Starting phenix.real_space_refine on Fri Jul 25 14:56:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k69_36919/07_2025/8k69_36919.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k69_36919/07_2025/8k69_36919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k69_36919/07_2025/8k69_36919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k69_36919/07_2025/8k69_36919.map" model { file = "/net/cci-nas-00/data/ceres_data/8k69_36919/07_2025/8k69_36919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k69_36919/07_2025/8k69_36919.cif" } resolution = 2.33 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 36 5.16 5 Na 6 4.78 5 C 5140 2.51 5 N 1140 2.21 5 O 1416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3574 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 458, 3574 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3657 Chain: "B" Number of atoms: 3577 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3574 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 458, 3574 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3657 Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 232 Unusual residues: {' NA': 3, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 232 Unusual residues: {' NA': 3, 'CLR': 1, 'PC1': 1, 'PTY': 1, 'T7X': 1, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Time building chain proxies: 10.80, per 1000 atoms: 1.39 Number of scatterers: 7744 At special positions: 0 Unit cell: (86.7227, 107.191, 84.0294, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Na 6 11.00 O 1416 8.00 N 1140 7.00 C 5140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG ACYS A 488 " distance=2.08 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG ACYS B 488 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.8 seconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 77.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 22 through 38 Processing helix chain 'A' and resid 39 through 62 Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 93 through 97 removed outlier: 3.543A pdb=" N VAL A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 179 through 214 Processing helix chain 'A' and resid 214 through 225 Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 258 through 273 Processing helix chain 'A' and resid 275 through 292 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 313 through 340 Processing helix chain 'A' and resid 342 through 346 Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 378 through 391 removed outlier: 3.537A pdb=" N LEU A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 425 through 441 Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.714A pdb=" N LEU A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 516 Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.583A pdb=" N THR A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 38 Processing helix chain 'B' and resid 39 through 62 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.543A pdb=" N VAL B 96 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 113 Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 179 through 214 Processing helix chain 'B' and resid 214 through 225 Proline residue: B 220 - end of helix Processing helix chain 'B' and resid 227 through 242 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 258 through 273 Processing helix chain 'B' and resid 275 through 292 Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 313 through 340 Processing helix chain 'B' and resid 342 through 346 Processing helix chain 'B' and resid 349 through 364 Processing helix chain 'B' and resid 373 through 377 Processing helix chain 'B' and resid 378 through 391 removed outlier: 3.537A pdb=" N LEU B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 425 through 441 Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 453 through 467 Processing helix chain 'B' and resid 475 through 481 removed outlier: 3.714A pdb=" N LEU B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'B' and resid 500 through 516 Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.582A pdb=" N THR B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 528 501 hydrogen bonds defined for protein. 