Starting phenix.real_space_refine on Mon Mar 18 19:13:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1u_13764/03_2024/7q1u_13764_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1u_13764/03_2024/7q1u_13764.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1u_13764/03_2024/7q1u_13764_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1u_13764/03_2024/7q1u_13764_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1u_13764/03_2024/7q1u_13764_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1u_13764/03_2024/7q1u_13764.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1u_13764/03_2024/7q1u_13764.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1u_13764/03_2024/7q1u_13764_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q1u_13764/03_2024/7q1u_13764_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= 1.000 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: 8 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 1 5.21 5 S 53 5.16 5 C 7198 2.51 5 N 1849 2.21 5 O 2010 1.98 5 H 10623 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21738 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7945 Classifications: {'peptide': 485} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 469} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'P1L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 13621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 13621 Classifications: {'peptide': 872} Link IDs: {'PTRANS': 42, 'TRANS': 829} Chain breaks: 1 Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 172 Unusual residues: {' MG': 1, 'CLR': 1, 'HD6': 1, 'HEM': 1, 'PLM': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5242 SG CYS A 324 49.621 58.920 115.967 1.00 42.74 S Time building chain proxies: 9.59, per 1000 atoms: 0.44 Number of scatterers: 21738 At special positions: 0 Unit cell: (96.1611, 91.7399, 149.215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 1 26.01 S 53 16.00 P 3 15.00 Mg 1 11.99 O 2010 8.00 N 1849 7.00 C 7198 6.00 H 10623 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 166 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 816 " - pdb=" SG CYS B 889 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.54 Conformation dependent library (CDL) restraints added in 2.2 seconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2510 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 9 sheets defined 46.9% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 4 through 31 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 58 through 69 Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 93 through 129 removed outlier: 7.368A pdb=" N THR A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.658A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.589A pdb=" N TRP A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 187 removed outlier: 3.733A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 237 through 264 Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 282 through 313 removed outlier: 3.514A pdb=" N VAL A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 360 through 378 Processing helix chain 'A' and resid 385 through 407 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 421 through 448 removed outlier: 3.579A pdb=" N CYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 468 through 487 Processing helix chain 'B' and resid 43 through 52 Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 96 through 99 Processing helix chain 'B' and resid 123 through 142 Processing helix chain 'B' and resid 146 through 166 Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 214 through 224 Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 315 through 327 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 505 through 508 No H-bonds generated for 'chain 'B' and resid 505 through 508' Processing helix chain 'B' and resid 583 through 598 removed outlier: 4.321A pdb=" N MET B 591 " --> pdb=" O SER B 587 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 618 Processing helix chain 'B' and resid 626 through 641 Processing helix chain 'B' and resid 671 through 683 removed outlier: 3.725A pdb=" N LYS B 676 " --> pdb=" O TRP B 672 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS B 683 " --> pdb=" O PHE B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 699 removed outlier: 4.269A pdb=" N TRP B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 744 through 755 Processing helix chain 'B' and resid 758 through 778 Proline residue: B 766 - end of helix Processing helix chain 'B' and resid 823 through 825 No H-bonds generated for 'chain 'B' and resid 823 through 825' Processing helix chain 'B' and resid 881 through 883 No H-bonds generated for 'chain 'B' and resid 881 through 883' Processing sheet with id= A, first strand: chain 'B' and resid 