Starting phenix.real_space_refine on Wed Sep 17 14:26:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7s_44322/09_2025/9b7s_44322.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7s_44322/09_2025/9b7s_44322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b7s_44322/09_2025/9b7s_44322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7s_44322/09_2025/9b7s_44322.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b7s_44322/09_2025/9b7s_44322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7s_44322/09_2025/9b7s_44322.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5799 2.51 5 N 1638 2.21 5 O 1805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9273 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 964 Classifications: {'peptide': 123} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain breaks: 8 Chain: "B" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 521 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Chain: "C" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2258 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 265} Chain breaks: 5 Chain: "D" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 112} Chain breaks: 8 Chain: "E" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 521 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Chain: "F" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2258 Classifications: {'peptide': 284} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 265} Chain breaks: 5 Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1001 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Time building chain proxies: 1.82, per 1000 atoms: 0.20 Number of scatterers: 9273 At special positions: 0 Unit cell: (128.148, 97.016, 82.536, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1805 8.00 N 1638 7.00 C 5799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 45 " - pdb=" SG CYS L 110 " distance=2.03 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: 0.80 Conformation dependent library (CDL) restraints added in 303.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 30 sheets defined 7.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 266 Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.580A pdb=" N PHE A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.214A pdb=" N HIS C 292 " --> pdb=" O ARG C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.833A pdb=" N ASN C 304 " --> pdb=" O ARG C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 Processing helix chain 'C' and resid 564 through 569 removed outlier: 4.054A pdb=" N THR C 568 " --> pdb=" O GLU C 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.762A pdb=" N PHE D 400 " --> pdb=" O LEU D 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 293 removed outlier: 4.010A pdb=" N HIS F 292 " --> pdb=" O ARG F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 431 through 435 removed outlier: 3.908A pdb=" N LEU F 435 " --> pdb=" O LEU F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 492 through 496 Processing helix chain 'F' and resid 554 through 556 No H-bonds generated for 'chain 'F' and resid 554 through 556' Processing helix chain 'F' and resid 564 through 569 removed outlier: 4.149A pdb=" N THR F 568 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.877A pdb=" N THR H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 261 Processing sheet with id=AA2, first strand: chain 'A' and resid 483 through 484 Processing sheet with id=AA3, first strand: chain 'A' and resid 515 through 517 removed outlier: 4.135A pdb=" N GLY C 578 " --> pdb=" O VAL C 596 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 451 removed outlier: 6.686A pdb=" N LYS B 462 " --> pdb=" O SER B 448 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR B 450 " --> pdb=" O THR B 460 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 593 through 596 removed outlier: 3.847A pdb=" N GLY B 578 " --> pdb=" O VAL B 596 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 305 through 307 removed outlier: 3.507A pdb=" N GLY C 307 " --> pdb=" O GLN C 688 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 427 through 428 removed outlier: 6.422A pdb=" N ALA C 427 " --> pdb=" O ARG C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 445 through 451 removed outlier: 6.751A pdb=" N LYS C 462 " --> pdb=" O SER C 448 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR C 450 " --> pdb=" O THR C 460 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 479 through 480 removed outlier: 6.156A pdb=" N ILE C 479 " --> pdb=" O VAL C 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 483 through 484 Processing sheet with id=AB2, first strand: chain 