1437 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: 2.22 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1105 1.32 - 1.44: 2053 1.44 - 1.57: 4570 1.57 - 1.69: 12 1.69 - 1.82: 62 Bond restraints: 7802 Sorted by residual: bond pdb=" N ILE A 92 " pdb=" CA ILE A 92 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N ILE B 92 " pdb=" CA ILE B 92 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.21e+01 bond pdb=" N CYS A 476 " pdb=" CA CYS A 476 " ideal model delta sigma weight residual 1.459 1.501 -0.041 1.21e-02 6.83e+03 1.18e+01 bond pdb=" N CYS B 476 " pdb=" CA CYS B 476 " ideal model delta sigma weight residual 1.459 1.501 -0.041 1.21e-02 6.83e+03 1.18e+01 bond pdb=" N VAL A 86 " pdb=" CA VAL A 86 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.89e+00 ... (remaining 7797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 9935 1.90 - 3.81: 573 3.81 - 5.71: 66 5.71 - 7.62: 12 7.62 - 9.52: 4 Bond angle restraints: 10590 Sorted by residual: angle pdb=" C CYS A 476 " pdb=" CA CYS A 476 " pdb=" CB CYS A 476 " ideal model delta sigma weight residual 110.79 102.52 8.27 1.66e+00 3.63e-01 2.48e+01 angle pdb=" C CYS B 476 " pdb=" CA CYS B 476 " pdb=" CB CYS B 476 " ideal model delta sigma weight residual 110.79 102.52 8.27 1.66e+00 3.63e-01 2.48e+01 angle pdb=" C LYS B 409 " pdb=" CA LYS B 409 " pdb=" CB LYS B 409 " ideal model delta sigma weight residual 116.63 111.03 5.60 1.16e+00 7.43e-01 2.33e+01 angle pdb=" C LYS A 409 " pdb=" CA LYS A 409 " pdb=" CB LYS A 409 " ideal model delta sigma weight residual 116.63 111.03 5.60 1.16e+00 7.43e-01 2.33e+01 angle pdb=" N SER B 87 " pdb=" CA SER B 87 " pdb=" C SER B 87 " ideal model delta sigma weight residual 112.04 106.52 5.52 1.44e+00 4.82e-01 1.47e+01 ... (remaining 10585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.38: 4574 26.38 - 52.76: 323 52.76 - 79.14: 57 79.14 - 105.52: 6 105.52 - 131.90: 4 Dihedral angle restraints: 4964 sinusoidal: 2300 harmonic: 2664 Sorted by residual: dihedral pdb=" C3 PTY B 705 " pdb=" O11 PTY B 705 " pdb=" P1 PTY B 705 " pdb=" O12 PTY B 705 " ideal model delta sinusoidal sigma weight residual -59.77 72.13 -131.90 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C3 PTY A 604 " pdb=" O11 PTY A 604 " pdb=" P1 PTY A 604 " pdb=" O12 PTY A 604 " ideal model delta sinusoidal sigma weight residual -59.77 72.11 -131.88 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C9 T7X A 603 " pdb=" C7 T7X A 603 " pdb=" C8 T7X A 603 " pdb=" O13 T7X A 603 " ideal model delta sinusoidal sigma weight residual 64.16 -173.35 -122.49 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 4961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1016 0.063 - 0.127: 197 0.127 - 0.190: 27 0.190 - 0.253: 12 0.253 - 0.316: 2 Chirality restraints: 1254 Sorted by residual: chirality pdb=" CBG Y01 B 702 " pdb=" CAQ Y01 B 702 " pdb=" CBD Y01 B 702 " pdb=" CBI Y01 B 702 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.65 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CBF Y01 A 601 " pdb=" CAS Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBH Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.45 -2.70 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 1251 not shown) Planarity restraints: 1222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 T7X B 704 " 0.219 2.00e-02 2.50e+03 2.19e-01 4.81e+02 pdb=" C18 T7X B 704 " -0.220 2.00e-02 2.50e+03 pdb=" C19 T7X B 704 " -0.219 2.00e-02 2.50e+03 pdb=" C20 T7X B 704 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 T7X A 603 " 0.219 2.00e-02 2.50e+03 2.19e-01 4.80e+02 pdb=" C18 T7X A 603 " -0.219 2.00e-02 2.50e+03 pdb=" C19 T7X A 603 " -0.219 2.00e-02 2.50e+03 pdb=" C20 T7X A 603 " 0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C14 T7X B 704 " 0.072 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C15 T7X B 704 " -0.183 2.00e-02 2.50e+03 pdb=" C16 T7X B 704 " 0.183 2.00e-02 2.50e+03 pdb=" C17 T7X B 704 " -0.072 2.00e-02 2.50e+03 ... (remaining 1219 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 96 2.61 - 3.18: 6733 3.18 - 3.76: 12788 3.76 - 4.33: 18580 4.33 - 4.90: 28343 Nonbonded interactions: 66540 Sorted by model distance: nonbonded pdb=" O HOH B 825 " pdb=" O HOH B 832 " model vdw 2.040 3.040 nonbonded pdb=" O ASN B 467 " pdb=" O HOH B 801 " model vdw 2.082 3.040 nonbonded pdb=" O ASN A 467 " pdb=" O HOH A 701 " model vdw 2.082 3.040 nonbonded pdb="NA NA B 708 " pdb=" O HOH B 801 " model vdw 2.100 2.470 nonbonded pdb="NA NA A 607 " pdb=" O HOH A 701 " model vdw 2.100 2.470 ... (remaining 66535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 487 or resid 489 through 530 or resid 602 or re \ sid 607 through 609)) selection = (chain 'B' and (resid 22 through 487 or resid 489 through 530 or resid 702 or re \ sid 707 through 709)) } 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=0.50 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: 6.