Starting phenix.real_space_refine on Fri Aug 22 14:17:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7b_38097/08_2025/8x7b_38097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7b_38097/08_2025/8x7b_38097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x7b_38097/08_2025/8x7b_38097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7b_38097/08_2025/8x7b_38097.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x7b_38097/08_2025/8x7b_38097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7b_38097/08_2025/8x7b_38097.map" } resolution = 3.0 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 12 5.16 5 C 2554 2.51 5 N 704 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4020 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "B" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "C" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "D" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "F" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "G" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "H" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "I" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "J" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 378 Classifications: {'peptide': 55} Link IDs: {'CIS': 3, 'TRANS': 51} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'TFX': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'TFX': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'TFX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'TFX': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'TFX': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'TFX': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.00, per 1000 atoms: 0.25 Number of scatterers: 4020 At special positions: 0 Unit cell: (80.51, 93.79, 44.82, 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 12 16.00 O 750 8.00 N 704 7.00 C 2554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.28 Conformation dependent library (CDL) restraints added in 170.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 46 through 48 removed outlier: 6.724A pdb=" N GLY A 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY I 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.422A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL I 63 " --> pdb=" O THR J 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.510A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL I 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.362A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR E 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ALA J 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL E 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA I 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 93 removed outlier: 8.873A pdb=" N ALA A 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N GLY B 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR A 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA A 91 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR E 92 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA E 91 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR J 92 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ALA I 90 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N GLY J 93 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N THR I 92 " --> pdb=" O GLY J 93 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 46 through 48 removed outlier: 6.725A pdb=" N GLY C 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY F 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 63 through 64 removed outlier: 6.422A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 63 " --> pdb=" O THR G 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.511A pdb=" N VAL C 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 78 removed outlier: 6.360A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 93 removed outlier: 8.873A pdb=" N ALA C 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLY D 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR C 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA C 91 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR G 92 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLY G 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR F 92 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA F 91 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR H 92 " --> pdb=" O ALA F 91 " (cutoff:3.500A) 33 hydrogen bonds defined for protein. 