Starting phenix.real_space_refine on Sun Jun 8 00:15:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b7s_44322/06_2025/9b7s_44322.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b7s_44322/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b7s_44322/06_2025/9b7s_44322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b7s_44322/06_2025/9b7s_44322.map" model { file = "/net/cci-nas-00/data/ceres_data/9b7s_44322/06_2025/9b7s_44322.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b7s_44322/06_2025/9b7s_44322.cif" } resolution = 2.84 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 ------------------------------------------------------------------------------- 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.86, per 1000 atoms: 0.63 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: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.19 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: 2.72 Time building geometry restraints manager: 2.61 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: 0.570 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.520 Find NCS groups from input model: 0.260 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:36.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (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 TRP 0.032 0.002 TRP H 138 HIS 0.014 0.003 HIS C 290 PHE 0.030 0.003 PHE F 367 TYR 0.027 0.003 TYR A 399 ARG 0.013 0.002 ARG F 734 Details of bonding type rmsd hydrogen bonds : bond 0.21485 ( 156) hydrogen bonds : angle 9.56990 ( 354) SS BOND : bond 0.00103 ( 2) SS BOND : angle 1.07977 ( 4) covalent geometry : bond 0.00810 ( 9498) covalent geometry : angle 0.96138 (12865) *********************** 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 : 1.240 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: 1.3041 time to fit residues: 276.7677 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 : 1.067 ------------------------------------------------------------------------------- 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 97 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN C 360 HIS ** 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 E 585 GLN F 360 HIS F 452 ASN F 470 ASN F 495 GLN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3185 r_free = 0.3185 target = 0.089228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.079565 restraints weight = 18956.171| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.03 r_work: 0.2934 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9500 Z= 0.154 Angle : 0.573 6.726 12869 Z= 0.306 Chirality : 0.043 0.140 1309 Planarity : 0.004 0.034 1702 Dihedral : 5.335 31.364 1271 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.12 % Allowed : 8.38 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1111 helix: -0.69 (0.88), residues: 32 sheet: -0.27 (0.35), residues: 180 loop : -0.78 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 138 HIS 0.006 0.001 HIS C 290 PHE 0.016 0.002 PHE F 367 TYR 0.018 0.002 TYR C 484 ARG 0.006 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 156) hydrogen bonds : angle 6.63405 ( 354) SS BOND : bond 0.00551 ( 2) SS BOND : angle 0.85569 ( 4) covalent geometry : bond 0.00355 ( 9498) covalent geometry : angle 0.57241 (12865) *********************** 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 175 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.199 Fit side-chains REVERT: C 300 ARG cc_start: 0.8399 (ttm110) cc_final: 0.7234 (ttt180) REVERT: C 462 LYS cc_start: 0.8067 (mmtt) cc_final: 0.6761 (tptt) REVERT: C 725 ARG cc_start: 0.8747 (ptt180) cc_final: 0.8142 (ptp-110) REVERT: D 485 ARG cc_start: 0.7540 (ttm170) cc_final: 0.5337 (ttt180) REVERT: E 470 ASN cc_start: 0.7936 (t0) cc_final: 0.7587 (t0) REVERT: F 300 ARG cc_start: 0.8419 (mtt180) cc_final: 0.6920 (ptt180) REVERT: F 462 LYS cc_start: 0.8586 (mmtt) cc_final: 0.6976 (tmtm) REVERT: F 514 ARG cc_start: 0.8550 (mtm180) cc_final: 0.7000 (mmt180) REVERT: F 689 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8395 (mttt) REVERT: H 31 VAL cc_start: 0.9106 (m) cc_final: 0.8765 (p) REVERT: H 62 LYS cc_start: 0.8448 (mmtt) cc_final: 0.7950 (mmtp) REVERT: H 78 ASP cc_start: 0.8797 (m-30) cc_final: 0.8570 (m-30) REVERT: H 110 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8929 (t) REVERT: L 67 ARG cc_start: 0.8445 (ptm-80) cc_final: 0.8183 (ptt90) REVERT: L 118 THR cc_start: 0.9345 (m) cc_final: 0.9104 (p) outliers start: 21 outliers final: 8 residues processed: 165 average time/residue: 1.1879 time to fit residues: 211.3527 Evaluate side-chains 141 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 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 110 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 40 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 100 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 457 ASN B 585 GLN C 497 ASN ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN F 470 ASN F 497 ASN F 585 GLN ** F 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN H 96 ASN L 59 GLN L 64 GLN L 101 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.086734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.076940 restraints weight = 19359.878| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.04 r_work: 0.2880 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1886 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 : 0.626 9.376 12869 Z= 0.332 Chirality : 0.046 0.149 1309 Planarity : 0.005 0.050 1702 Dihedral : 5.349 32.539 1268 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.53 % Allowed : 8.99 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1111 helix: 1.86 (1.15), residues: 20 sheet: -0.37 (0.37), residues: 167 loop : -0.71 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 138 HIS 0.010 0.002 HIS F 290 PHE 0.017 0.002 PHE F 367 TYR 0.018 0.002 TYR L 113 ARG 0.005 0.001 ARG D 391 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 156) hydrogen bonds : angle 6.35648 ( 354) SS BOND : bond 0.00559 ( 2) SS BOND : angle 1.12976 ( 4) covalent geometry : bond 0.00613 ( 9498) covalent geometry : angle 0.62551 (12865) *********************** 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 153 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.160 Fit side-chains REVERT: B 440 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6799 (mm) REVERT: B 575 GLU cc_start: 0.3508 (OUTLIER) cc_final: 0.2736 (pm20) REVERT: C 300 ARG cc_start: 0.8480 (ttm110) cc_final: 0.7235 (ttt180) REVERT: C 462 LYS cc_start: 0.8118 (mmtt) cc_final: 0.6792 (tptt) REVERT: D 398 GLU cc_start: 0.8392 (mp0) cc_final: 0.7931 (mp0) REVERT: D 485 ARG cc_start: 0.7470 (ttm170) cc_final: 0.5652 (ttt90) REVERT: F 300 ARG cc_start: 0.8469 (mtt180) cc_final: 0.6902 (ptt180) REVERT: F 462 LYS cc_start: 0.8568 (mmtt) cc_final: 0.6937 (tmtm) REVERT: F 689 LYS cc_start: 0.8822 (mmtm) cc_final: 0.8413 (mttt) REVERT: H 31 VAL cc_start: 0.9127 (m) cc_final: 0.8871 (p) REVERT: H 37 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8582 (pt) REVERT: H 62 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8345 (mmtp) REVERT: H 78 ASP cc_start: 0.8830 (m-30) cc_final: 0.8619 (m-30) REVERT: H 86 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.6812 (mtp85) REVERT: L 67 ARG cc_start: 0.8499 (ptm-80) cc_final: 0.8173 (ptt90) REVERT: L 118 THR cc_start: 0.9341 (m) cc_final: 0.9071 (p) outliers start: 25 outliers final: 13 residues processed: 143 average time/residue: 1.1539 time to fit residues: 177.2972 Evaluate side-chains 137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 575 GLU 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 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 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 115 ASN 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 107 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN ** C 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 470 ASN F 585 GLN F 588 GLN L 64 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 = 0.3152 r_free = 0.3152 target = 0.087451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.077729 restraints weight = 19102.280| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.00 r_work: 0.2893 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9500 Z= 0.193 Angle : 0.563 9.462 12869 Z= 0.296 Chirality : 0.043 0.141 1309 Planarity : 0.004 0.036 1702 Dihedral : 5.084 32.426 1268 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.83 % Allowed : 10.00 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.23), residues: 1111 helix: 2.37 (1.10), residues: 20 sheet: -0.26 (0.37), residues: 167 loop : -0.63 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 138 HIS 0.007 0.001 HIS C 290 PHE 0.013 0.002 PHE F 367 TYR 0.015 0.002 TYR L 113 ARG 0.004 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 156) hydrogen bonds : angle 6.07325 ( 354) SS BOND : bond 0.00583 ( 2) SS BOND : angle 0.92332 ( 4) covalent geometry : bond 0.00450 ( 9498) covalent geometry : angle 0.56280 (12865) *********************** 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 156 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 1.018 Fit side-chains REVERT: C 300 ARG cc_start: 0.8460 (ttm110) cc_final: 0.7096 (tmm160) REVERT: C 462 LYS cc_start: 0.8098 (mmtt) cc_final: 0.6737 (tptm) REVERT: D 398 GLU cc_start: 0.8382 (mp0) cc_final: 0.7918 (mp0) REVERT: D 485 ARG cc_start: 0.7439 (ttm170) cc_final: 0.5623 (ttt90) REVERT: F 300 ARG cc_start: 0.8389 (mtt180) cc_final: 0.6931 (ptt180) REVERT: F 462 LYS cc_start: 0.8557 (mmtt) cc_final: 0.6908 (tmtm) REVERT: F 689 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8405 (mttt) REVERT: F 707 LYS cc_start: 0.9120 (pttt) cc_final: 0.8905 (pttp) REVERT: H 31 VAL cc_start: 0.9144 (m) cc_final: 0.8894 (p) REVERT: H 37 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8501 (pt) REVERT: H 62 LYS cc_start: 0.8812 (mmtt) cc_final: 0.8406 (mmtp) REVERT: H 78 ASP cc_start: 0.8804 (m-30) cc_final: 0.8590 (m-30) REVERT: H 86 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.6668 (mtp85) REVERT: L 52 SER cc_start: 0.8497 (t) cc_final: 0.8121 (p) REVERT: L 67 ARG cc_start: 0.8488 (ptm-80) cc_final: 0.8223 (ptt90) REVERT: L 118 THR cc_start: 0.9321 (m) cc_final: 0.9029 (p) outliers start: 28 outliers final: 13 residues processed: 145 average time/residue: 1.1365 time to fit residues: 177.2186 Evaluate side-chains 138 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 E residue 465 VAL Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 24 LEU 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 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 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 20.0000 chunk 76 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 81 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 70 optimal weight: 0.1980 chunk 63 optimal weight: 9.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 624 HIS B 585 GLN C 430 GLN C 608 GLN F 470 ASN L 64 GLN L 101 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.088557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.078903 restraints weight = 19148.555| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.03 r_work: 0.2919 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9500 Z= 0.127 Angle : 0.514 9.302 12869 Z= 0.267 Chirality : 0.041 0.134 1309 Planarity : 0.004 0.031 1702 Dihedral : 4.698 31.583 1268 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.32 % Allowed : 11.01 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1111 helix: 2.90 (1.12), residues: 20 sheet: -0.09 (0.38), residues: 164 loop : -0.52 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 509 HIS 0.005 0.001 HIS C 290 PHE 0.010 0.001 PHE F 367 TYR 0.012 0.001 TYR L 113 ARG 0.003 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02664 ( 156) hydrogen bonds : angle 5.73881 ( 354) SS BOND : bond 0.00522 ( 2) SS BOND : angle 0.84838 ( 4) covalent geometry : bond 0.00295 ( 9498) covalent geometry : angle 0.51401 (12865) *********************** 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 151 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.177 Fit side-chains REVERT: B 575 GLU cc_start: 0.3497 (OUTLIER) cc_final: 0.2676 (pm20) REVERT: C 300 ARG cc_start: 0.8425 (ttm110) cc_final: 0.7076 (tmm160) REVERT: C 462 LYS cc_start: 0.8101 (mmtt) cc_final: 0.6785 (tptt) REVERT: D 398 GLU cc_start: 0.8293 (mp0) cc_final: 0.7709 (tm-30) REVERT: D 485 ARG cc_start: 0.7419 (ttm170) cc_final: 0.5476 (ttt180) REVERT: F 462 LYS cc_start: 0.8542 (mmtt) cc_final: 0.6916 (tmtm) REVERT: F 689 LYS cc_start: 0.8763 (mmtm) cc_final: 0.8343 (mttt) REVERT: F 707 LYS cc_start: 0.9134 (pttt) cc_final: 0.8922 (pttp) REVERT: H 31 VAL cc_start: 0.9138 (m) cc_final: 0.8929 (p) REVERT: H 37 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8452 (pt) REVERT: H 62 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8418 (mmtm) REVERT: H 78 ASP cc_start: 0.8773 (m-30) cc_final: 0.8553 (m-30) REVERT: H 92 ASP cc_start: 0.8593 (t0) cc_final: 0.8357 (t0) REVERT: L 52 SER cc_start: 0.8455 (t) cc_final: 0.8054 (p) REVERT: L 67 ARG cc_start: 0.8470 (ptm-80) cc_final: 0.8237 (ptt90) REVERT: L 118 THR cc_start: 0.9303 (m) cc_final: 0.8954 (p) outliers start: 23 outliers final: 12 residues processed: 141 average time/residue: 1.3294 time to fit residues: 201.4135 Evaluate side-chains 137 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 0.0970 chunk 67 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 21 optimal weight: 0.0070 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 overall best weight: 3.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 470 ASN F 608 GLN L 64 GLN L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.078733 restraints weight = 18960.067| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.01 r_work: 0.2905 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9500 Z= 0.141 Angle : 0.514 8.851 12869 Z= 0.267 Chirality : 0.041 0.136 1309 Planarity : 0.004 0.032 1702 Dihedral : 4.635 32.020 1268 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.32 % Allowed : 12.32 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.23), residues: 1111 helix: 2.96 (1.13), residues: 20 sheet: -0.00 (0.39), residues: 164 loop : -0.50 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 509 HIS 0.005 0.001 HIS C 290 PHE 0.011 0.001 PHE F 367 TYR 0.013 0.001 TYR L 113 ARG 0.003 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02708 ( 156) hydrogen bonds : angle 5.68268 ( 354) SS BOND : bond 0.00509 ( 2) SS BOND : angle 0.72209 ( 4) covalent geometry : bond 0.00327 ( 9498) covalent geometry : angle 0.51348 (12865) *********************** 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 145 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.796 Fit side-chains REVERT: B 575 GLU cc_start: 0.3341 (OUTLIER) cc_final: 0.2644 (pm20) REVERT: C 300 ARG cc_start: 0.8440 (ttm110) cc_final: 0.7065 (tmm160) REVERT: C 462 LYS cc_start: 0.8097 (mmtt) cc_final: 0.6699 (tptt) REVERT: D 398 GLU cc_start: 0.8280 (mp0) cc_final: 0.7703 (tm-30) REVERT: D 485 ARG cc_start: 0.7360 (ttm170) cc_final: 0.5448 (ttt180) REVERT: F 462 LYS cc_start: 0.8523 (mmtt) cc_final: 0.6865 (tmtm) REVERT: F 689 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8316 (mttt) REVERT: H 37 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8401 (pt) REVERT: H 62 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8405 (mmtm) REVERT: H 78 ASP cc_start: 0.8780 (m-30) cc_final: 0.8572 (m-30) REVERT: H 92 ASP cc_start: 0.8597 (t0) cc_final: 0.8280 (t0) REVERT: L 67 ARG cc_start: 0.8460 (ptm-80) cc_final: 0.8222 (ptt90) REVERT: L 118 THR cc_start: 0.9286 (m) cc_final: 0.8931 (p) outliers start: 23 outliers final: 13 