'C' and resid 488 through 490 Processing sheet with id=AB3, first strand: chain 'C' and resid 542 through 544 Processing sheet with id=AB4, first strand: chain 'D' and resid 258 through 261 Processing sheet with id=AB5, first strand: chain 'D' and resid 483 through 484 Processing sheet with id=AB6, first strand: chain 'D' and resid 514 through 517 removed outlier: 4.011A pdb=" N GLY F 578 " --> pdb=" O VAL F 596 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 445 through 451 removed outlier: 6.707A pdb=" N LYS E 462 " --> pdb=" O SER E 448 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR E 450 " --> pdb=" O THR E 460 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 593 through 596 removed outlier: 3.972A pdb=" N GLY E 578 " --> pdb=" O VAL E 596 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 305 through 307 removed outlier: 6.392A pdb=" N GLN F 688 " --> pdb=" O TRP F 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 427 through 428 removed outlier: 6.387A pdb=" N ALA F 427 " --> pdb=" O ARG F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 445 through 451 removed outlier: 5.775A pdb=" N LEU F 447 " --> pdb=" O SER F 464 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER F 464 " --> pdb=" O LEU F 447 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS F 449 " --> pdb=" O LYS F 462 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILE F 451 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N THR F 460 " --> pdb=" O ILE F 451 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 479 through 480 removed outlier: 6.430A pdb=" N ILE F 479 " --> pdb=" O VAL F 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 483 through 484 Processing sheet with id=AC5, first strand: chain 'F' and resid 488 through 490 Processing sheet with id=AC6, first strand: chain 'F' and resid 542 through 544 Processing sheet with id=AC7, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AC8, first strand: chain 'H' and resid 30 through 31 Processing sheet with id=AC9, first strand: chain 'H' and resid 77 through 79 removed outlier: 6.825A pdb=" N TRP H 55 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N MET H 53 " --> pdb=" O LEU H 69 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 26 through 28 removed outlier: 5.576A pdb=" N THR L 91 " --> pdb=" O ALA L 47 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N HIS L 49 " --> pdb=" O SER L 89 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N SER L 89 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 11.188A pdb=" N VAL L 51 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 10.972A pdb=" N SER L 87 " --> pdb=" O VAL L 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 32 through 35 removed outlier: 6.315A pdb=" N LEU L 33 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TRP L 57 " --> pdb=" O LEU L 69 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 32 through 35 removed outlier: 6.315A pdb=" N LEU L 33 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR L 118 " --> pdb=" O GLN L 112 " (cutoff:3.500A) 158 hydrogen bonds defined for protein. 354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2429 1.33 - 1.45: 2039 1.45 - 1.57: 4978 1.57 - 1.69: 0 1.69 - 1.80: 52 Bond restraints: 9498 Sorted by residual: bond pdb=" C GLU F 723 " pdb=" O GLU F 723 " ideal model delta sigma weight residual 1.246 1.224 0.023 9.20e-03 1.18e+04 6.02e+00 bond pdb=" C PRO C 365 " pdb=" O PRO C 365 " ideal model delta sigma weight residual 1.246 1.225 0.021 8.50e-03 1.38e+04 5.93e+00 bond pdb=" CG GLN L 112 " pdb=" CD GLN L 112 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.57e+00 bond pdb=" CA TYR H 127 " pdb=" C TYR H 127 " ideal model delta sigma weight residual 1.522 1.498 0.025 1.20e-02 6.94e+03 4.20e+00 bond pdb=" C ALA H 129 " pdb=" O ALA H 129 " ideal model delta sigma weight residual 1.234 1.208 0.026 1.27e-02 6.20e+03 4.12e+00 ... (remaining 9493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12163 1.90 - 3.80: 596 3.80 - 5.70: 85 5.70 - 7.60: 14 7.60 - 9.50: 7 Bond angle restraints: 12865 Sorted by residual: angle pdb=" N GLY F 539 " pdb=" CA GLY F 539 " pdb=" C GLY F 539 " ideal model delta sigma weight residual 112.77 121.75 -8.98 1.28e+00 6.10e-01 4.92e+01 angle pdb=" C GLY H 28 " pdb=" N GLY H 29 " pdb=" CA GLY H 29 " ideal model delta sigma weight residual 122.16 117.73 4.43 7.70e-01 1.69e+00 3.31e+01 angle pdb=" N ASN H 50 " pdb=" CA ASN H 50 " pdb=" C ASN H 50 " ideal model delta sigma weight residual 111.28 117.23 -5.95 1.09e+00 8.42e-01 2.98e+01 angle pdb=" N GLY C 539 " pdb=" CA GLY C 539 " pdb=" C GLY C 539 " ideal model delta sigma weight residual 112.73 119.16 -6.43 1.20e+00 