99 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.50 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.31: 680 1.31 - 1.41: 834 1.41 - 1.52: 1597 1.52 - 1.62: 919 1.62 - 1.72: 24 Bond restraints: 4054 Sorted by residual: bond pdb=" C2 TFX C 203 " pdb=" N2 TFX C 203 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C2 TFX E 201 " pdb=" N2 TFX E 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C2 TFX I 201 " pdb=" N2 TFX I 201 " ideal model delta sigma weight residual 1.346 1.452 -0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C2 TFX F 202 " pdb=" N2 TFX F 202 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C2 TFX J 202 " pdb=" N2 TFX J 202 " ideal model delta sigma weight residual 1.346 1.451 -0.105 2.00e-02 2.50e+03 2.76e+01 ... (remaining 4049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 4042 1.15 - 2.30: 858 2.30 - 3.45: 365 3.45 - 4.60: 98 4.60 - 5.75: 131 Bond angle restraints: 5494 Sorted by residual: angle pdb=" N ILE E 88 " pdb=" CA ILE E 88 " pdb=" C ILE E 88 " ideal model delta sigma weight residual 108.12 103.40 4.72 1.34e+00 5.57e-01 1.24e+01 angle pdb=" N ILE G 88 " pdb=" CA ILE G 88 " pdb=" C ILE G 88 " ideal model delta sigma weight residual 108.12 103.43 4.69 1.34e+00 5.57e-01 1.23e+01 angle pdb=" N ILE I 88 " pdb=" CA ILE I 88 " pdb=" C ILE I 88 " ideal model delta sigma weight residual 108.12 103.44 4.68 1.34e+00 5.57e-01 1.22e+01 angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 108.12 103.44 4.68 1.34e+00 5.57e-01 1.22e+01 angle pdb=" N ILE F 88 " pdb=" CA ILE F 88 " pdb=" C ILE F 88 " ideal model delta sigma weight residual 108.12 103.44 4.68 1.34e+00 5.57e-01 1.22e+01 ... (remaining 5489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 2057 16.38 - 32.76: 163 32.76 - 49.14: 26 49.14 - 65.51: 10 65.51 - 81.89: 32 Dihedral angle restraints: 2288 sinusoidal: 808 harmonic: 1480 Sorted by residual: dihedral pdb=" CA GLY D 67 " pdb=" C GLY D 67 " pdb=" N GLY D 68 " pdb=" CA GLY D 68 " ideal model delta harmonic sigma weight residual 0.00 25.12 -25.12 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLY I 67 " pdb=" C GLY I 67 " pdb=" N GLY I 68 " pdb=" CA GLY I 68 " ideal model delta harmonic sigma weight residual 0.00 25.06 -25.06 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY A 67 " pdb=" C GLY A 67 " pdb=" N GLY A 68 " pdb=" CA GLY A 68 " ideal model delta harmonic sigma weight residual 0.00 25.05 -25.05 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 2285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 362 0.052 - 0.103: 166 0.103 - 0.155: 102 0.155 - 0.207: 20 0.207 - 0.258: 20 Chirality restraints: 670 Sorted by residual: chirality pdb=" CA ILE E 88 " pdb=" N ILE E 88 " pdb=" C ILE E 88 " pdb=" CB ILE E 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ILE G 88 " pdb=" N ILE G 88 " pdb=" C ILE G 88 " pdb=" CB ILE G 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA ILE C 88 " pdb=" N ILE C 88 " pdb=" C ILE C 88 " pdb=" CB ILE C 88 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 667 not shown) Planarity restraints: 676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 TFX C 202 " -0.043 2.00e-02 2.50e+03 2.62e-02 2.05e+01 pdb=" C11 TFX C 202 " -0.009 2.00e-02 2.50e+03 pdb=" C12 TFX C 202 " 0.027 2.00e-02 2.50e+03 pdb=" C13 TFX C 202 " 0.028 2.00e-02 2.50e+03 pdb=" C14 TFX C 202 " -0.004 2.00e-02 2.50e+03 pdb=" C17 TFX C 202 " -0.008 2.00e-02 2.50e+03 pdb=" C18 TFX C 202 " 0.014 2.00e-02 2.50e+03 pdb=" C5 TFX C 202 " 0.052 2.00e-02 2.50e+03 pdb=" C8 TFX C 202 " 0.006 2.00e-02 2.50e+03 pdb=" C9 TFX C 202 " -0.039 2.00e-02 2.50e+03 pdb=" N1 TFX C 202 " -0.012 2.00e-02 2.50e+03 pdb=" S1 TFX C 202 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 TFX A 201 " -0.043 2.00e-02 2.50e+03 2.62e-02 2.05e+01 pdb=" C11 TFX A 201 " -0.009 2.00e-02 2.50e+03 pdb=" C12 TFX A 201 " 0.026 2.00e-02 2.50e+03 pdb=" C13 TFX A 201 " 0.028 2.00e-02 2.50e+03 pdb=" C14 TFX A 201 " -0.005 2.00e-02 2.50e+03 pdb=" C17 TFX A 201 " -0.008 2.00e-02 2.50e+03 pdb=" C18 TFX A 201 " 0.014 2.00e-02 2.50e+03 pdb=" C5 TFX A 201 " 0.052 2.00e-02 2.50e+03 pdb=" C8 TFX A 201 " 0.007 2.00e-02 2.50e+03 pdb=" C9 TFX A 201 " -0.039 2.00e-02 2.50e+03 pdb=" N1 TFX A 201 " -0.013 2.00e-02 2.50e+03 pdb=" S1 TFX A 201 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 TFX C 201 " -0.043 2.00e-02 2.50e+03 2.62e-02 2.05e+01 pdb=" C11 TFX C 201 " -0.008 2.00e-02 2.50e+03 pdb=" C12 TFX C 201 " 0.026 2.00e-02 2.50e+03 pdb=" C13 TFX C 201 " 0.028 2.00e-02 2.50e+03 pdb=" C14 TFX C 201 " -0.005 2.00e-02 2.50e+03 pdb=" C17 TFX C 201 " -0.008 2.00e-02 2.50e+03 pdb=" C18 TFX C 201 " 0.014 2.00e-02 2.50e+03 pdb=" C5 TFX C 201 " 0.052 2.00e-02 2.50e+03 pdb=" C8 TFX C 201 " 0.006 2.00e-02 2.50e+03 pdb=" C9 TFX C 201 " -0.039 2.00e-02 2.50e+03 pdb=" N1 TFX C 201 " -0.013 2.00e-02 2.50e+03 pdb=" S1 TFX C 201 " -0.010 2.00e-02 2.50e+03 ... (remaining 673 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1098 2.82 - 3.34: 3212 3.34 - 3.86: 6403 3.86 - 4.38: 7340 4.38 - 4.90: 14478 Nonbonded interactions: 32531 Sorted by model distance: nonbonded pdb=" CE1 HIS E 50 " pdb=" C15 TFX E 201 " model vdw 2.297 3.680 nonbonded pdb=" ND1 HIS C 50 " pdb=" C15 TFX C 201 " model vdw 2.322 3.540 nonbonded pdb=" ND1 HIS E 50 " pdb=" C15 TFX E 201 " model vdw 2.323 3.540 nonbonded pdb=" ND1 HIS A 50 " pdb=" C15 TFX A 201 " model vdw 2.349 3.540 nonbonded pdb=" CE1 HIS C 50 " pdb=" C15 TFX C 201 " model vdw 2.362 3.680 ... (remaining 32526 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.660 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:10.