26 through 30 Processing sheet with id= B, first strand: chain 'B' and resid 38 through 41 Processing sheet with id= C, first strand: chain 'B' and resid 368 through 370 Processing sheet with id= D, first strand: chain 'B' and resid 388 through 390 Processing sheet with id= E, first strand: chain 'B' and resid 422 through 426 Processing sheet with id= F, first strand: chain 'B' and resid 435 through 441 removed outlier: 6.582A pdb=" N THR B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 908 through 910 removed outlier: 5.890A pdb=" N ARG B 832 " --> pdb=" O LEU B 841 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU B 841 " --> pdb=" O ARG B 832 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 890 through 892 Processing sheet with id= I, first strand: chain 'B' and resid 103 through 107 551 hydrogen bonds defined for protein. 1530 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: 7.90 Time building geometry restraints manager: 19.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.09: 10611 1.09 - 1.34: 3459 1.34 - 1.58: 7898 1.58 - 1.83: 92 1.83 - 2.08: 6 Bond restraints: 22066 Sorted by residual: bond pdb=" CCJ HD6 A 603 " pdb=" OCK HD6 A 603 " ideal model delta sigma weight residual 1.300 1.510 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C5 HD6 A 603 " pdb=" N7 HD6 A 603 " ideal model delta sigma weight residual 1.337 1.526 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" CAP HD6 A 603 " pdb=" CCL HD6 A 603 " ideal model delta sigma weight residual 1.307 1.477 -0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" CCL HD6 A 603 " pdb=" OCK HD6 A 603 " ideal model delta sigma weight residual 1.618 1.499 0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" CAQ HD6 A 603 " pdb=" OAN HD6 A 603 " ideal model delta sigma weight residual 1.359 1.465 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 22061 not shown) Histogram of bond angle deviations from ideal: 73.65 - 94.36: 7 94.36 - 115.06: 26821 115.06 - 135.76: 12780 135.76 - 156.46: 1 156.46 - 177.17: 2 Bond angle restraints: 39611 Sorted by residual: angle pdb=" CB TYR B 130 " pdb=" CA TYR B 130 " pdb=" HA TYR B 130 " ideal model delta sigma weight residual 109.00 73.65 35.35 3.00e+00 1.11e-01 1.39e+02 angle pdb=" N TYR B 130 " pdb=" CA TYR B 130 " pdb=" HA TYR B 130 " ideal model delta sigma weight residual 110.00 74.67 35.33 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C TYR B 130 " pdb=" CA TYR B 130 " pdb=" HA TYR B 130 " ideal model delta sigma weight residual 109.00 74.18 34.82 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N1 HD6 A 603 " pdb=" C6 HD6 A 603 " pdb=" N6 HD6 A 603 " ideal model delta sigma weight residual 104.66 121.21 -16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" C5 HD6 A 603 " pdb=" C6 HD6 A 603 " pdb=" N6 HD6 A 603 " ideal model delta sigma weight residual 135.31 121.00 14.31 3.00e+00 1.11e-01 2.27e+01 ... (remaining 39606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.14: 10037 26.14 - 52.27: 380 52.27 - 78.41: 96 78.41 - 104.55: 7 104.55 - 130.68: 1 Dihedral angle restraints: 10521 sinusoidal: 5561 harmonic: 4960 Sorted by residual: dihedral pdb=" C2B HEM A 602 " pdb=" C3B HEM A 602 " pdb=" CAB HEM A 602 " pdb=" CBB HEM A 602 " ideal model delta sinusoidal sigma weight residual -0.00 45.40 -45.40 2 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CBI HD6 A 603 " pdb=" CBJ HD6 A 603 " pdb=" CBK HD6 A 603 " pdb=" CBL HD6 A 603 " ideal model delta sinusoidal sigma weight residual 180.43 49.75 130.68 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C2C HEM A 602 " pdb=" C3C HEM A 602 " pdb=" CAC HEM A 602 " pdb=" CBC HEM A 602 " ideal model delta sinusoidal sigma weight residual 180.00 145.58 34.42 2 1.00e+01 1.00e-02 1.53e+01 ... (remaining 10518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.001: 1635 1.001 - 2.001: 0 2.001 - 3.002: 0 3.002 - 4.003: 0 4.003 - 5.004: 1 Chirality restraints: 1636 Sorted by residual: chirality pdb=" CCA HD6 A 603 " pdb=" CBZ HD6 A 603 " pdb=" CCB HD6 A 603 " pdb=" OAX HD6 A 603 " both_signs ideal model delta sigma weight residual False 2.51 -2.50 5.00 2.00e-01 2.50e+01 6.26e+02 chirality pdb=" CA TYR B 130 " pdb=" N TYR B 130 " pdb=" C TYR B 130 " pdb=" CB TYR B 130 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA HIS B 134 " pdb=" N HIS B 134 " pdb=" C HIS B 134 " pdb=" CB HIS B 134 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 1633 not shown) Planarity restraints: 3248 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 352 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO A 353 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 643 " 0.007 2.00e-02 2.50e+03 9.87e-03 3.89e+00 pdb=" CG TRP B 643 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B 643 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 