Starting phenix.real_space_refine on Thu Dec 7 19:57:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/12_2023/8k6l_36922_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/12_2023/8k6l_36922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/12_2023/8k6l_36922.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/12_2023/8k6l_36922.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/12_2023/8k6l_36922_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k6l_36922/12_2023/8k6l_36922_updated.pdb" } resolution = 2.92 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= 0.092 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 34 5.16 5 Cl 2 4.86 5 C 2749 2.51 5 N 651 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A ARG 58": "NH1" <-> "NH2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 527": "OD1" <-> "OD2" Residue "A ASP 528": "OD1" <-> "OD2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 596": "OD1" <-> "OD2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A TYR 616": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4155 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4086 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 18, 'TRANS': 528} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "B" 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: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'IOQ': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.94, per 1000 atoms: 0.71 Number of scatterers: 4155 At special positions: 0 Unit cell: (65.24, 100.656, 87.608, 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) Cl 2 17.00 S 34 16.00 O 719 8.00 N 651 7.00 C 2749 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.04 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=1.71 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " 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 B 1 " - " NAG B 2 " NAG-ASN " NAG A 802 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 779.1 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 996 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 0 sheets defined 61.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 27 through 50 removed outlier: 3.725A pdb=" N ALA A 33 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.800A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.676A pdb=" N SER A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 117 removed outlier: 3.808A pdb=" N THR A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 171 through 198 removed outlier: 4.252A pdb=" N THR A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) Proline residue: A 187 - end of helix Proline residue: A 190 - end of helix removed outlier: 3.741A pdb=" N SER A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 232 removed outlier: 4.429A pdb=" N MET A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLY A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix removed outlier: 3.865A pdb=" N SER A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.922A pdb=" N VAL A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.810A pdb=" N ILE A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 366 removed outlier: 5.301A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 400 removed outlier: 3.865A pdb=" N VAL A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.514A pdb=" N ILE A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 427 removed outlier: 3.876A pdb=" N PHE A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 528 through 549 removed outlier: 3.542A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 587 through 598 removed outlier: 4.276A pdb=" N THR A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 650 210 hydrogen bonds defined for protein. 630 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: 0.97 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 881 1.33 - 1.45: 1009 1.45 - 1.57: 2315 1.57 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 4258 Sorted by residual: bond pdb=" C THR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.331 1.371 -0.039 7.90e-03 1.60e+04 2.44e+01 bond pdb=" C SER A 140 " pdb=" N THR A 141 " ideal model delta sigma weight residual 1.332 1.291 0.041 1.40e-02 5.10e+03 8.70e+00 bond pdb=" C PHE A 591 " pdb=" O PHE A 591 " ideal model delta sigma weight residual 1.237 1.210 0.026 1.17e-02 7.31e+03 5.05e+00 bond pdb=" C PRO A 588 " pdb=" O PRO A 588 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.16e-02 7.43e+03 4.98e+00 bond pdb=" C ILE A 589 " pdb=" O ILE A 589 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.13e-02 7.83e+03 4.97e+00 ... (remaining 4253 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.02: 112 107.02 - 113.77: 2343 113.77 - 120.51: 1776 120.51 - 127.26: 1513 127.26 - 134.01: 38 Bond