6.94e-01 2.87e+01 angle pdb=" N VAL L 117 " pdb=" CA VAL L 117 " pdb=" C VAL L 117 " ideal model delta sigma weight residual 109.30 116.26 -6.96 1.31e+00 5.83e-01 2.82e+01 ... (remaining 12860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 5260 17.74 - 35.48: 201 35.48 - 53.21: 35 53.21 - 70.95: 11 70.95 - 88.69: 13 Dihedral angle restraints: 5520 sinusoidal: 2166 harmonic: 3354 Sorted by residual: dihedral pdb=" CA THR C 729 " pdb=" C THR C 729 " pdb=" N ARG C 730 " pdb=" CA ARG C 730 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA SER L 74 " pdb=" C SER L 74 " pdb=" N THR L 75 " pdb=" CA THR L 75 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASN F 519 " pdb=" C ASN F 519 " pdb=" N PRO F 520 " pdb=" CA PRO F 520 " ideal model delta harmonic sigma weight residual 0.00 -21.86 21.86 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 5517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 970 0.061 - 0.122: 272 0.122 - 0.183: 44 0.183 - 0.244: 18 0.244 - 0.306: 5 Chirality restraints: 1309 Sorted by residual: chirality pdb=" CA ILE L 114 " pdb=" N ILE L 114 " pdb=" C ILE L 114 " pdb=" CB ILE L 114 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA TYR L 113 " pdb=" N TYR L 113 " pdb=" C TYR L 113 " pdb=" CB TYR L 113 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA TYR A 484 " pdb=" N TYR A 484 " pdb=" C TYR A 484 " pdb=" CB TYR A 484 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 1306 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 495 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C GLN F 495 " -0.041 2.00e-02 2.50e+03 pdb=" O GLN F 495 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN F 496 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 129 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C ALA H 129 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA H 129 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY H 130 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 138 " -0.015 2.00e-02 2.50e+03 1.27e-02 4.06e+00 pdb=" CG TRP H 138 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP H 138 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 138 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP H 138 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP H 138 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 138 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 138 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 138 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 138 " -0.000 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 135 2.64 - 3.21: 8283 3.21 - 3.77: 13958 3.77 - 4.34: 20572 4.34 - 4.90: 33355 Nonbonded interactions: 76303 Sorted by model distance: nonbonded pdb=" O ASN F 498 " pdb=" ND2 ASN F 498 " model vdw 2.076 3.120 nonbonded pdb=" NH2 ARG C 296 " pdb=" OE1 GLU F 690 " model vdw 2.219 3.120 nonbonded pdb=" OG1 THR D 279 " pdb=" O TYR D 377 " model vdw 2.233 3.040 nonbonded pdb=" O SER H 125 " pdb=" OG SER H 125 " model vdw 2.243 3.040 nonbonded pdb=" O GLN C 442 " pdb=" N LEU C 444 " model vdw 2.247 3.120 ... (remaining 76298 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 252 through 601 or resid 623 through 670)) selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.008 0.066 9500 Z= 0.388 Angle : 0.961 9.500 12869 Z= 0.599 Chirality : 0.062 0.306 1309 Planarity : 0.005 0.038 1702 Dihedral : 11.275 88.689 3376 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.11 % Allowed : 2.83 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.20), residues: 1111 helix: -1.86 (0.69), residues: 38 sheet: -0.93 (0.33), residues: 181 loop : -1.13 (0.17), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG F 734 TYR 0.027 0.003 TYR A 399 PHE 0.030 0.003 PHE F 367 TRP 0.032 0.002 TRP H 138 HIS 0.014 0.003 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00810 ( 9498) covalent geometry : angle 0.96138 (12865) SS BOND : bond 0.00103 ( 2) SS BOND : angle 1.07977 ( 4) hydrogen bonds : bond 0.21485 ( 156) hydrogen bonds : angle 9.56990 ( 354) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.308 Fit side-chains REVERT: C 300 ARG cc_start: 0.8379 (ttm110) cc_final: 0.7243 (tmt90) REVERT: C 462 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7237 (tptt) REVERT: C 725 ARG cc_start: 0.8626 (ptt180) cc_final: 0.8274 (ptp-110) REVERT: F 300 ARG cc_start: 0.8568 (mtt180) cc_final: 0.7005 (ptt180) REVERT: F 462 LYS cc_start: 0.8649 (mmtt) cc_final: 0.7228 (tmtm) REVERT: F 514 ARG cc_start: 0.8085 (mtm180) cc_final: 0.7091 (mmt180) REVERT: F 689 LYS cc_start: 0.8706 (mmtm) cc_final: 0.8466 (mttt) REVERT: H 24 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8861 (tt) REVERT: H 31 VAL cc_start: 0.9063 (m) cc_final: 0.8792 (p) outliers start: 11 outliers final: 2 residues processed: 198 average time/residue: 0.5272 time to fit residues: 111.3864 Evaluate side-chains 122 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 94 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS B 452 ASN ** C 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN C 700 GLN C 709 ASN D 259 GLN D 387 GLN D 519 ASN D 624 HIS E 452 ASN F 360 HIS F 452 ASN F 470 ASN F 495 GLN F 497 ASN F 498 ASN F 562 ASN F 608 GLN F 700 GLN F 709 ASN H 96 ASN L 59 GLN L 101 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.090240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.080633 restraints weight = 19064.561| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.02 r_work: 0.2952 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9500 Z= 0.117 Angle : 0.546 6.841 12869 Z= 0.290 Chirality : 0.042 0.135 1309 Planarity : 0.004 0.030 1702 Dihedral : 5.198 32.424 1271 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.02 % Allowed : 8.28 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.22), residues: 1111 helix: -0.81 (0.85), residues: 32 sheet: -0.18 (0.36), residues: 180 loop : -0.73 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 485 TYR 0.018 0.002 TYR C 484 PHE 0.014 0.001 PHE F 367 TRP 0.010 0.001 TRP H 138 HIS 0.004 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9498) covalent geometry : angle 0.54628 (12865) SS BOND : bond 0.00570 ( 2) SS BOND : angle 0.66193 ( 4) hydrogen bonds : bond 0.03394 ( 156) hydrogen bonds : angle 6.49844 ( 354) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.319 Fit side-chains REVERT: B 449 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8463 (ttpt) REVERT: C 300 ARG cc_start: 0.8364 (ttm110) cc_final: 0.7224 (ttt180) REVERT: C 462 LYS cc_start: 0.8019 (mmtt) cc_final: 0.6701 (tptt) REVERT: C 588 GLN cc_start: 0.8331 (pm20) cc_final: 0.8073 (pm20) REVERT: C 725 ARG cc_start: 0.8719 (ptt180) cc_final: 0.8135 (ptp-110) REVERT: D 485 ARG cc_start: 0.7321 (ttm170) cc_final: 0.5206 (ttt180) REVERT: E 470 ASN cc_start: 0.7907 (t0) cc_final: 0.7562 (t0) REVERT: F 300 ARG cc_start: 0.8342 (mtt180) cc_final: 0.6889 (ptt180) REVERT: F 462 LYS cc_start: 0.8567 (mmtt) cc_final: 0.6987 (tmtm) REVERT: F 514 ARG cc_start: 0.8523 (mtm180) cc_final: 0.6992 (mmt180) REVERT: F 554 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7644 (m-30) REVERT: F 689 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8410 (mttt) REVERT: H 31 VAL cc_start: 0.9099 (m) cc_final: 0.8744 (p) REVERT: H 62 LYS cc_start: 0.8376 (mmtt) cc_final: 0.7902 (mmtp) REVERT: H 78 ASP cc_start: 0.8767 (m-30) cc_final: 0.8544 (m-30) REVERT: H 110 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8956 (t) REVERT: L 67 ARG cc_start: 0.8416 (ptm-80) cc_final: 0.8163 (ptt90) REVERT: L 118 THR cc_start: 0.9311 (m) cc_final: 0.9058 (p) outliers start: 20 outliers final: 5 residues processed: 168 average time/residue: 0.4940 time to fit residues: 88.9662 Evaluate side-chains 133 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain F residue 554 ASP Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 115 ASN Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 457 ASN B 585 GLN C 360 HIS ** C 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 519 ASN F 456 GLN F 470 ASN F 562 ASN F 585 GLN F 588 GLN H 50 ASN H 96 ASN L 64 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.077229 restraints weight = 19234.534| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.00 r_work: 0.2884 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 9500 Z= 0.263 Angle : 0.628 9.445 12869 Z= 0.333 Chirality : 0.046 0.158 1309 Planarity : 0.005 0.050 1702 Dihedral : 5.311 32.700 1268 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.03 % Allowed : 9.19 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.22), residues: 1111 helix: 1.89 (1.16), residues: 20 sheet: -0.40 (0.37), residues: 167 loop : -0.67 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 485 TYR 0.021 0.002 TYR L 113 PHE 0.017 0.002 PHE F 367 TRP 0.020 0.002 TRP H 138 HIS 0.011 0.002 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00613 ( 9498) covalent geometry : angle 0.62798 (12865) SS BOND : bond 0.00601 ( 2) SS BOND : angle 1.12339 ( 4) hydrogen bonds : bond 0.03596 ( 156) hydrogen bonds : angle 6.30018 ( 354) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.404 Fit side-chains REVERT: B 440 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.6881 (mm) REVERT: C 300 ARG cc_start: 0.8479 (ttm110) cc_final: 0.7116 (tmm160) REVERT: C 462 LYS cc_start: 0.8106 (mmtt) cc_final: 