Starting phenix.real_space_refine on Mon Mar 11 00:08:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/03_2024/7mhz_23837_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/03_2024/7mhz_23837.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/03_2024/7mhz_23837_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/03_2024/7mhz_23837_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/03_2024/7mhz_23837_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/03_2024/7mhz_23837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/03_2024/7mhz_23837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/03_2024/7mhz_23837_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/03_2024/7mhz_23837_updated.pdb" } resolution = 3.2 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= 0.079 sd= 0.156 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 41 5.16 5 C 4149 2.51 5 N 933 2.21 5 O 1059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 34": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "P ARG 78": "NH1" <-> "NH2" 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: 6189 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 51 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "A" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3980 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 16, 'TRANS': 474} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "O" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 793 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 476 Unusual residues: {'AJP': 10, 'HEM': 1, 'PKZ': 3} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 667 Unresolved non-hydrogen angles: 997 Unresolved non-hydrogen dihedrals: 1351 Unresolved non-hydrogen chiralities: 248 Planarities with less than four sites: {'PKZ:plan-3': 2, 'PKZ:plan-2': 2, 'PKZ:plan-1': 2, 'PKZ:plan-5': 1, 'PKZ:plan-4': 2} Unresolved non-hydrogen planarities: 45 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2698 SG CYS A 324 41.620 48.101 81.893 1.00106.78 S Time building chain proxies: 4.16, per 1000 atoms: 0.67 Number of scatterers: 6189 At special positions: 0 Unit cell: (71.82, 79.8, 118.636, 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 41 16.00 P 6 15.00 O 1059 8.00 N 933 7.00 C 4149 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.0 seconds 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 6 sheets defined 54.1% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 4 through 31 Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 58 through 69 removed outlier: 3.741A pdb=" N GLU A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 93 through 130 removed outlier: 7.885A pdb=" N THR A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 4.257A pdb=" N PHE A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.962A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 164 through 189 removed outlier: 3.663A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' 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 230 removed outlier: 3.789A pdb=" N GLN A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 264 removed outlier: 3.691A pdb=" N CYS A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 274 through 279 removed outlier: 3.650A pdb=" N GLU A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 279' Processing helix chain 'A' and resid 282 through 314 removed outlier: 3.865A pdb=" N VAL A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix 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 357 through 379 removed outlier: 7.331A pdb=" N LEU A 361 " --> pdb=" O GLN A 358 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LEU A 362 " --> pdb=" O HIS A 359 " (cutoff:3.500A) 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 447 removed outlier: 3.933A pdb=" N MET A 438 " --> pdb=" O CYS A 434 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 468 through 488 removed outlier: 3.714A pdb=" N GLN A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 50 No H-bonds generated for 'chain 'O' and resid 48 through 50' Processing sheet with id= A, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= B, first strand: chain 'O' and resid 22 through 25 removed outlier: 3.554A pdb=" N VAL O 37 " --> pdb=" O ASN O 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN O 104 " --> pdb=" O VAL O 37 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR O 99 " --> pdb=" O GLU O 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'O' and resid 112 through 117 removed outlier: 6.592A pdb=" N ARG O 57 " --> pdb=" O TRP O 66 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N TRP O 66 " --> pdb=" O ARG O 57 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN O 71 " --> pdb=" O GLU O 76 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU O 76 " --> pdb=" O ASN O 71 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 23 through 26 Processing sheet with id= E, first strand: chain 'P' and resid 29 through 31 removed outlier: 6.485A pdb=" N LYS P 127 " --> pdb=" O LEU P 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'P' and resid 109 through 114 removed outlier: 