643 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 643 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 643 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 643 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 643 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 643 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 643 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP B 643 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP B 643 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP B 643 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 643 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 643 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 643 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 609 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C GLN B 609 " -0.032 2.00e-02 2.50e+03 pdb=" O GLN B 609 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG B 610 " 0.011 2.00e-02 2.50e+03 ... (remaining 3245 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 796 2.16 - 2.77: 42093 2.77 - 3.38: 64952 3.38 - 3.99: 86169 3.99 - 4.60: 133706 Nonbonded interactions: 327716 Sorted by model distance: nonbonded pdb=" OG SER B 315 " pdb="HD21 ASN B 642 " model vdw 1.551 1.850 nonbonded pdb=" O TYR B 752 " pdb=" H GLN B 756 " model vdw 1.559 1.850 nonbonded pdb=" HE2 HIS B 890 " pdb=" OD1 ASN B 902 " model vdw 1.567 1.850 nonbonded pdb=" HH TYR A 207 " pdb=" O LEU A 220 " model vdw 1.583 1.850 nonbonded pdb=" HA TYR B 130 " pdb=" HB3 TYR B 130 " model vdw 1.617 1.952 ... (remaining 327711 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.310 Extract box with map and model: 6.650 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 71.080 Find NCS groups from input model: 0.380 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: 0.000 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 0.210 11443 Z= 0.369 Angle : 0.559 16.550 15573 Z= 0.274 Chirality : 0.130 5.004 1636 Planarity : 0.003 0.053 1953 Dihedral : 14.377 130.683 4131 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 1.71 (0.24), residues: 1346 helix: 2.45 (0.20), residues: 659 sheet: 0.59 (0.42), residues: 157 loop : -0.40 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 643 HIS 0.008 0.001 HIS B 320 PHE 0.015 0.001 PHE A 17 TYR 0.028 0.001 TYR B 512 ARG 0.003 0.000 ARG A 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.815 Fit side-chains revert: symmetry clash REVERT: B 840 GLU cc_start: 0.7943 (pt0) cc_final: 0.7699 (pt0) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 2.7366 time to fit residues: 467.5756 Evaluate side-chains 126 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11443 Z= 0.306 Angle : 0.525 8.590 15573 Z= 0.273 Chirality : 0.040 0.298 1636 Planarity : 0.004 0.050 1953 Dihedral : 8.439 124.438 1634 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.05 % Allowed : 7.14 % Favored : 91.81 % 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: 1.52 (0.23), residues: 1346 helix: 2.25 (0.20), residues: 660 sheet: 0.50 (0.41), residues: 160 loop : -0.42 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 746 HIS 0.008 0.001 HIS B 320 PHE 0.031 0.002 PHE A 17 TYR 0.021 0.002 TYR B 512 ARG 0.005 0.000 ARG B 813 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: B 487 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: B 840 GLU cc_start: 0.7960 (pt0) cc_final: 0.7663 (pt0) outliers start: 12 outliers final: 3 residues processed: 129 average time/residue: 2.6868 time to fit residues: 375.4242 Evaluate side-chains 126 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11443 Z= 0.210 Angle : 0.480 6.787 15573 Z= 0.249 Chirality : 0.038 0.297 1636 Planarity : 0.004 0.049 1953 Dihedral : 8.011 118.869 1634 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.05 % Allowed : 8.01 % Favored : 90.94 % 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: 1.62 (0.23), residues: 1346 helix: 2.35 (0.20), residues: 661 sheet: 0.47 (0.40), residues: 160 loop : -0.38 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 746 HIS 0.007 0.001 HIS B 320 PHE 0.024 0.001 PHE A 17 TYR 0.019 0.001 TYR A 180 ARG 0.006 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8329 (tp) REVERT: A 246 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8257 (mp) REVERT: B 59 GLU cc_start: 0.7518 (tp30) cc_final: 0.7263 (tp30) REVERT: B 367 MET cc_start: 0.9010 (ttp) cc_final: 0.8771 (ttm) REVERT: B 840 GLU cc_start: 0.7922 (pt0) cc_final: 0.7645 (pt0) outliers start: 12 outliers final: 4 residues processed: 132 average time/residue: 2.7211 time to fit residues: 388.8308 Evaluate side-chains 126 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 52 LYS Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 116 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11443 Z= 