residues processed: 137 average time/residue: 1.5002 time to fit residues: 222.1714 Evaluate side-chains 132 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 E residue 469 SER Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 104 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- 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** ** F 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.085830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.076066 restraints weight = 19442.808| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.02 r_work: 0.2851 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 9500 Z= 0.329 Angle : 0.643 8.317 12869 Z= 0.338 Chirality : 0.047 0.155 1309 Planarity : 0.005 0.050 1702 Dihedral : 5.264 34.685 1268 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.63 % Allowed : 11.82 % 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 (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: -0.81 (0.23), residues: 1111 helix: 2.39 (1.09), residues: 20 sheet: -0.22 (0.40), residues: 162 loop : -0.71 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 509 HIS 0.010 0.002 HIS C 290 PHE 0.013 0.002 PHE F 367 TYR 0.017 0.002 TYR H 128 ARG 0.005 0.001 ARG D 391 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 156) hydrogen bonds : angle 6.20927 ( 354) SS BOND : bond 0.00699 ( 2) SS BOND : angle 0.90769 ( 4) covalent geometry : bond 0.00767 ( 9498) covalent geometry : angle 0.64310 (12865) *********************** 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 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: B 575 GLU cc_start: 0.3364 (OUTLIER) cc_final: 0.2521 (pm20) REVERT: C 300 ARG cc_start: 0.8491 (ttm110) cc_final: 0.7177 (ttp-170) REVERT: C 462 LYS cc_start: 0.8133 (mmtt) cc_final: 0.6697 (tptt) REVERT: D 398 GLU cc_start: 0.8351 (mp0) cc_final: 0.7916 (mp0) REVERT: D 485 ARG cc_start: 0.7645 (ttm170) cc_final: 0.5540 (ttt180) REVERT: F 462 LYS cc_start: 0.8478 (mmtt) cc_final: 0.7291 (mmmt) REVERT: F 689 LYS cc_start: 0.8798 (mmtm) cc_final: 0.8351 (mttt) REVERT: H 37 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8518 (pt) REVERT: H 62 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8511 (mmtm) REVERT: H 78 ASP cc_start: 0.8831 (m-30) cc_final: 0.8601 (m-30) REVERT: H 92 ASP cc_start: 0.8606 (t0) cc_final: 0.8285 (t0) REVERT: L 67 ARG cc_start: 0.8516 (ptm-80) cc_final: 0.8245 (ptt90) outliers start: 26 outliers final: 18 residues processed: 131 average time/residue: 1.6127 time to fit residues: 227.6154 Evaluate side-chains 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 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 37 LEU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 145 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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** L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.077103 restraints weight = 19505.103| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.06 r_work: 0.2870 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9500 Z= 0.207 Angle : 0.569 8.280 12869 Z= 0.297 Chirality : 0.043 0.142 1309 Planarity : 0.004 0.033 1702 Dihedral : 5.026 33.526 1268 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.42 % Allowed : 11.92 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.23), residues: 1111 helix: 2.57 (1.09), residues: 20 sheet: -0.18 (0.40), residues: 161 loop : -0.67 (0.19), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 509 HIS 0.007 0.001 HIS C 290 PHE 0.010 0.001 PHE F 367 TYR 0.015 0.002 TYR L 113 ARG 0.004 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 156) hydrogen bonds : angle 6.01516 ( 354) SS BOND : bond 0.00591 ( 2) SS BOND : angle 0.80625 ( 4) covalent geometry : bond 0.00482 ( 9498) covalent geometry : angle 0.56880 (12865) *********************** 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 140 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.507 