0.6778 (tptt) REVERT: C 588 GLN cc_start: 0.8363 (pm20) cc_final: 0.8143 (pm20) REVERT: D 398 GLU cc_start: 0.8393 (mp0) cc_final: 0.7974 (mp0) REVERT: D 485 ARG cc_start: 0.7403 (ttm170) cc_final: 0.5611 (ttt90) REVERT: F 462 LYS cc_start: 0.8567 (mmtt) cc_final: 0.6934 (tmtm) REVERT: F 689 LYS cc_start: 0.8825 (mmtm) cc_final: 0.8426 (mttt) REVERT: H 31 VAL cc_start: 0.9131 (m) cc_final: 0.8862 (p) REVERT: H 37 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8552 (pt) REVERT: H 62 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8322 (mmtp) REVERT: H 78 ASP cc_start: 0.8827 (m-30) cc_final: 0.8616 (m-30) REVERT: H 86 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.6845 (mtp85) REVERT: H 110 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8877 (t) REVERT: L 67 ARG cc_start: 0.8491 (ptm-80) cc_final: 0.8212 (ptt90) REVERT: L 92 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7934 (mp0) outliers start: 30 outliers final: 14 residues processed: 142 average time/residue: 0.5197 time to fit residues: 78.9212 Evaluate side-chains 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 31 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 0.0470 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 GLN C 497 ASN F 470 ASN F 585 GLN F 588 GLN H 96 ASN L 59 GLN L 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.080487 restraints weight = 19086.454| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.02 r_work: 0.2949 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9500 Z= 0.090 Angle : 0.492 9.199 12869 Z= 0.253 Chirality : 0.040 0.135 1309 Planarity : 0.003 0.030 1702 Dihedral : 4.559 30.278 1268 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.62 % Allowed : 10.51 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.23), residues: 1111 helix: 2.58 (1.10), residues: 20 sheet: -0.03 (0.38), residues: 156 loop : -0.47 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 53 TYR 0.010 0.001 TYR F 484 PHE 0.010 0.001 PHE F 367 TRP 0.008 0.001 TRP L 116 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 9498) covalent geometry : angle 0.49195 (12865) SS BOND : bond 0.00499 ( 2) SS BOND : angle 0.67262 ( 4) hydrogen bonds : bond 0.02480 ( 156) hydrogen bonds : angle 5.68163 ( 354) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.436 Fit side-chains REVERT: C 300 ARG cc_start: 0.8403 (ttm110) cc_final: 0.7332 (ttp-170) REVERT: C 462 LYS cc_start: 0.8065 (mmtt) cc_final: 0.6758 (tptt) REVERT: D 398 GLU cc_start: 0.8253 (mp0) cc_final: 0.7478 (tp30) REVERT: D 485 ARG cc_start: 0.7270 (ttm170) cc_final: 0.5309 (ttt180) REVERT: F 462 LYS cc_start: 0.8574 (mmtt) cc_final: 0.6981 (tmtm) REVERT: F 689 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8367 (mttt) REVERT: H 31 VAL cc_start: 0.9130 (m) cc_final: 0.8877 (p) REVERT: H 37 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8455 (pt) REVERT: H 62 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8344 (mmtm) REVERT: H 78 ASP cc_start: 0.8772 (m-30) cc_final: 0.8556 (m-30) REVERT: H 110 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8909 (t) REVERT: L 92 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7956 (mp0) REVERT: L 118 THR cc_start: 0.9301 (m) cc_final: 0.8959 (p) outliers start: 16 outliers final: 5 residues processed: 148 average time/residue: 0.5673 time to fit residues: 90.1291 Evaluate side-chains 127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 120 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 46 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 GLN ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 ASN L 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.089198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.079556 restraints weight = 19198.241| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.03 r_work: 0.2931 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9500 Z= 0.125 Angle : 0.504 9.336 12869 Z= 0.261 Chirality : 0.041 0.136 1309 Planarity : 0.003 0.031 1702 Dihedral : 4.489 31.280 1268 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.63 % Allowed : 11.01 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.23), residues: 1111 helix: 3.05 (1.13), residues: 20 sheet: -0.01 (0.38), residues: 156 loop : -0.42 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 485 TYR 0.013 0.001 TYR L 113 PHE 0.010 0.001 PHE F 367 TRP 0.011 0.001 TRP A 509 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9498) covalent geometry : angle 0.50338 (12865) SS BOND : bond 0.00498 ( 2) SS BOND : angle 0.86439 ( 4) hydrogen bonds : bond 0.02555 ( 156) hydrogen bonds : angle 5.51430 ( 354) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: B 