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 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 : 0.017 0.106 4054 Z= 0.809 Angle : 1.421 5.749 5494 Z= 0.775 Chirality : 0.081 0.258 670 Planarity : 0.006 0.026 676 Dihedral : 17.124 81.893 1348 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 30.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 15.79 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -4.07 (0.28), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.21), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.008 PHE B 94 HIS 0.003 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.01664 ( 4054) covalent geometry : angle 1.42095 ( 5494) hydrogen bonds : bond 0.19154 ( 33) hydrogen bonds : angle 8.64635 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 83 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6445 (mp0) REVERT: B 83 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7326 (mp0) REVERT: C 61 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6112 (tm-30) REVERT: D 83 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7260 (mp0) REVERT: E 83 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6663 (mm-30) REVERT: F 61 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6028 (tm-30) REVERT: G 61 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6033 (tm-30) REVERT: H 61 GLU cc_start: 0.6079 (mt-10) cc_final: 0.5581 (tm-30) REVERT: H 97 LYS cc_start: 0.6817 (mmtt) cc_final: 0.4822 (pmtt) REVERT: H 98 ASP cc_start: 0.5950 (m-30) cc_final: 0.5091 (p0) REVERT: I 60 LYS cc_start: 0.7014 (ttmt) cc_final: 0.6766 (mptm) REVERT: I 61 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6193 (tm-30) REVERT: I 97 LYS cc_start: 0.6924 (mmtt) cc_final: 0.4682 (pmtt) REVERT: J 61 GLU cc_start: 0.7465 (mt-10) cc_final: 0.6670 (tm-30) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.6398 time to fit residues: 63.8493 Evaluate side-chains 66 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 65 ASN J 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.164028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.112726 restraints weight = 4461.689| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.29 r_work: 0.3717 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4054 Z= 0.156 Angle : 0.666 5.501 5494 Z= 0.344 Chirality : 0.053 0.163 670 Planarity : 0.002 0.013 676 Dihedral : 13.874 65.324 588 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.89 % Allowed : 17.89 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.35 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE F 94 HIS 0.008 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4054) covalent geometry : angle 0.66616 ( 5494) hydrogen bonds : bond 0.01754 ( 33) hydrogen bonds : angle 5.54254 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.158 Fit side-chains REVERT: A 61 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7372 (tt0) REVERT: A 83 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7656 (mp0) REVERT: B 72 THR cc_start: 0.9287 (m) cc_final: 0.9044 (m) REVERT: C 61 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7435 (tt0) REVERT: C 83 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7684 (mp0) REVERT: D 83 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7936 (mp0) REVERT: E 61 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7503 (tm-30) REVERT: E 83 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7883 (mm-30) REVERT: F 61 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7847 (tm-30) REVERT: F 97 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7559 (mttt) REVERT: G 83 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7740 (mp0) REVERT: H 61 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8013 (tt0) REVERT: H 97 LYS cc_start: 0.8291 (mmtt) cc_final: 0.8085 (mttp) REVERT: I 61 GLU cc_start: 0.8416 (mt-10) cc_final: 0.7914 (tm-30) REVERT: J 61 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7761 (tt0) REVERT: J 83 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7660 (mp0) outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 