Fit side-chains REVERT: B 575 GLU cc_start: 0.3332 (OUTLIER) cc_final: 0.2540 (pm20) REVERT: C 300 ARG cc_start: 0.8486 (ttm110) cc_final: 0.7178 (ttt180) REVERT: C 462 LYS cc_start: 0.8140 (mmtt) cc_final: 0.6724 (tptt) REVERT: C 495 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: D 398 GLU cc_start: 0.8358 (mp0) cc_final: 0.7925 (mp0) REVERT: D 485 ARG cc_start: 0.7637 (ttm170) cc_final: 0.5517 (ttt180) REVERT: F 462 LYS cc_start: 0.8477 (mmtt) cc_final: 0.7312 (mmmt) REVERT: F 689 LYS cc_start: 0.8760 (mmtm) cc_final: 0.8312 (mttt) REVERT: H 37 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8405 (pt) REVERT: H 62 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8361 (mmtp) REVERT: H 78 ASP cc_start: 0.8817 (m-30) cc_final: 0.8575 (m-30) REVERT: H 86 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.6648 (mtp85) REVERT: H 92 ASP cc_start: 0.8613 (t0) cc_final: 0.8259 (t0) REVERT: L 52 SER cc_start: 0.8585 (t) cc_final: 0.8265 (p) REVERT: L 67 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8237 (ptt90) outliers start: 24 outliers final: 14 residues processed: 132 average time/residue: 1.5868 time to fit residues: 226.8047 Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 495 GLN 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 94 SER Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.076613 restraints weight = 19138.311| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.03 r_work: 0.2869 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9500 Z= 0.254 Angle : 0.601 8.083 12869 Z= 0.314 Chirality : 0.045 0.250 1309 Planarity : 0.005 0.038 1702 Dihedral : 5.113 34.262 1268 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.12 % Allowed : 12.32 % 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 (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: -0.80 (0.23), residues: 1111 helix: 2.27 (1.09), residues: 20 sheet: -0.18 (0.40), residues: 162 loop : -0.70 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 509 HIS 0.008 0.001 HIS C 290 PHE 0.011 0.002 PHE F 367 TYR 0.016 0.002 TYR H 128 ARG 0.004 0.001 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 156) hydrogen bonds : angle 6.08863 ( 354) SS BOND : bond 0.00642 ( 2) SS BOND : angle 0.89867 ( 4) covalent geometry : bond 0.00593 ( 9498) covalent geometry : angle 0.60124 (12865) *********************** 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 135 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.452 Fit side-chains REVERT: B 575 GLU cc_start: 0.3340 (OUTLIER) cc_final: 0.2482 (pm20) REVERT: C 300 ARG cc_start: 0.8469 (ttm110) cc_final: 0.7188 (ttt180) REVERT: C 462 LYS cc_start: 0.8166 (mmtt) cc_final: 0.6750 (tptt) REVERT: C 495 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: D 398 GLU cc_start: 0.8398 (mp0) cc_final: 0.7962 (mp0) REVERT: D 485 ARG cc_start: 0.7651 (ttm170) cc_final: 0.5562 (ttt180) REVERT: F 462 LYS cc_start: 0.8475 (mmtt) cc_final: 0.7276 (mmmt) REVERT: F 689 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8347 (mttt) REVERT: H 37 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8342 (pt) REVERT: H 62 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8456 (mmtm) REVERT: H 78 ASP cc_start: 0.8820 (m-30) cc_final: 0.8583 (m-30) REVERT: H 86 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.6678 (mtp85) REVERT: H 92 ASP cc_start: 0.8620 (t0) cc_final: 0.8265 (t0) REVERT: L 67 ARG cc_start: 0.8510 (ptm-80) cc_final: 0.8187 (ptt90) outliers start: 21 outliers final: 15 residues processed: 127 average time/residue: 1.1362 time to fit residues: 155.9300 Evaluate side-chains 125 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 495 GLN 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 37 LEU Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 LYS Chi-restraints excluded: chain H residue 104 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 6.9990 chunk 106 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- 