3.656A pdb=" N ILE P 72 " --> pdb=" O TRP P 59 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU P 61 " --> pdb=" O LEU P 70 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU P 70 " --> pdb=" O LEU P 61 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 864 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: 1.78 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 1743 1.35 - 1.53: 3718 1.53 - 1.70: 907 1.70 - 1.87: 63 1.87 - 2.04: 4 Bond restraints: 6435 Sorted by residual: bond pdb=" C1 PLM B 101 " pdb=" O2 PLM B 101 " ideal model delta sigma weight residual 1.249 1.183 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CBP PKZ A 502 " pdb=" CDP PKZ A 502 " ideal model delta sigma weight residual 1.572 1.524 0.048 2.00e-02 2.50e+03 5.86e+00 bond pdb=" CBP PKZ A 503 " pdb=" CDP PKZ A 503 " ideal model delta sigma weight residual 1.572 1.524 0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" O3B PKZ A 503 " pdb=" P3B PKZ A 503 " ideal model delta sigma weight residual 1.689 1.650 0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" O3B PKZ A 502 " pdb=" P3B PKZ A 502 " ideal model delta sigma weight residual 1.689 1.650 0.039 2.00e-02 2.50e+03 3.73e+00 ... (remaining 6430 not shown) Histogram of bond angle deviations from ideal: 89.44 - 107.38: 370 107.38 - 125.32: 8322 125.32 - 143.26: 212 143.26 - 161.21: 0 161.21 - 179.15: 2 Bond angle restraints: 8906 Sorted by residual: angle pdb=" C07 AJP A 512 " pdb=" C08 AJP A 512 " pdb=" C10 AJP A 512 " ideal model delta sigma weight residual 107.39 98.10 9.29 3.00e+00 1.11e-01 9.58e+00 angle pdb=" C06 AJP A 512 " pdb=" C07 AJP A 512 " pdb=" C12 AJP A 512 " ideal model delta sigma weight residual 120.30 129.05 -8.75 3.00e+00 1.11e-01 8.51e+00 angle pdb=" C08 AJP A 512 " pdb=" C07 AJP A 512 " pdb=" C12 AJP A 512 " ideal model delta sigma weight residual 106.21 97.60 8.61 3.00e+00 1.11e-01 8.24e+00 angle pdb=" C07 AJP A 512 " pdb=" C08 AJP A 512 " pdb=" O09 AJP A 512 " ideal model delta sigma weight residual 107.32 99.42 7.90 3.00e+00 1.11e-01 6.94e+00 angle pdb=" CA TYR A 300 " pdb=" CB TYR A 300 " pdb=" CG TYR A 300 " ideal model delta sigma weight residual 113.90 109.68 4.22 1.80e+00 3.09e-01 5.49e+00 ... (remaining 8901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 3608 35.93 - 71.86: 255 71.86 - 107.79: 149 107.79 - 143.72: 241 143.72 - 179.65: 57 Dihedral angle restraints: 4310 sinusoidal: 2221 harmonic: 2089 Sorted by residual: dihedral pdb=" C22 AJP A 512 " pdb=" C20 AJP A 512 " pdb=" C21 AJP A 512 " pdb=" C80 AJP A 512 " ideal model delta sinusoidal sigma weight residual 65.75 -114.60 -179.65 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C22 AJP A 513 " pdb=" C20 AJP A 513 " pdb=" C21 AJP A 513 " pdb=" C80 AJP A 513 " ideal model delta sinusoidal sigma weight residual 65.75 -113.84 179.59 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C22 AJP A 505 " pdb=" C20 AJP A 505 " pdb=" C21 AJP A 505 " pdb=" C80 AJP A 505 " ideal model delta sinusoidal sigma weight residual 65.75 -113.12 178.87 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 4307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.204: 922 1.204 - 2.408: 0 2.408 - 3.612: 0 3.612 - 4.815: 10 4.815 - 6.019: 88 Chirality restraints: 1020 Sorted by residual: chirality pdb=" C12 AJP A 505 " pdb=" C07 AJP A 505 " pdb=" C11 AJP A 505 " pdb=" C13 AJP A 505 " both_signs ideal model delta sigma weight residual False 3.01 -3.01 6.02 2.00e-01 2.50e+01 9.06e+02 chirality pdb=" C12 AJP A 509 " pdb=" C07 AJP A 509 " pdb=" C11 AJP A 509 " pdb=" C13 AJP A 509 " both_signs ideal model delta sigma weight residual False 3.01 -3.01 6.01 2.00e-01 2.50e+01 9.04e+02 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 -3.00 6.01 2.00e-01 2.50e+01 9.03e+02 ... (remaining 1017 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 373 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C ALA A 373 " -0.041 2.00e-02 2.50e+03 pdb=" O ALA A 373 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A 374 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 69 " -0.012 2.00e-02 2.50e+03 1.10e-02 3.00e+00 pdb=" CG TRP O 69 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP O 69 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP O 69 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP O 69 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 69 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP O 69 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 69 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 69 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP O 69 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 371 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C THR A 371 " 0.029 2.00e-02 2.50e+03 pdb=" O THR A 371 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE A 372 " -0.010 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 756 2.75 - 3.29: 5964 3.29 - 3.82: 10577 3.82 - 4.36: 11937 4.36 - 4.90: 21455 Nonbonded interactions: 50689 Sorted by model distance: nonbonded pdb=" NZ LYS P 63 " pdb=" O GLU P 105 " model vdw 2.210 2.520 nonbonded pdb=" NH2 