575 GLU cc_start: 0.3523 (OUTLIER) cc_final: 0.2882 (pm20) REVERT: C 300 ARG cc_start: 0.8411 (ttm110) cc_final: 0.7184 (tmm160) REVERT: C 462 LYS cc_start: 0.8098 (mmtt) cc_final: 0.6765 (tptt) REVERT: D 398 GLU cc_start: 0.8224 (mp0) cc_final: 0.7720 (tm-30) REVERT: D 485 ARG cc_start: 0.7147 (ttm170) cc_final: 0.5379 (ttt180) REVERT: F 462 LYS cc_start: 0.8571 (mmtt) cc_final: 0.6960 (tmtm) REVERT: F 689 LYS cc_start: 0.8751 (mmtm) cc_final: 0.8324 (mttt) REVERT: H 31 VAL cc_start: 0.9141 (m) cc_final: 0.8925 (p) REVERT: H 37 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8407 (pt) REVERT: H 62 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8387 (mmtm) REVERT: H 78 ASP cc_start: 0.8791 (m-30) cc_final: 0.8587 (m-30) REVERT: H 110 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8895 (t) REVERT: L 92 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7981 (mp0) REVERT: L 118 THR cc_start: 0.9309 (m) cc_final: 0.8973 (p) outliers start: 26 outliers final: 14 residues processed: 138 average time/residue: 0.5876 time to fit residues: 87.0634 Evaluate side-chains 135 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 21 optimal weight: 0.0770 chunk 57 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 ASN F 608 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.077961 restraints weight = 19276.178| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.04 r_work: 0.2901 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9500 Z= 0.175 Angle : 0.530 5.622 12869 Z= 0.278 Chirality : 0.042 0.140 1309 Planarity : 0.004 0.033 1702 Dihedral : 4.664 32.066 1268 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.83 % Allowed : 11.21 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.23), residues: 1111 helix: 2.92 (1.12), residues: 20 sheet: -0.00 (0.39), residues: 162 loop : -0.47 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 53 TYR 0.015 0.002 TYR L 113 PHE 0.010 0.001 PHE F 367 TRP 0.012 0.001 TRP A 509 HIS 0.006 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 9498) covalent geometry : angle 0.52943 (12865) SS BOND : bond 0.00554 ( 2) SS BOND : angle 0.79654 ( 4) hydrogen bonds : bond 0.02814 ( 156) hydrogen bonds : angle 5.64197 ( 354) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.387 Fit side-chains REVERT: B 575 GLU cc_start: 0.3377 (OUTLIER) cc_final: 0.2757 (pm20) REVERT: C 300 ARG cc_start: 0.8429 (ttm110) cc_final: 0.7058 (tmm160) REVERT: C 462 LYS cc_start: 0.8090 (mmtt) cc_final: 0.6699 (tptt) REVERT: D 398 GLU cc_start: 0.8287 (mp0) cc_final: 0.7758 (tm-30) REVERT: D 485 ARG cc_start: 0.7263 (ttm170) cc_final: 0.5573 (ttt90) REVERT: F 462 LYS cc_start: 0.8517 (mmtt) cc_final: 0.6865 (tmtm) REVERT: F 689 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8323 (mttt) REVERT: H 37 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8335 (pt) REVERT: H 62 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8387 (mmtm) REVERT: H 78 ASP cc_start: 0.8792 (m-30) cc_final: 0.8580 (m-30) REVERT: H 86 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.6742 (mtp85) REVERT: H 110 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8924 (t) REVERT: L 118 THR cc_start: 0.9309 (m) cc_final: 0.8992 (p) outliers start: 28 outliers final: 17 residues processed: 137 average time/residue: 0.5790 time to fit residues: 85.1703 Evaluate side-chains 134 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 575 GLU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 GLN ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN F 470 ASN F 588 GLN L 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.076590 restraints weight = 19411.278| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.03 r_work: 0.2868 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 9500 Z= 0.285 Angle : 0.614 9.010 12869 Z= 0.323 Chirality : 0.046 0.149 1309 Planarity : 0.005 0.045 1702 Dihedral : 5.108 34.026 1268 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.43 % Allowed : 11.01 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.23), residues: 1111 helix: 2.31 (1.09), residues: 20 sheet: -0.18 (0.40), residues: 161 loop : -0.62 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 391 TYR 0.018 0.002 TYR L 113 PHE 0.012 0.002 PHE F 367 TRP 0.016 0.002 TRP A 509 HIS 0.009 0.002 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 9498) covalent geometry : angle 0.61436 (12865) SS BOND : bond 0.00648 ( 2) SS BOND : angle 0.82425 ( 4) hydrogen bonds : bond 0.03349 ( 156) hydrogen bonds : angle 6.02999 ( 354) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.416 Fit side-chains REVERT: C 300 ARG cc_start: 0.8465 (ttm110) cc_final: 0.7040 (tmm160) REVERT: C 462 