0.8094 time to fit residues: 46.5117 Evaluate side-chains 43 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.161285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.109138 restraints weight = 4284.027| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.07 r_work: 0.3695 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4054 Z= 0.125 Angle : 0.557 4.602 5494 Z= 0.292 Chirality : 0.051 0.163 670 Planarity : 0.002 0.011 676 Dihedral : 13.400 75.624 588 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.63 % Allowed : 21.05 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.21 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE D 94 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4054) covalent geometry : angle 0.55738 ( 5494) hydrogen bonds : bond 0.01528 ( 33) hydrogen bonds : angle 5.39405 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.153 Fit side-chains REVERT: A 83 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7595 (mp0) REVERT: A 97 LYS cc_start: 0.7678 (mttm) cc_final: 0.7463 (mttp) REVERT: B 96 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7195 (mtpp) REVERT: C 83 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7662 (mp0) REVERT: D 83 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7885 (mp0) REVERT: F 61 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7669 (tm-30) REVERT: F 83 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: H 61 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7864 (tt0) REVERT: I 61 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7822 (tt0) REVERT: J 61 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7643 (tm-30) outliers start: 10 outliers final: 0 residues processed: 38 average time/residue: 0.8072 time to fit residues: 31.5571 Evaluate side-chains 30 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain F residue 83 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 0.0980 chunk 13 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.156104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.101733 restraints weight = 4187.533| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 3.08 r_work: 0.3600 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4054 Z= 0.150 Angle : 0.571 4.643 5494 Z= 0.297 Chirality : 0.051 0.155 670 Planarity : 0.002 0.012 676 Dihedral : 12.521 72.850 588 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.47 % Allowed : 18.16 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.20 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4054) covalent geometry : angle 0.57136 ( 5494) hydrogen bonds : bond 0.00971 ( 33) hydrogen bonds : angle 5.34192 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.165 Fit side-chains REVERT: A 83 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7733 (mp0) REVERT: C 99 GLN cc_start: 0.6181 (mt0) cc_final: 0.5645 (tm-30) REVERT: D 83 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7971 (mp0) REVERT: E 99 GLN cc_start: 0.6137 (mt0) cc_final: 0.5785 (tm-30) REVERT: G 83 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8113 (mp0) REVERT: G 99 GLN cc_start: 0.6209 (OUTLIER) cc_final: 0.5780 (tm-30) REVERT: H 61 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7893 (tt0) REVERT: J 61 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7408 (tm-30) REVERT: J 99 GLN cc_start: 0.5861 (tm-30) cc_final: 0.5492 (tm-30) outliers start: 17 outliers final: 4 residues processed: 44 average time/residue: 0.9412 time to fit residues: 42.3301 Evaluate side-chains 34 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN C 79 GLN D 79 GLN E 79 GLN I 99 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.154491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.099672 restraints weight = 4165.529| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 3.06 r_work: 0.3557 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4054 Z= 0.193 Angle : 0.587 4.473 5494 Z= 0.306 Chirality : 0.052 0.158 670 Planarity : 0.002 0.014 676 Dihedral : 13.170 77.713 588 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.74 % Allowed : 17.37 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.38 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 4054) covalent geometry : angle 0.58717 ( 5494) hydrogen bonds : bond 0.01008 ( 33) hydrogen bonds : angle 5.67750 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.174 Fit side-chains REVERT: A 83 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7920 (mp0) REVERT: C 98 ASP cc_start: 0.7747 (m-30) cc_final: 0.7494 (m-30) REVERT: C 99 GLN cc_start: 0.6546 (mt0) cc_final: 0.6188 (tm-30) REVERT: D 61 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7541 (tt0) REVERT: D 83 