ARG A 176 " pdb=" O VAL A 213 " model vdw 2.252 2.520 nonbonded pdb=" OE2 GLU P 58 " pdb=" OH TYR P 60 " model vdw 2.268 2.440 nonbonded pdb=" OG1 THR O 36 " pdb=" O ASN O 104 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR A 207 " pdb=" O LEU A 220 " model vdw 2.271 2.440 ... (remaining 50684 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 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: 12.740 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.360 Find NCS groups from input model: 0.160 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 6435 Z= 0.306 Angle : 0.769 9.286 8906 Z= 0.348 Chirality : 1.632 6.019 1020 Planarity : 0.004 0.032 992 Dihedral : 49.488 179.647 2976 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.32), residues: 713 helix: 1.89 (0.27), residues: 391 sheet: 0.25 (0.49), residues: 119 loop : -0.36 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP O 69 HIS 0.004 0.001 HIS A 263 PHE 0.015 0.001 PHE A 17 TYR 0.024 0.002 TYR A 180 ARG 0.002 0.000 ARG O 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: O 119 TRP cc_start: 0.7507 (t-100) cc_final: 0.7069 (t-100) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1550 time to fit residues: 12.7397 Evaluate side-chains 47 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6435 Z= 0.222 Angle : 2.580 35.804 8906 Z= 0.878 Chirality : 0.242 1.835 1020 Planarity : 0.004 0.031 992 Dihedral : 40.960 179.926 1807 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.52 % Allowed : 5.71 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.52 (0.32), residues: 713 helix: 1.97 (0.27), residues: 390 sheet: 0.23 (0.47), residues: 132 loop : -0.36 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 69 HIS 0.010 0.001 HIS A 481 PHE 0.017 0.001 PHE A 17 TYR 0.021 0.002 TYR A 180 ARG 0.001 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.620 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.1647 time to fit residues: 12.4140 Evaluate side-chains 49 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 9.9990 chunk 20 optimal weight: 0.0060 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.0020 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.3608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6435 Z= 0.199 Angle : 2.525 34.456 8906 Z= 0.859 Chirality : 0.244 1.834 1020 Planarity : 0.004 0.031 992 Dihedral : 40.825 179.633 1807 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.87 % Allowed : 7.27 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.52 (0.32), residues: 713 helix: 2.07 (0.27), residues: 384 sheet: 0.24 (0.47), residues: 132 loop : -0.52 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 69 HIS 0.007 0.001 HIS A 481 PHE 0.018 0.001 PHE A 17 TYR 0.020 0.001 TYR A 180 ARG 0.001 0.000 ARG O 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 49 time to evaluate : 0.766 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.1576 time to fit residues: 11.7831 Evaluate side-chains 50 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6435 Z= 0.153 Angle : 2.516 34.110 8906 Z= 0.854 Chirality : 0.244 1.830 1020 Planarity : 0.004 0.031 992 Dihedral : 40.818 179.978 1807 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.04 % Allowed : 9.52 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.72 (0.32), residues: 713 helix: 2.27 (0.27), residues: 382 sheet: 0.43 (0.47), residues: 129 loop : -0.56 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 486 HIS 0.007 0.001 HIS A 481 PHE 0.017 0.001 PHE A 17 TYR 0.020 0.001 TYR A 180 ARG 0.001 0.000 ARG P 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.683 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.1474 time to fit residues: 12.5627 Evaluate side-chains 52 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 28 optimal weight: 0.0040 chunk 59 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6435 Z= 0.275 Angle : 2.531 34.824 8906 Z= 0.865 Chirality : 0.243 1.831 1020 Planarity : 0.004 0.030 992 Dihedral : 40.843 179.988 1807 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.56 % Allowed : 9.86 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.50 (0.32), residues: 713 helix: 1.97 (0.27), residues: 390 sheet: 0.22 (0.47), residues: 132 loop : -0.40 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 69 HIS 0.007 0.001 HIS A 481 PHE 0.019 0.001 PHE A 17 TYR 0.021 0.002 TYR A 300 ARG 0.002 0.000 ARG O 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.643 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.1535 time to fit residues: 12.2746 Evaluate side-chains 55 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6435 Z= 0.182 Angle : 2.516 34.332 8906 Z= 0.856 Chirality : 0.244 1.833 1020 Planarity : 0.004 0.032 992 Dihedral : 40.866 179.898 1807 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.08 % Allowed : 10.21 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.58 (0.32), residues: 713 helix: 2.17 (0.27), residues: 384 sheet: 0.21 (0.47), residues: 132 loop : -0.59 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 128 HIS 0.007 0.001 HIS A 481 PHE 0.019 0.001 PHE A 17 TYR 0.019 0.001 TYR