LYS cc_start: 0.8140 (mmtt) cc_final: 0.6731 (tptt) REVERT: D 398 GLU cc_start: 0.8378 (mp0) cc_final: 0.7927 (mp0) REVERT: D 485 ARG cc_start: 0.7393 (ttm170) cc_final: 0.5560 (ttt180) REVERT: F 462 LYS cc_start: 0.8484 (mmtt) cc_final: 0.7324 (mmmt) REVERT: F 689 LYS cc_start: 0.8812 (mmtm) cc_final: 0.8354 (mttt) REVERT: H 37 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8343 (pt) REVERT: H 62 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8466 (mmtm) REVERT: H 78 ASP cc_start: 0.8814 (m-30) cc_final: 0.8581 (m-30) REVERT: H 86 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.6762 (mtp85) REVERT: H 110 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8909 (t) outliers start: 34 outliers final: 18 residues processed: 135 average time/residue: 0.5573 time to fit residues: 80.8835 Evaluate side-chains 132 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 20.0000 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 0.0030 chunk 73 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 GLN C 608 GLN F 470 ASN F 588 GLN L 59 GLN L 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.089834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.080157 restraints weight = 18913.991| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.02 r_work: 0.2937 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9500 Z= 0.085 Angle : 0.486 7.715 12869 Z= 0.249 Chirality : 0.040 0.134 1309 Planarity : 0.003 0.031 1702 Dihedral : 4.399 31.037 1268 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.72 % Allowed : 12.53 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.24), residues: 1111 helix: 2.98 (1.14), residues: 20 sheet: 0.09 (0.39), residues: 162 loop : -0.47 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 485 TYR 0.010 0.001 TYR F 484 PHE 0.007 0.001 PHE C 535 TRP 0.010 0.001 TRP L 116 HIS 0.003 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 9498) covalent geometry : angle 0.48574 (12865) SS BOND : bond 0.00484 ( 2) SS BOND : angle 0.61420 ( 4) hydrogen bonds : bond 0.02293 ( 156) hydrogen bonds : angle 5.47225 ( 354) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: C 300 ARG cc_start: 0.8388 (ttm110) cc_final: 0.7039 (tmm160) REVERT: C 462 LYS cc_start: 0.7997 (mmtt) cc_final: 0.6755 (tptm) REVERT: D 398 GLU cc_start: 0.8196 (mp0) cc_final: 0.7717 (tm-30) REVERT: D 485 ARG cc_start: 0.7309 (ttm170) cc_final: 0.5640 (ttt180) REVERT: F 462 LYS cc_start: 0.8542 (mmtt) cc_final: 0.7403 (mmmt) REVERT: F 689 LYS cc_start: 0.8715 (mmtm) cc_final: 0.8295 (mttt) REVERT: H 37 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8197 (pt) REVERT: H 62 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8381 (mmtm) REVERT: H 78 ASP cc_start: 0.8766 (m-30) cc_final: 0.8549 (m-30) REVERT: H 92 ASP cc_start: 0.8583 (t0) cc_final: 0.8332 (t0) REVERT: H 110 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8909 (t) REVERT: L 118 THR cc_start: 0.9301 (m) cc_final: 0.8928 (p) outliers start: 17 outliers final: 10 residues processed: 143 average time/residue: 0.5416 time to fit residues: 83.5857 Evaluate side-chains 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain C residue 565 GLU Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 102 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 90 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 470 ASN F 588 GLN H 32 GLN L 59 GLN L 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.087753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.078019 restraints weight = 18977.545| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.01 r_work: 0.2897 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9500 Z= 0.186 Angle : 0.549 10.490 12869 Z= 0.283 Chirality : 0.043 0.139 1309 Planarity : 0.004 0.033 1702 Dihedral : 4.666 32.685 1268 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.92 % Allowed : 13.13 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.24), residues: 1111 helix: 2.91 (1.11), residues: 20 sheet: -0.05 (0.38), residues: 170 loop : -0.48 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 550 TYR 0.016 0.002 TYR L 113 PHE 0.010 0.001 PHE F 367 TRP 0.013 0.001 TRP A 509 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 9498) covalent geometry : angle 0.54846 (12865) SS BOND : bond 0.00580 ( 2) SS BOND : angle 0.84541 ( 4) hydrogen bonds : bond 0.02822 ( 156) hydrogen bonds : angle 5.62337 ( 354) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.400 Fit side-chains REVERT: C 300 ARG cc_start: 0.8461 (ttm110) cc_final: 0.7067 (tmm160) REVERT: C 462 LYS cc_start: 0.8109 (mmtt) cc_final: 0.6725 (tptt) REVERT: D 398 GLU cc_start: 0.8290 (mp0) cc_final: 0.7777 (tm-30) REVERT: D 