Starting phenix.real_space_refine on Fri Feb 16 20:04:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iro_35681/02_2024/8iro_35681_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iro_35681/02_2024/8iro_35681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iro_35681/02_2024/8iro_35681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iro_35681/02_2024/8iro_35681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iro_35681/02_2024/8iro_35681_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iro_35681/02_2024/8iro_35681_trim_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 5300 2.51 5 N 1316 2.21 5 O 1474 1.98 5 H 8208 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16350 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "A" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 8130 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'ZEA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.82, per 1000 atoms: 0.48 Number of scatterers: 16350 At special positions: 0 Unit cell: (94.461, 108.077, 101.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1474 8.00 N 1316 7.00 C 5300 6.00 H 8208 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 123 " distance=2.04 Simple disulfide: pdb=" SG CYS B 83 " - pdb=" SG CYS B 111 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 123 " distance=2.04 Simple disulfide: pdb=" SG CYS A 83 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 254 " - pdb=" SG CYS A 287 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN A 270 " " NAG D 1 " - " ASN B 270 " Time building additional restraints: 14.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1940 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 2 sheets defined 60.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 32 through 36 Processing helix chain 'B' and resid 39 through 42 No H-bonds generated for 'chain 'B' and resid 39 through 42' Processing helix chain 'B' and resid 47 through 73 removed outlier: 5.271A pdb=" N TYR B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA B 65 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 109 through 112 Processing helix chain 'B' and resid 118 through 149 Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.952A pdb=" N ALA B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 200 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 213 through 231 removed outlier: 4.400A pdb=" N SER B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 295 through 312 Processing helix chain 'B' and resid 318 through 331 Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 377 through 405 Processing helix chain 'B' and resid 417 through 434 Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'B' and resid 473 through 476 No H-bonds generated for 'chain 'B' and resid 473 through 476' Processing helix chain 'B' and resid 481 through 501 Proline residue: B 486 - end of helix removed outlier: 4.115A pdb=" N LYS B 497 " --> pdb=" O VAL B 493 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER B 498 " --> pdb=" O MET B 494 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL B 499 " --> pdb=" O MET B 495 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N THR B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU B 501 " --> pdb=" O LYS B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 522 Proline residue: B 512 - end of helix removed outlier: 3.771A pdb=" N MET B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Proline residue: B 521 - end of helix Processing helix chain 'B' and resid 526 through 540 Processing helix chain 'B' and resid 542 through 553 Processing helix chain 'A' and resid 20 through 29 Processing helix chain 'A' and resid 32 through 36 Processing helix chain 'A' and resid 39 through 42 No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 47 through 73 removed outlier: 5.271A pdb=" N TYR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ALA A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 82 No H-bonds generated for 'chain 'A' and resid 80 through 82' Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 109 through 112 Processing helix chain 'A' and resid 118 through 149 Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.953A pdb=" N ALA A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 213 through 231 removed outlier: 4.399A pdb=" N SER A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ALA A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 295 through 312 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 344 through 354 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 377 through 405 