A 180 ARG 0.001 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 49 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.7766 (mtt) cc_final: 0.7296 (mtt) REVERT: O 121 TYR cc_start: 0.7555 (p90) cc_final: 0.7291 (p90) outliers start: 12 outliers final: 9 residues processed: 59 average time/residue: 0.1484 time to fit residues: 12.9485 Evaluate side-chains 55 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6435 Z= 0.351 Angle : 2.543 35.576 8906 Z= 0.873 Chirality : 0.243 1.842 1020 Planarity : 0.004 0.031 992 Dihedral : 40.822 179.685 1807 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.73 % Allowed : 11.76 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.26 (0.32), residues: 713 helix: 1.82 (0.26), residues: 390 sheet: 0.01 (0.46), residues: 132 loop : -0.51 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 69 HIS 0.007 0.001 HIS A 481 PHE 0.033 0.002 PHE A 17 TYR 0.023 0.002 TYR A 300 ARG 0.003 0.000 ARG O 117 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.680 Fit side-chains REVERT: A 311 MET cc_start: 0.7940 (mtt) cc_final: 0.7606 (mtt) outliers start: 10 outliers final: 9 residues processed: 55 average time/residue: 0.1652 time to fit residues: 12.9051 Evaluate side-chains 54 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6435 Z= 0.225 Angle : 2.522 34.914 8906 Z= 0.859 Chirality : 0.244 1.837 1020 Planarity : 0.004 0.033 992 Dihedral : 40.780 179.876 1807 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.56 % Allowed : 12.98 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.32), residues: 713 helix: 2.03 (0.27), residues: 384 sheet: -0.01 (0.46), residues: 131 loop : -0.64 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 128 HIS 0.007 0.001 HIS A 481 PHE 0.033 0.001 PHE A 17 TYR 0.018 0.001 TYR A 300 ARG 0.001 0.000 ARG P 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.664 Fit side-chains REVERT: A 311 MET cc_start: 0.7912 (mtt) cc_final: 0.7603 (mtt) outliers start: 9 outliers final: 8 residues processed: 51 average time/residue: 0.1571 time to fit residues: 11.6972 Evaluate side-chains 51 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 136 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.0010 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 68 optimal weight: 9.9990 chunk 41 optimal weight: 0.0980 overall best weight: 0.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6435 Z= 0.143 Angle : 2.506 34.002 8906 Z= 0.851 Chirality : 0.245 1.847 1020 Planarity : 0.004 0.032 992 Dihedral : 40.623 179.927 1807 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.38 % Allowed : 13.32 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.60 (0.33), residues: 713 helix: 2.27 (0.27), residues: 382 sheet: 0.12 (0.47), residues: 131 loop : -0.65 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.007 0.001 HIS A 481 PHE 0.030 0.001 PHE A 17 TYR 0.020 0.001 TYR A 180 ARG 0.001 0.000 ARG O 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.584 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 52 average time/residue: 0.1534 time to fit residues: 11.4731 Evaluate side-chains 54 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 7.9990 chunk 66 optimal weight: 0.0270 chunk 57 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6435 Z= 0.156 Angle : 2.504 33.835 8906 Z= 0.850 Chirality : 0.245 1.847 1020 Planarity : 0.004 0.030 992 Dihedral : 40.458 179.860 1807 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.21 % Allowed : 13.15 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.75 (0.33), residues: 713 helix: 2.33 (0.27), residues: 384 sheet: 0.20 (0.47), residues: 131 loop : -0.49 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.005 0.001 HIS A 481 PHE 0.035 0.001 PHE A 17 TYR 0.020 0.001 TYR A 180 ARG 0.002 0.000 ARG A 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.663 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 7 residues processed: 52 average time/residue: 0.1555 time to fit residues: 11.9076 Evaluate side-chains 53 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 TYR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 41 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.095819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.075885 restraints weight = 11797.861| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.71 r_work: 0.3002 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6435 Z= 0.148 Angle : 2.499 33.684 8906 Z= 0.848 Chirality : 0.246 1.848 1020 Planarity : 0.004 0.031 992 Dihedral : 40.453 179.978 1807 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.73 % Allowed : 12.46 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.33), residues: 713 helix: 2.40 (0.27), residues: 385 sheet: 0.20 (0.47), residues: 131 loop : -0.44 (0.45), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 486 HIS 0.005 0.001 HIS A 481 PHE 0.032 0.001 PHE A 17 TYR 0.021 0.001 TYR A 180 ARG 0.001 0.000 ARG P 74 =============================================================================== Job complete usr+sys time: 1810.21 seconds wall clock time: 33 minutes 23.54 seconds (2003.54 seconds total)