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.640 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 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 : 0.007 0.057 7804 Z= 0.447 Angle : 0.977 16.374 10594 Z= 0.590 Chirality : 0.057 0.316 1254 Planarity : 0.012 0.219 1222 Dihedral : 17.641 131.899 3242 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.86 % Favored : 96.92 % Rotamer: Outliers : 5.85 % Allowed : 8.78 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 0.30 (0.25), residues: 910 helix: 0.65 (0.19), residues: 642 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 527 HIS 0.004 0.002 HIS B 483 PHE 0.011 0.002 PHE A 196 TYR 0.019 0.002 TYR B 195 ARG 0.004 0.001 ARG B 32 Details of bonding type rmsd hydrogen bonds : bond 0.12889 ( 501) hydrogen bonds : angle 4.63346 ( 1437) SS BOND : bond 0.05149 ( 2) SS BOND : angle 13.83437 ( 4) covalent geometry : bond 0.00731 ( 7802) covalent geometry : angle 0.93917 (10590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 124 time to evaluate : 0.910 Fit side-chains REVERT: A 63 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6718 (tmtm) REVERT: A 125 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7374 (ptm160) REVERT: A 414 LYS cc_start: 0.5785 (OUTLIER) cc_final: 0.4874 (tmtm) REVERT: A 415 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6355 (tm) REVERT: A 442 ARG cc_start: 0.7155 (ptt-90) cc_final: 0.5915 (ptm160) REVERT: A 478 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.6498 (mtm-85) REVERT: A 480 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7068 (mt0) REVERT: A 525 GLU cc_start: 0.7474 (tp30) cc_final: 0.7187 (tp30) REVERT: B 63 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6720 (tmtm) REVERT: B 125 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7372 (ptm160) REVERT: B 414 LYS cc_start: 0.5790 (OUTLIER) cc_final: 0.4874 (tmtm) REVERT: B 415 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6352 (tm) REVERT: B 442 ARG cc_start: 0.7153 (ptt-90) cc_final: 0.5914 (ptm160) REVERT: B 478 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6496 (mtm-85) REVERT: B 480 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7071 (mt0) REVERT: B 525 GLU cc_start: 0.7471 (tp30) cc_final: 0.7183 (tp30) outliers start: 44 outliers final: 14 residues processed: 152 average time/residue: 1.3057 time to fit residues: 209.1558 Evaluate side-chains 145 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 480 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.0270 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 200 HIS A 251 ASN A 421 ASN B 39 HIS B 200 HIS B 251 ASN B 421 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.097479 restraints weight = 8152.090| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.22 r_work: 0.2828 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7804 Z= 0.108 Angle : 0.519 4.831 10594 Z= 0.271 Chirality : 0.037 0.126 1254 Planarity : 0.004 0.040 1222 Dihedral : 15.149 121.185 1704 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.67 % Allowed : 12.09 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 2.09 (0.27), residues: 910 helix: 2.14 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 186 HIS 0.002 0.001 HIS A 37 PHE 0.008 0.001 PHE B 196 TYR 0.015 0.002 TYR A 195 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 501) hydrogen bonds : angle 3.96160 ( 1437) SS BOND : bond 0.00921 ( 2) SS BOND : angle 3.75379 ( 4) covalent geometry : bond 0.00214 ( 7802) covalent geometry : angle 0.51367 (10590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.886 Fit side-chains REVERT: A 414 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.5333 (tmtm) REVERT: A 415 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6518 (tm) REVERT: A 442 ARG cc_start: 0.8658 (ptt-90) cc_final: 0.7961 (ptm160) REVERT: A 478 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8051 (mtm-85) REVERT: A 480 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7935 (mt0) REVERT: B 414 LYS cc_start: 0.6370 (OUTLIER) cc_final: 0.5343 (tmtm) REVERT: B 415 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6524 (tm) REVERT: B 442 ARG cc_start: 0.8666 (ptt-90) cc_final: 0.7965 (ptm160) REVERT: B 478 ARG cc_start: 0.8474 (mtm-85) cc_final: 0.8053 (mtm-85) REVERT: B 480 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7953 (mt0) outliers start: 21 outliers final: 6 residues processed: 138 average