Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 07:18:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/04_2023/7mhz_23837_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/04_2023/7mhz_23837.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/04_2023/7mhz_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_23837/04_2023/7mhz_23837_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/04_2023/7mhz_23837_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/04_2023/7mhz_23837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/04_2023/7mhz_23837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/04_2023/7mhz_23837_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mhz_23837/04_2023/7mhz_23837_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-1.21rc1-4938/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: 94 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: 3.98, per 1000 atoms: 0.64 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: 2.59 Conformation dependent library (CDL) restraints added in 854.8 milliseconds 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: 0.66 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: 1.76 Time building geometry restraints manager: 2.82 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 - 24.95: 3169 24.95 - 49.89: 176 49.89 - 74.84: 16 74.84 - 99.78: 2 99.78 - 124.73: 30 Dihedral angle restraints: 3393 sinusoidal: 1304 harmonic: 2089 Sorted by residual: dihedral pdb=" C02 AJP A 505 " pdb=" C85 AJP A 505 " pdb=" O84 AJP A 505 " pdb=" C05 AJP A 505 " ideal model delta sinusoidal sigma weight residual -57.60 67.13 -124.73 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C02 AJP A 511 " pdb=" C85 AJP A 511 " pdb=" O84 AJP A 511 " pdb=" C05 AJP A 511 " ideal model delta sinusoidal sigma weight residual -57.60 66.69 -124.29 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C02 AJP A 510 " pdb=" C03 AJP A 510 " pdb=" C04 AJP A 510 " pdb=" C05 AJP A 510 " ideal model delta sinusoidal sigma weight residual 52.15 -63.07 115.22 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 3390 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.280 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.390 Find NCS groups from input model: 0.150 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.950 ------------------------------------------------------------------------------- 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 : 19.461 124.730 2059 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 % 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 *********************** 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 : 0.733 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1703 time to fit residues: 13.7455 Evaluate side-chains 47 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8901 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6435 Z= 0.222 Angle : 2.555 35.998 8906 Z= 0.870 Chirality : 0.254 1.936 1020 Planarity : 0.004 0.031 992 Dihedral : 12.712 106.840 890 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.52 % 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: 1.53 (0.32), residues: 713 helix: 1.97 (0.27), residues: 390 sheet: 0.23 (0.47), residues: 132 loop : -0.33 (0.44), residues: 191 *********************** 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 : 0.660 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 52 average time/residue: 0.1539 time to fit residues: 11.7611 Evaluate side-chains 49 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0774 time to fit residues: 1.1545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7549 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6435 Z= 0.185 Angle : 2.498 33.715 8906 Z= 0.850 Chirality : 0.258 1.936 1020 Planarity : 0.004 0.031 992 Dihedral : 12.265 108.319 890 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.52 % 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 (0.33), residues: 713 helix: 2.11 (0.27), residues: 384 sheet: 0.29 (0.47), residues: 132 loop : -0.50 (0.44), residues: 197 *********************** 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 57 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.809 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 54 average time/residue: 0.1556 time to fit residues: 12.3546 Evaluate side-chains 50 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0839 time to fit residues: 1.1281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7519 moved from start: 0.1238 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= 0.159 Angle : 2.481 32.980 8906 Z= 0.842 Chirality : 0.260 2.000 1020 Planarity : 0.004 0.030 992 Dihedral : 12.063 106.887 890 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 1.21 % 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: 1.76 (0.33), residues: 713 helix: 2.30 (0.27), residues: 382 sheet: 0.45 (0.47), residues: 129 loop : -0.55 (0.43), residues: 202 *********************** 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 59 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 52 time to evaluate : 0.705 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 57 average time/residue: 0.1507 time to fit residues: 12.5304 Evaluate side-chains 51 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0675 time to fit residues: 1.4903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 62 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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: 0.7621 moved from start: 0.1313 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= 0.347 Angle : 2.509 34.887 8906 Z= 0.862 Chirality : 0.258 1.944 1020 Planarity : 0.004 0.031 992 Dihedral : 12.379 107.405 890 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 1.21 % 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: 1.41 (0.32), residues: 713 helix: 1.87 (0.26), residues: 