485 ARG cc_start: 0.7377 (ttm170) cc_final: 0.5435 (ttt180) REVERT: F 462 LYS cc_start: 0.8522 (mmtt) cc_final: 0.7373 (mmmt) REVERT: F 689 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8294 (mttt) REVERT: H 37 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8286 (pt) REVERT: H 62 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8426 (mmtm) REVERT: H 78 ASP cc_start: 0.8808 (m-30) cc_final: 0.8585 (m-30) REVERT: H 86 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.6827 (mtp85) REVERT: H 92 ASP cc_start: 0.8595 (t0) cc_final: 0.8324 (t0) REVERT: H 110 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8926 (t) REVERT: L 52 SER cc_start: 0.8550 (t) cc_final: 0.8161 (p) REVERT: L 118 THR cc_start: 0.9329 (m) cc_final: 0.9006 (p) outliers start: 19 outliers final: 11 residues processed: 132 average time/residue: 0.5540 time to fit residues: 78.6565 Evaluate side-chains 128 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain C residue 689 LYS Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 40.0000 chunk 75 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 GLN F 470 ASN F 588 GLN H 32 GLN L 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.078063 restraints weight = 19101.272| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.02 r_work: 0.2894 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9500 Z= 0.187 Angle : 0.552 9.765 12869 Z= 0.286 Chirality : 0.043 0.138 1309 Planarity : 0.004 0.032 1702 Dihedral : 4.760 32.619 1268 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.92 % Allowed : 12.93 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.23), residues: 1111 helix: 2.86 (1.10), residues: 20 sheet: -0.11 (0.40), residues: 161 loop : -0.53 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 550 TYR 0.015 0.002 TYR L 113 PHE 0.009 0.001 PHE F 367 TRP 0.012 0.001 TRP A 509 HIS 0.007 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9498) covalent geometry : angle 0.55173 (12865) SS BOND : bond 0.00585 ( 2) SS BOND : angle 0.74280 ( 4) hydrogen bonds : bond 0.02856 ( 156) hydrogen bonds : angle 5.72024 ( 354) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.393 Fit side-chains REVERT: A 398 GLU cc_start: 0.8643 (mp0) cc_final: 0.8438 (mp0) REVERT: C 300 ARG cc_start: 0.8414 (ttm110) cc_final: 0.7040 (tmm160) REVERT: C 462 LYS cc_start: 0.8149 (mmtt) cc_final: 0.6751 (tptt) REVERT: D 398 GLU cc_start: 0.8291 (mp0) cc_final: 0.7779 (tm-30) REVERT: D 485 ARG cc_start: 0.7362 (ttm170) cc_final: 0.5451 (ttt180) REVERT: F 462 LYS cc_start: 0.8484 (mmtt) cc_final: 0.7310 (mmmt) REVERT: F 689 LYS cc_start: 0.8764 (mmtm) cc_final: 0.8302 (mttt) REVERT: H 37 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8261 (pt) REVERT: H 62 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8390 (mmtm) REVERT: H 78 ASP cc_start: 0.8818 (m-30) cc_final: 0.8597 (m-30) REVERT: H 86 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.6838 (mtp85) REVERT: H 92 ASP cc_start: 0.8601 (t0) cc_final: 0.8320 (t0) REVERT: H 110 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8901 (t) REVERT: L 52 SER cc_start: 0.8596 (t) cc_final: 0.8216 (p) outliers start: 19 outliers final: 11 residues processed: 127 average time/residue: 0.5535 time to fit residues: 75.6447 Evaluate side-chains 123 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 81 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 470 ASN ** F 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN L 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.087189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.077363 restraints weight = 19114.567| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.04 r_work: 0.2876 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9500 Z= 0.218 Angle : 0.580 10.028 12869 Z= 0.301 Chirality : 0.044 0.249 1309 Planarity : 0.004 0.034 1702 Dihedral : 4.884 33.184 1268 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.92 % Allowed : 12.83 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.23), residues: 1111 helix: 2.64 (1.08), residues: 20 sheet: -0.13 (0.40), residues: 161 loop : -0.58 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 550 TYR 0.017 0.002 TYR L 113 PHE 0.010 0.002 PHE F 367 TRP 0.013 0.001 TRP A 509 HIS 0.008 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 9498) covalent geometry : angle 0.57973 (12865) SS BOND : bond 0.00613 ( 2) SS BOND : angle 0.85909 ( 4) hydrogen bonds : bond 0.03018 ( 156) hydrogen bonds : angle 5.83504 ( 354) =============================================================================== Job complete usr+sys time: 3201.79 seconds wall clock time: 55 minutes 27.13 seconds (3327.13 seconds total)