time/residue: 1.4545 time to fit residues: 210.7829 Evaluate side-chains 133 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 480 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 54 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS B 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.129238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.094605 restraints weight = 8258.406| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.26 r_work: 0.2783 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7804 Z= 0.119 Angle : 0.538 4.943 10594 Z= 0.280 Chirality : 0.038 0.125 1254 Planarity : 0.004 0.040 1222 Dihedral : 13.860 113.829 1676 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.67 % Allowed : 12.21 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 2.37 (0.27), residues: 910 helix: 2.39 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.53 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 186 HIS 0.002 0.001 HIS A 483 PHE 0.012 0.001 PHE B 196 TYR 0.017 0.002 TYR A 73 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 501) hydrogen bonds : angle 3.92019 ( 1437) SS BOND : bond 0.00942 ( 2) SS BOND : angle 3.26669 ( 4) covalent geometry : bond 0.00241 ( 7802) covalent geometry : angle 0.53477 (10590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.832 Fit side-chains REVERT: A 49 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8299 (tt) REVERT: A 61 PHE cc_start: 0.7785 (m-10) cc_final: 0.7262 (t80) REVERT: A 179 LYS cc_start: 0.5900 (OUTLIER) cc_final: 0.5141 (mmpt) REVERT: A 414 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5485 (tmtm) REVERT: A 415 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6538 (tm) REVERT: A 442 ARG cc_start: 0.8707 (ptt-90) cc_final: 0.8004 (ptm160) REVERT: A 478 ARG cc_start: 0.8526 (mtm-85) cc_final: 0.8162 (mtp180) REVERT: B 49 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8303 (tt) REVERT: B 61 PHE cc_start: 0.7783 (m-10) cc_final: 0.7260 (t80) REVERT: B 179 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.5134 (mmpt) REVERT: B 414 LYS cc_start: 0.6512 (OUTLIER) cc_final: 0.5473 (tmtm) REVERT: B 415 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6552 (tm) REVERT: B 442 ARG cc_start: 0.8700 (ptt-90) cc_final: 0.7999 (ptm160) REVERT: B 478 ARG cc_start: 0.8528 (mtm-85) cc_final: 0.8164 (mtp180) outliers start: 21 outliers final: 4 residues processed: 130 average time/residue: 1.4779 time to fit residues: 201.5758 Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 414 LYS Chi-restraints excluded: chain B residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.127695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.090926 restraints weight = 12268.668| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.49 r_work: 0.2726 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7804 Z= 0.134 Angle : 0.568 5.270 10594 Z= 0.295 Chirality : 0.039 0.133 1254 Planarity : 0.004 0.039 1222 Dihedral : 13.569 114.234 1664 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.78 % Allowed : 13.74 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 2.36 (0.27), residues: 910 helix: 2.37 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 498 HIS 0.002 0.001 HIS B 200 PHE 0.012 0.001 PHE A 196 TYR 0.018 0.002 TYR B 73 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 501) hydrogen bonds : angle 3.96780 ( 1437) SS BOND : bond 0.00817 ( 2) SS BOND : angle 2.99384 ( 4) covalent geometry : bond 0.00280 ( 7802) covalent geometry : angle 0.56503 (10590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.835 Fit side-chains REVERT: A 49 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8356 (tt) REVERT: A 61 PHE cc_start: 0.7913 (m-10) cc_final: 0.7319 (t80) REVERT: A 179 LYS cc_start: 0.5925 (OUTLIER) cc_final: 0.5513 (pptt) REVERT: A 414 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.5596 (tmtm) REVERT: A 442 ARG cc_start: 0.8746 (ptt-90) cc_final: 0.8005 (ptm160) REVERT: A 478 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8199 (mtm-85) REVERT: B 49 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8359 (tt) REVERT: B 61 PHE cc_start: 0.7914 (m-10) cc_final: 0.7326 (t80) REVERT: B 179 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5513 (pptt) REVERT: B 414 LYS cc_start: 0.6659 (OUTLIER) cc_final: 0.5621 (tmtm) REVERT: B 442 ARG cc_start: 0.8744 (ptt-90) cc_final: 0.8004 (ptm160) REVERT: B 478 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.8195 (mtm-85) outliers start: 14 outliers final: 