Processing helix chain 'A' and resid 417 through 434 Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 457 through 469 Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 481 through 501 Proline residue: A 486 - end of helix removed outlier: 4.116A pdb=" N LYS A 497 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR A 500 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 522 Proline residue: A 512 - end of helix removed outlier: 3.770A pdb=" N MET A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Proline residue: A 521 - end of helix Processing helix chain 'A' and resid 526 through 540 Processing helix chain 'A' and resid 542 through 553 Processing sheet with id= A, first strand: chain 'B' and resid 156 through 158 Processing sheet with id= B, first strand: chain 'A' and resid 156 through 158 414 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 14.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8204 1.03 - 1.23: 39 1.23 - 1.42: 3387 1.42 - 1.62: 4822 1.62 - 1.82: 84 Bond restraints: 16536 Sorted by residual: bond pdb=" C6 ZEA B 701 " pdb=" N10 ZEA B 701 " ideal model delta sigma weight residual 1.336 1.464 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C6 ZEA A 701 " pdb=" N10 ZEA A 701 " ideal model delta sigma weight residual 1.336 1.464 -0.128 2.00e-02 2.50e+03 4.12e+01 bond pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 1.502 1.589 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 1.502 1.588 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.73e+00 ... (remaining 16531 not shown) Histogram of bond angle deviations from ideal: 79.23 - 96.72: 4 96.72 - 114.22: 20468 114.22 - 131.71: 9430 131.71 - 149.21: 18 149.21 - 166.70: 2 Bond angle restraints: 29922 Sorted by residual: angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C15 ZEA B 701 " ideal model delta sigma weight residual 125.58 166.70 -41.12 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 125.58 166.66 -41.08 3.00e+00 1.11e-01 1.88e+02 angle pdb=" C12 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C14 ZEA A 701 " ideal model delta sigma weight residual 121.92 87.45 34.47 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C12 ZEA B 701 " pdb=" C13 ZEA B 701 " pdb=" C14 ZEA B 701 " ideal model delta sigma weight residual 121.92 87.48 34.44 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C14 ZEA A 701 " pdb=" C13 ZEA A 701 " pdb=" C15 ZEA A 701 " ideal model delta sigma weight residual 112.50 79.23 33.27 3.00e+00 1.11e-01 1.23e+02 ... (remaining 29917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.96: 7423 24.96 - 49.93: 328 49.93 - 74.89: 123 74.89 - 99.86: 6 99.86 - 124.82: 2 Dihedral angle restraints: 7882 sinusoidal: 4248 harmonic: 3634 Sorted by residual: dihedral pdb=" CA VAL A 484 " pdb=" C VAL A 484 " pdb=" N GLY A 485 " pdb=" CA GLY A 485 " ideal model delta harmonic sigma weight residual 180.00 141.09 38.91 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA VAL B 484 " pdb=" C VAL B 484 " pdb=" N GLY B 485 " pdb=" CA GLY B 485 " ideal model delta harmonic sigma weight residual 180.00 141.10 38.90 0 5.00e+00 4.00e-02 6.05e+01 dihedral pdb=" CA PHE A 332 " pdb=" C PHE A 332 " pdb=" N ARG A 333 " pdb=" CA ARG A 333 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 7879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1303 0.097 - 0.194: 49 0.194 - 0.291: 3 0.291 - 0.388: 0 0.388 - 0.486: 1 Chirality restraints: 1356 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 270 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.89 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 270 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 250 " pdb=" CA THR A 250 " pdb=" OG1 THR A 250 " pdb=" CG2 THR A 250 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1353 not shown) Planarity restraints: 2434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 270 " -0.091 2.00e-02 2.50e+03 6.88e-02 7.09e+01 pdb=" CG ASN A 270 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 270 " 0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN A 270 " 0.073 2.00e-02 2.50e+03 pdb="HD21 ASN A 270 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG C 1 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 486 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO A 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 487 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 486 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO B 487 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 487 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 487 " -0.035 5.00e-02 4.00e+02 ... (remaining 