angle restraints: 5782 Sorted by residual: angle pdb=" C ILE A 585 " pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta sigma weight residual 111.30 101.87 9.43 9.60e-01 1.09e+00 9.65e+01 angle pdb=" N ILE A 52 " pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 110.62 117.58 -6.96 1.02e+00 9.61e-01 4.65e+01 angle pdb=" N ASN A 375 " pdb=" CA ASN A 375 " pdb=" C ASN A 375 " ideal model delta sigma weight residual 111.02 120.98 -9.96 1.52e+00 4.33e-01 4.30e+01 angle pdb=" C ALA A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta sigma weight residual 120.28 129.02 -8.74 1.34e+00 5.57e-01 4.25e+01 angle pdb=" C THR A 186 " pdb=" N PRO A 187 " pdb=" CA PRO A 187 " ideal model delta sigma weight residual 121.00 113.85 7.15 1.16e+00 7.43e-01 3.80e+01 ... (remaining 5777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 2317 21.07 - 42.14: 131 42.14 - 63.21: 43 63.21 - 84.28: 4 84.28 - 105.35: 16 Dihedral angle restraints: 2511 sinusoidal: 947 harmonic: 1564 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -157.45 71.45 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS A 599 " pdb=" SG CYS A 599 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -155.91 69.91 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" C TYR A 590 " pdb=" N TYR A 590 " pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " ideal model delta harmonic sigma weight residual -122.60 -139.33 16.73 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 2508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 672 0.243 - 0.486: 2 0.486 - 0.729: 2 0.729 - 0.972: 1 0.972 - 1.215: 1 Chirality restraints: 678 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 503 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.69e+01 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 ... (remaining 675 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.094 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.310 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG B 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.448 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " 0.309 2.00e-02 2.50e+03 2.60e-01 8.48e+02 pdb=" C7 NAG A 802 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.030 2.00e-02 2.50e+03 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1281 2.82 - 3.34: 3843 3.34 - 3.86: 6430 3.86 - 4.38: 7227 4.38 - 4.90: 12370 Nonbonded interactions: 31151 Sorted by model distance: nonbonded pdb=" O SER A 85 " pdb=" OG SER A 89 " model vdw 2.297 2.440 nonbonded pdb=" O GLY A 324 " pdb=" OG SER A 328 " model vdw 2.387 2.440 nonbonded pdb=" O LEU A 507 " pdb=" CD1 LEU A 507 " model vdw 2.400 3.460 nonbonded pdb=" O SER A 491 " pdb=" CD1 PHE A 501 " model vdw 2.463 3.340 nonbonded pdb=" O SER A 371 " pdb=" OG SER A 371 " model vdw 2.475 2.440 ... (remaining 31146 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.770 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.780 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 35.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 0.041 4258 Z= 0.346 Angle : 1.005 11.983 5782 Z= 0.659 Chirality : 0.086 1.215 678 Planarity : 0.019 0.294 700 Dihedral : 17.751 105.346 1494 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.17 % Allowed : 13.98 % Favored : 83.86 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.31), residues: 539 helix: -0.93 (0.25), residues: 333 sheet: None (None), residues: 0 loop : -2.71 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 171 HIS 0.002 0.001 HIS A 575 PHE 0.012 0.001 PHE A 621 TYR 0.026 0.002 TYR A 625 ARG 0.002 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.468 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 1.0624 time to fit residues: 91.6727 Evaluate side-chains 58 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.6166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.0060 chunk 49 optimal weight: 6.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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: 0.7788 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4258 Z= 0.190 Angle : 0.647 9.063 5782 Z= 0.318 Chirality : 0.055 0.788 678 Planarity : 0.004 0.045 700 Dihedral : 8.990 52.372 659 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.61 % Allowed : 20.72 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.36), residues: 539 helix: 0.82 (0.28), residues: 342 sheet: None (None), residues: 0 loop : -2.21 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 171 HIS 0.002 0.001 HIS A 115 PHE 0.012 0.001 PHE A 501 TYR 0.022 0.001 TYR A 625 ARG 0.002 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.601 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 63 average time/residue: 0.9696 time to fit residues: 63.7215 Evaluate side-chains 54 