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** L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.087805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.078025 restraints weight = 19269.801| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.05 r_work: 0.2891 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9500 Z= 0.145 Angle : 0.530 7.791 12869 Z= 0.275 Chirality : 0.042 0.236 1309 Planarity : 0.004 0.033 1702 Dihedral : 4.778 32.511 1268 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.62 % Allowed : 13.03 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.23), residues: 1111 helix: 2.61 (1.10), residues: 20 sheet: 0.01 (0.39), residues: 168 loop : -0.58 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 509 HIS 0.005 0.001 HIS C 290 PHE 0.009 0.001 PHE F 367 TYR 0.014 0.001 TYR L 113 ARG 0.004 0.000 ARG C 485 Details of bonding type rmsd hydrogen bonds : bond 0.02715 ( 156) hydrogen bonds : angle 5.79096 ( 354) SS BOND : bond 0.00555 ( 2) SS BOND : angle 0.77773 ( 4) covalent geometry : bond 0.00340 ( 9498) covalent geometry : angle 0.52993 (12865) ********************** 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: 16 poor density : 115 time to evaluate : 1.106 Fit side-chains REVERT: A 398 GLU cc_start: 0.8614 (mp0) cc_final: 0.8394 (mp0) REVERT: B 575 GLU cc_start: 0.3301 (OUTLIER) cc_final: 0.2516 (pm20) REVERT: C 300 ARG cc_start: 0.8499 (ttm110) cc_final: 0.7227 (ttt180) REVERT: C 462 LYS cc_start: 0.8090 (mmtt) cc_final: 0.6775 (tptm) REVERT: D 398 GLU cc_start: 0.8268 (mp0) cc_final: 0.7440 (tp30) REVERT: D 485 ARG cc_start: 0.7600 (ttm170) cc_final: 0.5449 (ttt180) REVERT: F 462 LYS cc_start: 0.8495 (mmtt) cc_final: 0.7298 (mmmt) REVERT: F 689 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8231 (mttt) REVERT: H 37 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8260 (pt) REVERT: H 62 LYS cc_start: 0.8756 (mmtt) cc_final: 0.8378 (mmtm) REVERT: H 78 ASP cc_start: 0.8807 (m-30) cc_final: 0.8572 (m-30) REVERT: H 92 ASP cc_start: 0.8599 (t0) cc_final: 0.8237 (t0) REVERT: L 52 SER cc_start: 0.8519 (t) cc_final: 0.8153 (p) REVERT: L 67 ARG cc_start: 0.8472 (ptm-80) cc_final: 0.8227 (ptt90) outliers start: 16 outliers final: 13 residues processed: 124 average time/residue: 1.2404 time to fit residues: 165.6580 Evaluate side-chains 124 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 E residue 465 VAL Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain F residue 565 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 95 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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** L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.087401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.077604 restraints weight = 19075.340| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.04 r_work: 0.2881 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2546 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= 0.187 Angle : 0.551 7.860 12869 Z= 0.287 Chirality : 0.043 0.232 1309 Planarity : 0.004 0.035 1702 Dihedral : 4.838 33.198 1268 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.92 % Allowed : 13.03 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.23), residues: 1111 helix: 2.61 (1.09), residues: 20 sheet: 0.04 (0.39), residues: 170 loop : -0.57 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 509 HIS 0.006 0.001 HIS C 290 PHE 0.010 0.001 PHE F 367 TYR 0.016 0.002 TYR L 113 ARG 0.007 0.001 ARG C 550 Details of bonding type rmsd hydrogen bonds : bond 0.02889 ( 156) hydrogen bonds : angle 5.84486 ( 354) SS BOND : bond 0.00624 ( 2) SS BOND : angle 0.63760 ( 4) covalent geometry : bond 0.00438 ( 9498) covalent geometry : angle 0.55143 (12865) =============================================================================== Job complete usr+sys time: 7136.57 seconds wall clock time: 129 minutes 8.55 seconds (7748.55 seconds total)