4 residues processed: 121 average time/residue: 1.6243 time to fit residues: 205.8259 Evaluate side-chains 125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 414 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 414 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.128334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.091756 restraints weight = 11552.602| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.44 r_work: 0.2758 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2641 r_free = 0.2641 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7804 Z= 0.127 Angle : 0.548 5.145 10594 Z= 0.285 Chirality : 0.039 0.126 1254 Planarity : 0.004 0.039 1222 Dihedral : 12.927 113.718 1660 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.91 % Allowed : 13.36 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 2.48 (0.27), residues: 910 helix: 2.45 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.46 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 186 HIS 0.003 0.001 HIS A 200 PHE 0.012 0.001 PHE A 196 TYR 0.017 0.002 TYR A 73 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 501) hydrogen bonds : angle 3.91246 ( 1437) SS BOND : bond 0.00955 ( 2) SS BOND : angle 2.80564 ( 4) covalent geometry : bond 0.00263 ( 7802) covalent geometry : angle 0.54576 (10590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.873 Fit side-chains REVERT: A 49 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 61 PHE cc_start: 0.7787 (m-10) cc_final: 0.7583 (m-10) REVERT: A 179 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5589 (pmtt) REVERT: A 442 ARG cc_start: 0.8690 (ptt-90) cc_final: 0.7894 (ptm160) REVERT: A 478 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.8073 (mtp180) REVERT: B 49 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8278 (tt) REVERT: B 61 PHE cc_start: 0.7787 (m-10) cc_final: 0.7583 (m-10) REVERT: B 179 LYS cc_start: 0.5917 (OUTLIER) cc_final: 0.5601 (pmtt) REVERT: B 442 ARG cc_start: 0.8689 (ptt-90) cc_final: 0.7889 (ptm160) REVERT: B 478 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8069 (mtp180) outliers start: 13 outliers final: 5 residues processed: 120 average time/residue: 1.9740 time to fit residues: 248.2474 Evaluate side-chains 124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 33 optimal weight: 50.0000 chunk 18 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN B 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.128413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.093333 restraints weight = 7460.191| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.29 r_work: 0.2785 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7804 Z= 0.130 Angle : 0.555 4.982 10594 Z= 0.289 Chirality : 0.039 0.127 1254 Planarity : 0.004 0.039 1222 Dihedral : 12.788 113.638 1652 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.04 % Allowed : 13.23 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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 (0.27), residues: 910 helix: 2.43 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.48 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 498 HIS 0.003 0.001 HIS B 200 PHE 0.012 0.001 PHE A 196 TYR 0.018 0.002 TYR B 73 ARG 0.003 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 501) hydrogen bonds : angle 3.92821 ( 1437) SS BOND : bond 0.00896 ( 2) SS BOND : angle 2.83909 ( 4) covalent geometry : bond 0.00271 ( 7802) covalent geometry : angle 0.55261 (10590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.820 Fit side-chains REVERT: A 49 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8262 (tt) REVERT: A 179 LYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5587 (pmtt) REVERT: A 442 ARG cc_start: 0.8626 (ptt-90) cc_final: 0.7834 (ptm160) REVERT: A 478 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.7975 (mtp180) REVERT: B 49 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8253 (tt) REVERT: B 179 LYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5590 (pmtt) REVERT: B 442 ARG cc_start: 0.8623 (ptt-90) cc_final: 0.7830 (ptm160) REVERT: B 478 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.7966 (mtp180) outliers start: 14 outliers final: 4 residues processed: 119 average time/residue: 1.5834 time to fit residues: 197.5508 Evaluate side-chains 123 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 76 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 50.0000 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.091770 restraints weight = 