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 0.4479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7823 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4258 Z= 0.181 Angle : 0.575 8.808 5782 Z= 0.288 Chirality : 0.051 0.665 678 Planarity : 0.004 0.045 700 Dihedral : 6.915 59.624 659 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.86 % Allowed : 19.52 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.37), residues: 539 helix: 1.53 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.85 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 254 HIS 0.001 0.001 HIS A 575 PHE 0.013 0.001 PHE A 621 TYR 0.022 0.001 TYR A 625 ARG 0.012 0.001 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.426 Fit side-chains outliers start: 16 outliers final: 10 residues processed: 64 average time/residue: 0.9472 time to fit residues: 63.5258 Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 2 average time/residue: 0.5474 time to fit residues: 1.7777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.0020 chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4258 Z= 0.160 Angle : 0.533 6.505 5782 Z= 0.272 Chirality : 0.049 0.638 678 Planarity : 0.004 0.046 700 Dihedral : 6.392 53.474 659 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.61 % Allowed : 20.24 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.37), residues: 539 helix: 1.80 (0.29), residues: 338 sheet: None (None), residues: 0 loop : -1.68 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 254 HIS 0.001 0.001 HIS A 575 PHE 0.014 0.001 PHE A 501 TYR 0.021 0.001 TYR A 625 ARG 0.003 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 50 time to evaluate : 0.439 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 60 average time/residue: 0.9204 time to fit residues: 57.8748 Evaluate side-chains 55 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.3965 time to fit residues: 1.9193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 26 optimal weight: 0.0570 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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: 0.7832 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4258 Z= 0.178 Angle : 0.538 7.936 5782 Z= 0.275 Chirality : 0.049 0.619 678 Planarity : 0.004 0.044 700 Dihedral : 6.334 54.139 659 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.89 % Allowed : 21.45 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.37), residues: 539 helix: 2.02 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.63 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 254 HIS 0.001 0.001 HIS A 520 PHE 0.014 0.001 PHE A 386 TYR 0.021 0.001 TYR A 625 ARG 0.004 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.474 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 1.0428 time to fit residues: 59.9447 Evaluate side-chains 55 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.461 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 2 average time/residue: 0.0826 time to fit residues: 0.8594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.3980 chunk 50 optimal weight: 0.0870 chunk 5 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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: 0.7835 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4258 Z= 0.176 Angle : 0.532 7.183 5782 Z= 0.273 Chirality : 0.048 0.603 678 Planarity : 0.004 0.043 700 Dihedral : 6.236 53.829 659 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.86 % Allowed : 20.00 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.37), residues: 539 helix: 2.14 (0.29), residues: 331 sheet: None (None), residues: 0 loop : -1.50 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 254 HIS 0.002 0.001 HIS A 520 PHE 0.012 0.001 PHE A 621 TYR 0.020 0.001 TYR A 625 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.459 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 57 average time/residue: 1.1076 time to fit residues: 66.1059 Evaluate side-chains 54 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.467 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.7391 time to fit residues: 2.4316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4258 Z= 0.158 Angle : 0.514 7.902 5782 Z= 0.261 Chirality : 0.048 0.598 678 Planarity : 0.004 0.043 700 Dihedral : 6.136 53.792 659 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.13 % Allowed : 20.96 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.37), residues: 539 helix: 2.35 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.45 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 254 HIS 0.001 0.001 HIS A 520 PHE 0.014 0.001 PHE A 386 TYR 0.019 0.001 TYR A 625 ARG 0.001 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 0.464 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 59 average time/residue: 