2431 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 474 2.13 - 2.74: 30756 2.74 - 3.36: 50506 3.36 - 3.98: 64948 3.98 - 4.60: 102015 Nonbonded interactions: 248699 Sorted by model distance: nonbonded pdb="HD22 ASN B 67 " pdb=" OG1 THR B 135 " model vdw 1.507 1.850 nonbonded pdb="HD22 ASN A 67 " pdb=" OG1 THR A 135 " model vdw 1.507 1.850 nonbonded pdb="HH22 ARG B 333 " pdb=" OD1 ASP B 347 " model vdw 1.550 1.850 nonbonded pdb="HH22 ARG A 333 " pdb=" OD1 ASP A 347 " model vdw 1.550 1.850 nonbonded pdb=" O PHE B 419 " pdb=" HG SER B 423 " model vdw 1.553 1.850 ... (remaining 248694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.980 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: 0.250 Extract box with map and model: 4.020 Check model and map are aligned: 0.210 Set scattering table: 0.160 Process input model: 56.170 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.128 8328 Z= 0.401 Angle : 1.088 41.124 11334 Z= 0.454 Chirality : 0.045 0.486 1356 Planarity : 0.005 0.062 1400 Dihedral : 13.581 124.823 2938 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1076 helix: 1.28 (0.21), residues: 664 sheet: -4.84 (0.53), residues: 20 loop : -0.47 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.002 0.001 HIS B 350 PHE 0.012 0.002 PHE A 414 TYR 0.013 0.002 TYR B 524 ARG 0.002 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7851 (m-30) cc_final: 0.7624 (m-30) REVERT: B 440 THR cc_start: 0.8584 (p) cc_final: 0.8325 (t) REVERT: A 390 ASP cc_start: 0.7851 (m-30) cc_final: 0.7631 (m-30) REVERT: A 440 THR cc_start: 0.8581 (p) cc_final: 0.8315 (t) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 2.0767 time to fit residues: 205.0247 Evaluate side-chains 75 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 0.0870 chunk 45 optimal weight: 0.1980 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- 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: 0.8339 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8328 Z= 0.187 Angle : 0.985 36.818 11334 Z= 0.390 Chirality : 0.039 0.157 1356 Planarity : 0.004 0.061 1400 Dihedral : 8.279 106.304 1236 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.82 % Allowed : 5.24 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1076 helix: 1.48 (0.20), residues: 666 sheet: -4.82 (0.53), residues: 20 loop : -0.49 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 380 HIS 0.002 0.001 HIS B 350 PHE 0.011 0.001 PHE B 414 TYR 0.009 0.001 TYR B 399 ARG 0.001 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7781 (m-30) cc_final: 0.7548 (m-30) REVERT: B 440 THR cc_start: 0.8591 (p) cc_final: 0.8112 (t) REVERT: B 494 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7259 (mtp) REVERT: A 390 ASP cc_start: 0.7763 (m-30) cc_final: 0.7547 (m-30) REVERT: A 440 THR cc_start: 0.8583 (p) cc_final: 0.8075 (t) REVERT: A 494 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7255 (mtp) outliers start: 7 outliers final: 0 residues processed: 80 average time/residue: 2.4190 time to fit residues: 208.2740 Evaluate side-chains 80 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.8355 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8328 Z= 0.226 Angle : 0.984 36.857 11334 Z= 0.389 Chirality : 0.039 0.152 1356 Planarity : 0.004 0.061 1400 Dihedral : 7.829 98.748 1236 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.28 % Allowed : 5.48 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1076 helix: 1.53 (0.20), residues: 666 sheet: -4.64 (0.61), residues: 20 loop : -0.53 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.002 0.001 HIS B 350 PHE 0.011 0.001 PHE B 414 TYR 0.009 0.001 TYR A 399 ARG 0.001 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7785 (m-30) cc_final: 0.7561 (m-30) REVERT: B 440 THR cc_start: 0.8607 (p) cc_final: 0.8093 (t) REVERT: B 494 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7160 (mtp) REVERT: A 390 ASP cc_start: 0.7771 (m-30) cc_final: 0.7548 (m-30) REVERT: A 440 THR cc_start: 0.8589 (p) cc_final: 0.8070 (t) REVERT: A 494 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7165 (mtp) outliers start: 11 outliers final: 6 residues processed: 82 average time/residue: 2.2649 time to fit residues: 199.7686 Evaluate side-chains 84 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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: 0.8374 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8328 Z= 0.243 Angle : 0.993 37.104 11334 Z= 0.395 Chirality : 0.040 0.156 1356 Planarity : 0.004 0.061 1400 Dihedral : 7.479 90.523 1236 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.63 % Allowed : 6.64 