0.251 Angle : 0.490 7.487 15573 Z= 0.255 Chirality : 0.039 0.296 1636 Planarity : 0.004 0.047 1953 Dihedral : 7.981 106.157 1634 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.31 % Allowed : 8.36 % Favored : 90.33 % 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: 1.59 (0.23), residues: 1346 helix: 2.31 (0.20), residues: 661 sheet: 0.37 (0.38), residues: 164 loop : -0.36 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 746 HIS 0.007 0.001 HIS B 320 PHE 0.024 0.001 PHE A 17 TYR 0.019 0.001 TYR A 180 ARG 0.006 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 121 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8213 (mp) REVERT: B 59 GLU cc_start: 0.7459 (tp30) cc_final: 0.7255 (tp30) REVERT: B 367 MET cc_start: 0.9043 (ttp) cc_final: 0.8798 (ttm) REVERT: B 487 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: B 560 ARG cc_start: 0.7817 (ptt90) cc_final: 0.7569 (mtm-85) REVERT: B 840 GLU cc_start: 0.7916 (pt0) cc_final: 0.7632 (pt0) outliers start: 15 outliers final: 5 residues processed: 131 average time/residue: 2.6180 time to fit residues: 371.8885 Evaluate side-chains 127 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.0010 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11443 Z= 0.221 Angle : 0.478 7.557 15573 Z= 0.248 Chirality : 0.038 0.299 1636 Planarity : 0.003 0.046 1953 Dihedral : 7.696 91.851 1634 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.61 % Allowed : 9.58 % Favored : 89.81 % 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: 1.62 (0.23), residues: 1346 helix: 2.35 (0.20), residues: 661 sheet: 0.36 (0.38), residues: 164 loop : -0.36 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 746 HIS 0.006 0.001 HIS B 320 PHE 0.022 0.001 PHE A 17 TYR 0.019 0.001 TYR A 180 ARG 0.007 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.545 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8820 (mt) cc_final: 0.8459 (tt) REVERT: B 59 GLU cc_start: 0.7528 (tp30) cc_final: 0.7324 (tp30) REVERT: B 367 MET cc_start: 0.9048 (ttp) cc_final: 0.8791 (ttm) REVERT: B 840 GLU cc_start: 0.7909 (pt0) cc_final: 0.7632 (pt0) outliers start: 7 outliers final: 5 residues processed: 124 average time/residue: 2.5943 time to fit residues: 349.4666 Evaluate side-chains 124 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 855 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11443 Z= 0.232 Angle : 0.484 8.093 15573 Z= 0.250 Chirality : 0.038 0.299 1636 Planarity : 0.003 0.045 1953 Dihedral : 7.622 89.136 1634 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.13 % Allowed : 9.23 % Favored : 89.63 % 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: 1.63 (0.23), residues: 1346 helix: 2.37 (0.20), residues: 661 sheet: 0.35 (0.38), residues: 164 loop : -0.34 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 746 HIS 0.006 0.001 HIS B 320 PHE 0.022 0.001 PHE A 17 TYR 0.019 0.001 TYR A 180 ARG 0.004 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 119 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8818 (mt) cc_final: 0.8457 (tt) REVERT: A 246 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8189 (mp) REVERT: B 59 GLU cc_start: 0.7454 (tp30) cc_final: 0.7252 (tp30) REVERT: B 367 MET cc_start: 0.9059 (ttp) cc_final: 0.8799 (ttm) REVERT: B 520 ARG cc_start: 0.8075 (ptm-80) cc_final: 0.7838 (ptt90) REVERT: B 840 GLU cc_start: 0.7912 (pt0) cc_final: 0.7637 (pt0) outliers start: 13 outliers final: 5 residues processed: 125 average time/residue: 2.6960 time to fit residues: 368.4471 Evaluate side-chains 122 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 81 optimal weight: 0.0040 chunk 79 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11443 Z= 0.230 Angle : 0.481 8.533 15573 Z= 0.249 Chirality : 0.038 0.300 1636 Planarity : 0.003 0.044 1953 Dihedral : 7.548 89.188 1634 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.05 % Allowed : 9.58 % Favored : 89.37 % 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: 1.62 (0.23), residues: 1346 helix: 2.36 (0.20), residues: 661 sheet: 0.35 (0.38), residues: 164 loop : -0.35 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 746 HIS 0.006 0.001 HIS B 320 PHE 0.021 0.001 PHE A 17 TYR 0.019 0.001 TYR A 180 ARG 0.004 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.587 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8807 (mt) cc_final: 0.8442 (tt) REVERT: A 246 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8184 (mp) REVERT: B 59 GLU cc_start: 0.7519 (tp30) cc_final: 0.7307 (tp30) REVERT: B 367 MET cc_start: 0.9054 (ttp) cc_final: 0.8794 (ttm) REVERT: B 493 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7336 (pm20) REVERT: B 520 ARG cc_start: 0.8072 (ptm-80) cc_final: 0.7840 (ptt90) REVERT: B 840 GLU cc_start: 0.7914 (pt0) cc_final: 0.7642 (pt0) outliers start: 12 outliers final: 