE 0.023 0.002 PHE A 17 TYR 0.021 0.001 TYR A 180 ARG 0.001 0.000 ARG M 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.853 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 148 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7933 (ptp-170) REVERT: P 58 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7171 (mp0) outliers start: 24 outliers final: 15 residues processed: 144 average time/residue: 1.0768 time to fit residues: 165.6568 Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 89 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.0030 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN A 450 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8203 Z= 0.158 Angle : 2.692 34.073 11363 Z= 0.914 Chirality : 0.261 1.870 1331 Planarity : 0.003 0.030 1243 Dihedral : 41.515 179.887 2548 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.24 % Allowed : 15.11 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.62 (0.29), residues: 888 helix: 2.65 (0.26), residues: 383 sheet: 0.78 (0.37), residues: 202 loop : -0.83 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 467 HIS 0.003 0.001 HIS A 481 PHE 0.019 0.001 PHE A 17 TYR 0.023 0.001 TYR A 180 ARG 0.001 0.000 ARG M 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.923 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7989 (mm) REVERT: A 148 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7979 (ptp-170) REVERT: N 73 TYR cc_start: 0.7625 (p90) cc_final: 0.7419 (p90) REVERT: N 77 ASN cc_start: 0.8474 (t0) cc_final: 0.8242 (t0) REVERT: P 58 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7095 (mp0) outliers start: 24 outliers final: 15 residues processed: 147 average time/residue: 1.1508 time to fit residues: 180.2614 Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain M residue 36 SER Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 89 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN A 450 ASN N 54 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8203 Z= 0.235 Angle : 2.713 34.520 11363 Z= 0.926 Chirality : 0.260 1.855 1331 Planarity : 0.004 0.035 1243 Dihedral : 41.516 179.997 2548 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.10 % Allowed : 15.25 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.40 (0.28), residues: 888 helix: 2.38 (0.26), residues: 389 sheet: 0.70 (0.37), residues: 202 loop : -0.89 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 388 HIS 0.005 0.001 HIS A 428 PHE 0.025 0.002 PHE N 113 TYR 0.019 0.002 TYR A 180 ARG 0.002 0.000 ARG M 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 0.832 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 148 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7970 (ptp-170) REVERT: N 77 ASN cc_start: 0.8556 (t0) cc_final: 0.8350 (t0) REVERT: P 58 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7203 (mp0) outliers start: 23 outliers final: 17 residues processed: 142 average time/residue: 1.0623 time to fit residues: 160.8772 Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 89 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN A 450 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8203 Z= 0.225 Angle : 2.711 34.709 11363 Z= 0.925 Chirality : 0.260 1.849 1331 Planarity : 0.004 0.034 1243 Dihedral : 41.508 179.947 2548 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.64 % Allowed : 15.65 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.36 (0.28), residues: 888 helix: 2.34 (0.26), residues: 389 sheet: 0.65 (0.37), residues: 202 loop : -0.90 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 467 HIS 0.004 0.001 HIS A 428 PHE 0.022 0.002 PHE N 113 TYR 0.020 0.002 TYR A 180 ARG 0.002 0.000 ARG M 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.776 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 34 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: A 148 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8012 (ptp-170) REVERT: M 101 GLN cc_start: 0.8413 (tt0) cc_final: 0.8161 (tt0) REVERT: P 58 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7202 (mp0) outliers start: 27 outliers final: 20 residues processed: 144 average time/residue: 1.0809 time to fit residues: 166.0150 Evaluate side-chains 150 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 82 LYS Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 89 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN A 450 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8203 Z= 0.174 Angle : 2.697 34.381 11363 Z= 0.917 Chirality : 0.261 1.848 1331 Planarity : 0.003 0.032 1243 Dihedral : 41.498 179.843 2548 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.10 % Allowed : 16.06 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.45 (0.29), residues: 888 helix: 