1.0645 time to fit residues: 65.5484 Evaluate side-chains 56 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.476 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 1 average time/residue: 0.0968 time to fit residues: 0.7438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.0170 chunk 25 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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: 0.7849 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4258 Z= 0.190 Angle : 0.535 8.467 5782 Z= 0.274 Chirality : 0.048 0.592 678 Planarity : 0.004 0.043 700 Dihedral : 6.167 53.997 659 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.89 % Allowed : 20.96 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.37), residues: 539 helix: 2.26 (0.30), residues: 331 sheet: None (None), residues: 0 loop : -1.31 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.002 0.001 HIS A 520 PHE 0.014 0.001 PHE A 386 TYR 0.022 0.001 TYR A 625 ARG 0.001 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.436 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 54 average time/residue: 1.0797 time to fit residues: 60.9317 Evaluate side-chains 53 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 1 average time/residue: 0.0905 time to fit residues: 0.7680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.0370 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 49 optimal weight: 0.0040 chunk 42 optimal weight: 0.9980 overall best weight: 0.4670 ------------------------------------------------------------------------------- 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: 0.7809 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4258 Z= 0.156 Angle : 0.510 8.860 5782 Z= 0.259 Chirality : 0.047 0.585 678 Planarity : 0.004 0.044 700 Dihedral : 6.025 53.573 659 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.93 % Allowed : 21.93 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.37), residues: 539 helix: 2.46 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -1.35 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.002 0.001 HIS A 520 PHE 0.015 0.001 PHE A 386 TYR 0.018 0.001 TYR A 625 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.419 Fit side-chains outliers start: 8 outliers final: 8 residues processed: 51 average time/residue: 1.1237 time to fit residues: 59.7072 Evaluate side-chains 52 residues out of total 473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 1 average time/residue: 0.1129 time to fit residues: 0.7666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.5731 > 50: distance: 2 - 26: 23.424 distance: 6 - 35: 18.883 distance: 11 - 44: 23.964 distance: 21 - 26: 19.995 distance: 26 - 27: 8.469 distance: 27 - 28: 36.120 distance: 27 - 30: 39.003 distance: 28 - 29: 22.085 distance: 28 - 35: 46.993 distance: 30 - 31: 34.972 distance: 31 - 32: 25.464 distance: 32 - 33: 23.489 distance: 32 - 34: 49.231 distance: 35 - 36: 18.458 distance: 36 - 37: 25.227 distance: 36 - 39: 25.027 distance: 37 - 38: 15.764 distance: 37 - 44: 16.082 distance: 39 - 40: 15.446 distance: 40 - 41: 16.486 distance: 41 - 42: 20.890 distance: 41 - 43: 8.485 distance: 44 - 45: 20.477 distance: 45 - 46: 33.528 distance: 45 - 48: 33.628 distance: 46 - 47: 4.675 distance: 46 - 53: 63.148 distance: 48 - 49: 13.342 distance: 49 - 50: 26.413 distance: 50 - 51: 21.338 distance: 50 - 52: 23.184 distance: 53 - 54: 35.510 distance: 54 - 55: 26.593 distance: 54 - 57: 27.266 distance: 55 - 56: 58.072 distance: 55 - 65: 21.069 distance: 57 - 58: 16.416 distance: 58 - 59: 18.826 distance: 58 - 60: 11.705 distance: 59 - 61: 3.116 distance: 60 - 62: 12.407 distance: 61 - 63: 15.597 distance: 62 - 63: 17.228 distance: 63 - 64: 20.036 distance: 65 - 66: 21.734 distance: 66 - 67: 42.643 distance: 67 - 68: 41.414 distance: 67 - 69: 43.954 distance: 69 - 70: 52.910 distance: 70 - 71: 9.018 distance: 70 - 73: 44.864 distance: 71 - 78: 45.723 distance: 73 - 74: 53.728 distance: 74 - 75: 5.815 distance: 75 - 76: 56.299 distance: 75 - 77: 33.508 distance: 78 - 79: 28.318 distance: 78 - 84: 18.911 distance: 79 - 80: 27.818 distance: 79 - 82: 7.453 distance: 80 - 81: 15.035 distance: 80 - 85: 40.786 distance: 82 - 83: 7.979 distance: 83 - 84: 41.127 distance: 85 - 86: 7.650 distance: 86 - 87: 33.804 distance: 86 - 89: 31.865 distance: 87 - 88: 33.953 distance: 87 - 91: 43.028 distance: 89 - 90: 13.867 distance: 91 - 92: 30.480 distance: 92 - 93: 33.465 distance: 92 - 95: 26.797 distance: 93 - 94: 27.516 distance: 93 - 97: 26.826 distance: 95 - 96: 25.229 distance: 97 - 98: 8.041 distance: 98 - 99: 20.999 distance: 98 - 101: 27.432 distance: 99 - 100: 11.826 distance: 99 - 106: 29.205 distance: 101 - 102: 23.171 distance: 102 - 103: 27.879 distance: 103 - 104: 26.828 distance: 104 - 105: 21.365