10287.312| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 1.53 r_work: 0.2745 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7804 Z= 0.131 Angle : 0.557 4.978 10594 Z= 0.289 Chirality : 0.039 0.128 1254 Planarity : 0.004 0.038 1222 Dihedral : 12.792 113.906 1652 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.78 % Allowed : 13.74 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 2.46 (0.27), residues: 910 helix: 2.44 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.46 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 498 HIS 0.003 0.001 HIS A 200 PHE 0.012 0.001 PHE B 196 TYR 0.018 0.002 TYR B 73 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04700 ( 501) hydrogen bonds : angle 3.91729 ( 1437) SS BOND : bond 0.00872 ( 2) SS BOND : angle 2.86202 ( 4) covalent geometry : bond 0.00273 ( 7802) covalent geometry : angle 0.55396 (10590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 1.051 Fit side-chains REVERT: A 49 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8262 (tt) REVERT: A 61 PHE cc_start: 0.7679 (m-10) cc_final: 0.7036 (t80) REVERT: A 179 LYS cc_start: 0.5878 (OUTLIER) cc_final: 0.5524 (pmtt) REVERT: A 442 ARG cc_start: 0.8665 (ptt-90) cc_final: 0.7831 (ptm160) REVERT: A 478 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8013 (mtp180) REVERT: B 49 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8264 (tt) REVERT: B 61 PHE cc_start: 0.7679 (m-10) cc_final: 0.7034 (t80) REVERT: B 179 LYS cc_start: 0.5880 (OUTLIER) cc_final: 0.5529 (pmtt) REVERT: B 442 ARG cc_start: 0.8666 (ptt-90) cc_final: 0.7830 (ptm160) REVERT: B 478 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.7999 (mtp180) outliers start: 12 outliers final: 6 residues processed: 117 average time/residue: 1.9972 time to fit residues: 245.0040 Evaluate side-chains 123 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 29 optimal weight: 0.1980 chunk 41 optimal weight: 0.0370 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.093523 restraints weight = 7349.420| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.27 r_work: 0.2789 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7804 Z= 0.128 Angle : 0.550 4.972 10594 Z= 0.286 Chirality : 0.039 0.127 1254 Planarity : 0.004 0.038 1222 Dihedral : 12.696 113.202 1652 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.78 % Allowed : 13.74 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 2.49 (0.27), residues: 910 helix: 2.47 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.45 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 186 HIS 0.003 0.001 HIS B 200 PHE 0.012 0.001 PHE A 196 TYR 0.018 0.002 TYR B 73 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 501) hydrogen bonds : angle 3.89835 ( 1437) SS BOND : bond 0.00901 ( 2) SS BOND : angle 2.77712 ( 4) covalent geometry : bond 0.00266 ( 7802) covalent geometry : angle 0.54775 (10590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.870 Fit side-chains REVERT: A 49 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8245 (tt) REVERT: A 61 PHE cc_start: 0.7635 (m-10) cc_final: 0.7034 (t80) REVERT: A 179 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5589 (pmtt) REVERT: A 442 ARG cc_start: 0.8613 (ptt-90) cc_final: 0.7820 (ptm160) REVERT: A 478 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.7967 (mtp180) REVERT: B 49 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8254 (tt) REVERT: B 61 PHE cc_start: 0.7637 (m-10) cc_final: 0.7033 (t80) REVERT: B 179 LYS cc_start: 0.5926 (OUTLIER) cc_final: 0.5588 (pmtt) REVERT: B 442 ARG cc_start: 0.8615 (ptt-90) cc_final: 0.7818 (ptm160) REVERT: B 478 ARG cc_start: 0.8360 (mtm-85) cc_final: 0.7954 (mtp180) outliers start: 12 outliers final: 8 residues processed: 119 average time/residue: 1.9517 time to fit residues: 243.2369 Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.126899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.091386 restraints weight = 8053.999| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.32 r_work: 0.2743 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7804 Z= 0.165 Angle : 0.619 5.207 10594 Z= 0.318 Chirality : 0.042 0.137 1254 Planarity : 0.004 0.042 1222 Dihedral : 13.251 115.489 1652 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.78 % Allowed : 13.61 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 2.26 (0.27), residues: 910 helix: 2.27 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.47 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 498 HIS 0.004 0.002 HIS