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.02 (0.26), residues: 1076 helix: 1.52 (0.20), residues: 664 sheet: -4.62 (0.63), residues: 20 loop : -0.41 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.002 0.001 HIS B 350 PHE 0.011 0.001 PHE B 414 TYR 0.009 0.001 TYR B 388 ARG 0.001 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7772 (m-30) cc_final: 0.7539 (m-30) REVERT: B 440 THR cc_start: 0.8577 (p) cc_final: 0.8049 (t) REVERT: B 494 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7074 (mtp) REVERT: A 390 ASP cc_start: 0.7744 (m-30) cc_final: 0.7523 (m-30) REVERT: A 440 THR cc_start: 0.8584 (p) cc_final: 0.8022 (t) REVERT: A 494 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7089 (mtp) outliers start: 14 outliers final: 7 residues processed: 80 average time/residue: 2.3165 time to fit residues: 199.4405 Evaluate side-chains 84 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8328 Z= 0.379 Angle : 1.029 37.530 11334 Z= 0.421 Chirality : 0.043 0.129 1356 Planarity : 0.005 0.059 1400 Dihedral : 7.052 73.819 1236 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.00 % Favored : 95.82 % Rotamer: Outliers : 1.63 % Allowed : 7.34 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1076 helix: 1.21 (0.20), residues: 668 sheet: -4.36 (0.70), residues: 20 loop : -0.54 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 380 HIS 0.003 0.001 HIS B 350 PHE 0.013 0.002 PHE B 414 TYR 0.011 0.002 TYR B 388 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7769 (m-30) cc_final: 0.7564 (m-30) REVERT: B 440 THR cc_start: 0.8628 (p) cc_final: 0.8028 (t) REVERT: A 440 THR cc_start: 0.8618 (p) cc_final: 0.8012 (t) outliers start: 14 outliers final: 8 residues processed: 84 average time/residue: 2.2170 time to fit residues: 200.8570 Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 250 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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: 0.8388 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8328 Z= 0.236 Angle : 0.993 37.399 11334 Z= 0.395 Chirality : 0.039 0.132 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.966 45.371 1236 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.75 % Allowed : 8.04 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.26), residues: 1076 helix: 1.36 (0.20), residues: 668 sheet: -4.54 (0.68), residues: 20 loop : -0.46 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 380 HIS 0.002 0.001 HIS B 350 PHE 0.012 0.001 PHE A 414 TYR 0.010 0.001 TYR B 388 ARG 0.001 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7751 (m-30) cc_final: 0.7526 (m-30) REVERT: B 440 THR cc_start: 0.8599 (p) cc_final: 0.8012 (t) REVERT: B 494 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.6739 (mpp) REVERT: A 440 THR cc_start: 0.8604 (p) cc_final: 0.7966 (t) REVERT: A 494 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.6772 (mpp) outliers start: 15 outliers final: 6 residues processed: 86 average time/residue: 2.2031 time to fit residues: 204.9839 Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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: 0.8383 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8328 Z= 0.226 Angle : 0.986 37.275 11334 Z= 0.392 Chirality : 0.039 0.137 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.492 41.437 1236 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.52 % Allowed : 8.39 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1076 helix: 1.43 (0.20), residues: 670 sheet: -4.44 (0.71), residues: 20 loop : -0.51 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 380 HIS 0.002 0.001 HIS B 350 PHE 0.012 0.001 PHE A 414 TYR 0.009 0.001 TYR B 388 ARG 0.001 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7741 (m-30) cc_final: 0.7530 (m-30) REVERT: B 440 THR cc_start: 0.8606 (p) cc_final: 0.7994 (t) REVERT: B 494 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.6715 (mpp) REVERT: A 440 THR cc_start: 0.8611 (p) cc_final: 0.7970 (t) REVERT: A 494 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.6714 (mpp) outliers start: 13 outliers final: 4 residues processed: 84 average time/residue: 2.3174 time to fit residues: 209.9311 Evaluate side-chains 84 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.0270 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- 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: 0.8386 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8328 Z= 0.245 Angle : 0.986 37.356 11334 Z= 0.393 Chirality : 0.039 0.144 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.384 41.971 1236 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.52 % Allowed : 8.51 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1076 helix: 1.43 (0.20), residues: 668 sheet: -4.46 (0.70), residues: 20 loop : -0.43 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 380 HIS 0.002 0.001 HIS B 350 PHE 0.012 0.001 PHE A 414 TYR 0.009 0.001 TYR B 399 ARG 0.001 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 390 ASP cc_start: 0.7747 (m-30) cc_final: 0.7531 (m-30) REVERT: B 440 THR cc_start: 0.8591 (p) cc_final: 0.7984 (t) REVERT: A 440 THR cc_start: 0.8644 (p) cc_final: 0.7930 (t) outliers start: 13 outliers final: 9 residues processed: 85 average time/residue: 2.2216 time to fit residues: 203.5493 Evaluate side-chains 88 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 123 CYS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 470 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.8361 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8328 Z= 0.180 Angle : 0.970 37.152 11334 Z= 0.381 Chirality : 0.038 0.154 1356 Planarity : 0.004 0.059 1400 Dihedral : 5.190 40.704 1236 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.52 % Allowed : 8.62 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.08 (0.26), residues: 1076 helix: 1.57 (0.20), residues: 670 sheet: -4.41 (0.75), residues: 20 loop : -0.47 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 482 HIS 0.001 0.000 HIS B 350 PHE 0.011 0.001 PHE A 414 TYR 0.008 0.001 TYR B 388 ARG 0.001 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.228 Fit side-chains REVERT: B 390 ASP cc_start: 0.7754 (m-30) cc_final: 0.7521 (m-30) REVERT: B 440 THR cc_start: 0.8536 (p) cc_final: 0.7936 (t) REVERT: B 494 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.6672 (mpp) REVERT: A 440 THR cc_start: 0.8531 (p) cc_final: 0.7945 (t) REVERT: A 494 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.6666 (mpp) outliers start: 13 outliers final: 4 residues processed: 86 average time/residue: 2.2356 time to fit residues: 207.2710 Evaluate side-chains 85 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.0170 chunk 68 optimal weight: 0.9980 overall best weight: 1.0022 ------------------------------------------------------------------------------- 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: 0.8349 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8328 Z= 0.176 Angle : 0.972 37.061 11334 Z= 0.382 Chirality : 0.038 0.155 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.170 40.715 1236 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.82 % Allowed : 9.44 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.11 (0.26), residues: 1076 helix: 1.59 (0.20), residues: 670 sheet: -4.30 (0.78), residues: 20 loop : -0.43 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 482 HIS 0.002 0.000 HIS B 350 PHE 0.010 0.001 PHE A 414 TYR 0.008 0.001 TYR B 388 ARG 0.001 0.000 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2152 Ramachandran restraints generated. 1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.432 Fit side-chains REVERT: B 390 ASP cc_start: 0.7746 (m-30) cc_final: 0.7521 (m-30) REVERT: B 494 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.6649 (mpp) REVERT: A 440 THR cc_start: 0.8561 (p) cc_final: 0.7896 (t) REVERT: A 494 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.6620 (mpp) outliers start: 7 outliers final: 4 residues processed: 84 average time/residue: 2.2954 time to fit residues: 207.3655 Evaluate side-chains 86 residues out of total 858 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 470 MET Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 494 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** 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 = 0.3376 r_free = 0.3376 target = 0.125094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.102500 restraints weight = 25034.779| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.51 r_work: 0.2963 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8328 Z= 0.252 Angle : 0.989 37.281 11334 Z= 0.395 Chirality : 0.040 0.148 1356 Planarity : 0.004 0.060 1400 Dihedral : 5.293 41.822 1236 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.05 % Allowed : 9.56 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.02 (0.26), residues: 1076 helix: 1.49 (0.20), residues: 668 sheet: -4.33 (0.73), residues: 20 loop : -0.38 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 380 HIS 0.002 0.001 HIS A 350 PHE 0.011 0.002 PHE B 414 TYR 0.009 0.001 TYR B 388 ARG 0.001 0.000 ARG A 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5145.62 seconds wall clock time: 91 minutes 29.87 seconds (5489.87 seconds total)