390 sheet: 0.23 (0.47), residues: 132 loop : -0.40 (0.45), residues: 191 *********************** 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 56 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.684 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.1698 time to fit residues: 12.6284 Evaluate side-chains 51 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0815 time to fit residues: 1.4250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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: 0.7571 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 6435 Z= 0.190 Angle : 2.482 33.642 8906 Z= 0.845 Chirality : 0.260 1.938 1020 Planarity : 0.004 0.032 992 Dihedral : 12.192 106.005 890 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 1.04 % 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: 1.53 (0.33), residues: 713 helix: 2.11 (0.27), residues: 384 sheet: 0.22 (0.47), residues: 131 loop : -0.57 (0.44), residues: 198 *********************** 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 55 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.686 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 54 average time/residue: 0.1644 time to fit residues: 12.8060 Evaluate side-chains 48 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0756 time to fit residues: 1.1668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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: 0.7614 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 6435 Z= 0.298 Angle : 2.494 34.109 8906 Z= 0.853 Chirality : 0.259 1.944 1020 Planarity : 0.004 0.031 992 Dihedral : 12.252 106.225 890 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.52 % 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: 1.41 (0.32), residues: 713 helix: 1.94 (0.27), residues: 390 sheet: 0.09 (0.47), residues: 131 loop : -0.47 (0.45), residues: 192 *********************** 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 52 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.692 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.1691 time to fit residues: 12.3699 Evaluate side-chains 49 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0752 time to fit residues: 1.1463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.0270 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 0.2980 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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** P 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6435 Z= 0.174 Angle : 2.473 32.913 8906 Z= 0.841 Chirality : 0.261 1.945 1020 Planarity : 0.004 0.032 992 Dihedral : 12.060 105.714 890 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.87 % 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: 1.57 (0.33), residues: 713 helix: 2.23 (0.27), residues: 383 sheet: 0.15 (0.47), residues: 131 loop : -0.67 (0.44), residues: 199 *********************** 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 52 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.674 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1578 time to fit residues: 11.1625 Evaluate side-chains 50 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0942 time to fit residues: 1.5638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.0270 chunk 50 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- 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** P 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1561 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= 0.164 Angle : 2.463 32.461 8906 Z= 0.837 Chirality : 0.262 1.951 1020 Planarity : 0.004 0.032 992 Dihedral : 11.877 106.593 890 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.52 % 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: 1.73 (0.33), residues: 713 helix: 2.33 (0.27), residues: 385 sheet: 0.21 (0.47), residues: 131 loop : -0.56 (0.45), residues: 197 *********************** 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 50 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.699 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 48 average time/residue: 0.1634 time to fit residues: 11.5948 Evaluate side-chains 44 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 71 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7537 moved from start: 0.1654 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= 0.164 Angle : 2.458 32.413 8906 Z= 0.835 Chirality : 0.262 1.954 1020 Planarity : 0.004 0.032 992 Dihedral : 11.911 106.619 890 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.17 % 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: 2.38 (0.27), residues: 383 sheet: 0.23 (0.47), residues: 131 loop : -0.60 (0.44), residues: 199 ********************** 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 47 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.721 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.1875 time to fit residues: 12.7190 Evaluate side-chains 45 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0874 time to fit residues: 1.0931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.094479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.074172 restraints weight = 11846.865| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.75 r_work: 0.2971 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 6435 Z= 0.177 Angle : 2.461 32.631 8906 Z= 0.837 Chirality : 0.262 1.954 1020 Planarity : 0.004 0.034 992 Dihedral : 11.913 106.706 890 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 0.35 % 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: 1.74 (0.33), residues: 713 helix: 2.35 (0.27), residues: 383 sheet: 0.22 (0.47), residues: 131 loop : -0.56 (0.45), residues: 199 =============================================================================== Job complete usr+sys time: 1645.74 seconds wall clock time: 30 minutes 27.66 seconds (1827.66 seconds total)