B 200 PHE 0.012 0.002 PHE B 196 TYR 0.020 0.002 TYR B 73 ARG 0.003 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 501) hydrogen bonds : angle 4.01167 ( 1437) SS BOND : bond 0.00844 ( 2) SS BOND : angle 2.97070 ( 4) covalent geometry : bond 0.00356 ( 7802) covalent geometry : angle 0.61642 (10590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.815 Fit side-chains REVERT: A 49 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8322 (tt) REVERT: A 61 PHE cc_start: 0.7718 (m-10) cc_final: 0.7096 (t80) REVERT: A 179 LYS cc_start: 0.5926 (OUTLIER) cc_final: 0.5578 (pmtt) REVERT: A 442 ARG cc_start: 0.8653 (ptt-90) cc_final: 0.7845 (ptm160) REVERT: A 478 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.7966 (mtp180) REVERT: B 49 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8333 (tt) REVERT: B 61 PHE cc_start: 0.7718 (m-10) cc_final: 0.7097 (t80) REVERT: B 179 LYS cc_start: 0.5921 (OUTLIER) cc_final: 0.5575 (pmtt) REVERT: B 442 ARG cc_start: 0.8653 (ptt-90) cc_final: 0.7841 (ptm160) REVERT: B 478 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.7954 (mtp180) outliers start: 12 outliers final: 6 residues processed: 119 average time/residue: 1.5431 time to fit residues: 192.2873 Evaluate side-chains 125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 67 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.129208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.093758 restraints weight = 8091.337| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.34 r_work: 0.2791 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7804 Z= 0.117 Angle : 0.533 4.972 10594 Z= 0.277 Chirality : 0.038 0.124 1254 Planarity : 0.004 0.038 1222 Dihedral : 12.807 114.644 1652 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.53 % Allowed : 13.74 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 2.53 (0.27), residues: 910 helix: 2.51 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.48 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 186 HIS 0.002 0.001 HIS A 200 PHE 0.012 0.001 PHE B 196 TYR 0.016 0.002 TYR A 195 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 501) hydrogen bonds : angle 3.87968 ( 1437) SS BOND : bond 0.00949 ( 2) SS BOND : angle 2.69823 ( 4) covalent geometry : bond 0.00239 ( 7802) covalent geometry : angle 0.53036 (10590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.822 Fit side-chains REVERT: A 49 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8262 (tt) REVERT: A 61 PHE cc_start: 0.7668 (m-10) cc_final: 0.7044 (t80) REVERT: A 179 LYS cc_start: 0.5907 (OUTLIER) cc_final: 0.5574 (pmtt) REVERT: A 442 ARG cc_start: 0.8611 (ptt-90) cc_final: 0.7802 (ptm160) REVERT: A 478 ARG cc_start: 0.8378 (mtm-85) cc_final: 0.7974 (mtp180) REVERT: B 49 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8264 (tt) REVERT: B 61 PHE cc_start: 0.7667 (m-10) cc_final: 0.7044 (t80) REVERT: B 179 LYS cc_start: 0.5907 (OUTLIER) cc_final: 0.5574 (pmtt) REVERT: B 442 ARG cc_start: 0.8615 (ptt-90) cc_final: 0.7801 (ptm160) REVERT: B 478 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.7969 (mtp180) outliers start: 10 outliers final: 6 residues processed: 118 average time/residue: 1.5492 time to fit residues: 191.4422 Evaluate side-chains 124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 305 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.129101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.092725 restraints weight = 9747.353| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 1.42 r_work: 0.2767 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7804 Z= 0.124 Angle : 0.545 4.964 10594 Z= 0.283 Chirality : 0.038 0.126 1254 Planarity : 0.004 0.038 1222 Dihedral : 12.727 113.683 1652 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.53 % Allowed : 13.74 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.23 % 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: 2.50 (0.27), residues: 910 helix: 2.49 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -0.49 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 186 HIS 0.003 0.001 HIS B 200 PHE 0.012 0.001 PHE B 196 TYR 0.017 0.002 TYR B 73 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 501) hydrogen bonds : angle 3.87964 ( 1437) SS BOND : bond 0.00925 ( 2) SS BOND : angle 2.75462 ( 4) covalent geometry : bond 0.00255 ( 7802) covalent geometry : angle 0.54236 (10590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8929.49 seconds wall clock time: 156 minutes 54.96 seconds (9414.96 seconds total)