6 residues processed: 124 average time/residue: 2.6193 time to fit residues: 352.5204 Evaluate side-chains 125 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 124 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11443 Z= 0.186 Angle : 0.468 8.327 15573 Z= 0.242 Chirality : 0.038 0.304 1636 Planarity : 0.003 0.044 1953 Dihedral : 7.285 87.164 1634 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.78 % Allowed : 9.76 % Favored : 89.46 % 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: 1.72 (0.23), residues: 1346 helix: 2.46 (0.20), residues: 661 sheet: 0.43 (0.38), residues: 163 loop : -0.34 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 746 HIS 0.006 0.001 HIS B 320 PHE 0.018 0.001 PHE A 17 TYR 0.019 0.001 TYR A 180 ARG 0.003 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8822 (mt) cc_final: 0.8462 (tt) REVERT: B 367 MET cc_start: 0.9061 (ttp) cc_final: 0.8760 (ttm) REVERT: B 520 ARG cc_start: 0.8047 (ptm-80) cc_final: 0.7819 (ptt90) REVERT: B 840 GLU cc_start: 0.7906 (pt0) cc_final: 0.7643 (pt0) outliers start: 9 outliers final: 7 residues processed: 121 average time/residue: 2.7119 time to fit residues: 355.2864 Evaluate side-chains 122 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 115 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 114 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11443 Z= 0.224 Angle : 0.478 8.747 15573 Z= 0.247 Chirality : 0.038 0.299 1636 Planarity : 0.003 0.044 1953 Dihedral : 7.380 88.516 1634 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.96 % Allowed : 9.84 % Favored : 89.20 % 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: 1.70 (0.23), residues: 1346 helix: 2.44 (0.20), residues: 661 sheet: 0.41 (0.38), residues: 164 loop : -0.34 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 746 HIS 0.006 0.001 HIS B 772 PHE 0.021 0.001 PHE A 17 TYR 0.018 0.001 TYR A 180 ARG 0.003 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8850 (mt) cc_final: 0.8499 (tp) REVERT: B 316 TRP cc_start: 0.8618 (OUTLIER) cc_final: 0.8076 (t60) REVERT: B 367 MET cc_start: 0.9047 (ttp) cc_final: 0.8738 (ttm) REVERT: B 493 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7338 (pm20) REVERT: B 520 ARG cc_start: 0.8045 (ptm-80) cc_final: 0.7820 (ptt90) REVERT: B 840 GLU cc_start: 0.7920 (pt0) cc_final: 0.7651 (pt0) outliers start: 11 outliers final: 6 residues processed: 124 average time/residue: 2.7319 time to fit residues: 366.9751 Evaluate side-chains 124 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11443 Z= 0.340 Angle : 0.521 9.128 15573 Z= 0.270 Chirality : 0.040 0.291 1636 Planarity : 0.004 0.045 1953 Dihedral : 7.843 86.417 1634 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.05 % Allowed : 9.93 % Favored : 89.02 % 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: 1.51 (0.23), residues: 1346 helix: 2.25 (0.20), residues: 662 sheet: 0.31 (0.37), residues: 164 loop : -0.38 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 316 HIS 0.007 0.001 HIS B 772 PHE 0.027 0.002 PHE A 17 TYR 0.016 0.002 TYR A 180 ARG 0.002 0.000 ARG B 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 LEU cc_start: 0.8852 (mt) cc_final: 0.8497 (tp) REVERT: A 246 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8201 (mp) REVERT: B 367 MET cc_start: 0.9064 (ttp) cc_final: 0.8815 (ttm) REVERT: B 493 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7282 (pm20) REVERT: B 520 ARG cc_start: 0.8047 (ptm-80) cc_final: 0.7832 (ptt90) REVERT: B 840 GLU cc_start: 0.7941 (pt0) cc_final: 0.7654 (pt0) outliers start: 12 outliers final: 7 residues processed: 126 average time/residue: 2.7051 time to fit residues: 370.0349 Evaluate side-chains 124 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 134 HIS Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 316 TRP Chi-restraints excluded: chain B residue 493 GLU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 902 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.081234 restraints weight = 45056.441| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.76 r_work: 0.2853 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11443 Z= 0.243 Angle : 0.489 8.645 15573 Z= 0.253 Chirality : 0.039 0.303 1636 Planarity : 0.003 0.044 1953 Dihedral : 7.625 88.783 1634 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.78 % Allowed : 10.19 % Favored : 89.02 % 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: 1.57 (0.23), residues: 1346 helix: 2.32 (0.20), residues: 662 sheet: 0.32 (0.37), residues: 164 loop : -0.38 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 316 HIS 0.005 0.001 HIS B 772 PHE 0.021 0.001 PHE A 17 TYR 0.019 0.001 TYR A 180 ARG 0.003 0.000 ARG B 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7600.85 seconds wall clock time: 133 minutes 41.60 seconds (8021.60 seconds total)