2.45 (0.26), residues: 389 sheet: 0.61 (0.37), residues: 205 loop : -0.85 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 467 HIS 0.003 0.001 HIS A 481 PHE 0.019 0.001 PHE A 17 TYR 0.021 0.001 TYR A 180 ARG 0.001 0.000 ARG N 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.914 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7967 (mm) REVERT: A 148 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7942 (ptp-170) REVERT: M 101 GLN cc_start: 0.8384 (tt0) cc_final: 0.8077 (tt0) REVERT: P 58 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7196 (mp0) outliers start: 23 outliers final: 16 residues processed: 142 average time/residue: 1.0876 time to fit residues: 164.7124 Evaluate side-chains 146 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 89 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 75 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8203 Z= 0.225 Angle : 2.710 34.818 11363 Z= 0.924 Chirality : 0.261 1.844 1331 Planarity : 0.004 0.033 1243 Dihedral : 41.489 179.995 2548 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.24 % Allowed : 16.33 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.33 (0.29), residues: 888 helix: 2.35 (0.26), residues: 389 sheet: 0.52 (0.37), residues: 205 loop : -0.88 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 467 HIS 0.004 0.001 HIS A 428 PHE 0.022 0.002 PHE A 17 TYR 0.020 0.002 TYR A 180 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 0.864 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 34 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7639 (tp30) REVERT: A 148 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8034 (ptp-170) REVERT: M 101 GLN cc_start: 0.8411 (tt0) cc_final: 0.8168 (tt0) REVERT: P 58 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7219 (mp0) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 1.1193 time to fit residues: 164.6607 Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 89 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.5980 chunk 81 optimal weight: 9.9990 chunk 70 optimal weight: 0.0670 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN N 77 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8203 Z= 0.165 Angle : 2.696 34.444 11363 Z= 0.917 Chirality : 0.261 1.845 1331 Planarity : 0.003 0.032 1243 Dihedral : 41.488 179.975 2548 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.56 % Allowed : 17.41 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.45 (0.29), residues: 888 helix: 2.47 (0.26), residues: 389 sheet: 0.58 (0.37), residues: 205 loop : -0.85 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 467 HIS 0.003 0.001 HIS A 481 PHE 0.018 0.001 PHE A 17 TYR 0.021 0.001 TYR A 180 ARG 0.002 0.000 ARG N 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 0.857 Fit side-chains TARDY: cannot create tardy model for: "ILE A 462 " (corrupted residue). Skipping it. REVERT: A 34 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7625 (tp30) REVERT: A 76 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7967 (mm) REVERT: A 148 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7933 (ptp-170) REVERT: A 403 ARG cc_start: 0.7493 (ttm110) cc_final: 0.7187 (ttm110) REVERT: M 101 GLN cc_start: 0.8390 (tt0) cc_final: 0.8089 (tt0) REVERT: P 58 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7211 (mp0) outliers start: 19 outliers final: 14 residues processed: 137 average time/residue: 1.0596 time to fit residues: 155.1087 Evaluate side-chains 143 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 24 THR Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 121 THR Chi-restraints excluded: chain O residue 47 THR Chi-restraints excluded: chain O residue 120 ASN Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 89 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.0070 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108546 restraints weight = 9641.510| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.80 r_work: 0.3047 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8203 Z= 0.183 Angle : 2.698 34.523 11363 Z= 0.918 Chirality : 0.261 1.842 1331 Planarity : 0.003 0.033 1243 Dihedral : 41.481 179.946 2548 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.83 % Allowed : 17.14 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.43 (0.29), residues: 888 helix: 2.46 (0.26), residues: 389 sheet: 0.55 (0.37), residues: 205 loop : -0.86 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 467 HIS 0.003 0.001 HIS A 18 PHE 0.019 0.001 PHE A 17 TYR 0.021 0.001 TYR A 180 ARG 0.001 0.000 ARG M 119 =============================================================================== Job complete usr+sys time: 3491.72 seconds wall clock time: 62 minutes 39.39 seconds (3759.39 seconds total)