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8062 (mp0) REVERT: E 83 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8117 (mt-10) REVERT: E 99 GLN cc_start: 0.6493 (mt0) cc_final: 0.6146 (tm-30) REVERT: F 83 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: F 97 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8204 (mmtp) REVERT: G 83 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: G 99 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.6114 (tm-30) REVERT: H 61 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7867 (tt0) REVERT: J 61 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7601 (tm-30) REVERT: J 83 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8174 (mp0) REVERT: J 99 GLN cc_start: 0.6271 (tm-30) cc_final: 0.5899 (tm-30) outliers start: 18 outliers final: 7 residues processed: 52 average time/residue: 0.8363 time to fit residues: 44.5663 Evaluate side-chains 46 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 36 optimal weight: 0.0010 chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN F 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.156529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.101742 restraints weight = 4321.614| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.96 r_work: 0.3653 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.044 4054 Z= 0.356 Angle : 0.745 5.381 5494 Z= 0.388 Chirality : 0.056 0.172 670 Planarity : 0.003 0.008 676 Dihedral : 15.042 86.675 588 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 5.00 % Allowed : 17.89 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.69 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE C 94 HIS 0.005 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00791 ( 4054) covalent geometry : angle 0.74457 ( 5494) hydrogen bonds : bond 0.01012 ( 33) hydrogen bonds : angle 5.83947 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.159 Fit side-chains REVERT: A 83 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7985 (mp0) REVERT: A 98 ASP cc_start: 0.7782 (m-30) cc_final: 0.7457 (m-30) REVERT: C 83 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8259 (mm-30) REVERT: C 98 ASP cc_start: 0.7985 (m-30) cc_final: 0.7649 (m-30) REVERT: C 99 GLN cc_start: 0.6738 (mt0) cc_final: 0.6360 (tm-30) REVERT: D 50 HIS cc_start: 0.6021 (t-90) cc_final: 0.5643 (m90) REVERT: D 61 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7514 (tt0) REVERT: D 83 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8073 (mp0) REVERT: E 83 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8101 (mt-10) REVERT: E 99 GLN cc_start: 0.6816 (mt0) cc_final: 0.6380 (tm-30) REVERT: F 83 GLU cc_start: 0.8317 (mp0) cc_final: 0.7768 (mp0) REVERT: F 97 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8314 (mmtp) REVERT: G 83 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: G 99 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.6275 (tm-30) REVERT: I 58 LYS cc_start: 0.7836 (mmtp) cc_final: 0.7142 (mmtp) REVERT: I 97 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8624 (mttp) REVERT: I 99 GLN cc_start: 0.5955 (tm-30) cc_final: 0.5317 (mp10) REVERT: J 61 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7435 (tm-30) REVERT: J 99 GLN cc_start: 0.6362 (tm-30) cc_final: 0.6020 (tm-30) outliers start: 19 outliers final: 9 residues processed: 56 average time/residue: 0.7385 time to fit residues: 42.4939 Evaluate side-chains 56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 97 LYS Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN D 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.160798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.106613 restraints weight = 4191.242| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.99 r_work: 0.3731 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.7455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4054 Z= 0.167 Angle : 0.573 4.566 5494 Z= 0.294 Chirality : 0.052 0.155 670 Planarity : 0.002 0.007 676 Dihedral : 13.964 83.017 588 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 5.00 % Allowed : 18.68 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.60 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE G 94 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 4054) covalent geometry : angle 0.57263 ( 5494) hydrogen bonds : bond 0.00765 ( 33) hydrogen bonds : angle 5.27858 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 41 time to evaluate : 0.108 Fit side-chains REVERT: A 83 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7810 (mp0) REVERT: A 98 ASP cc_start: 0.7600 (m-30) cc_final: 0.7223 (m-30) REVERT: C 83 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8127 (mm-30) REVERT: C 98 ASP cc_start: 0.7753 (m-30) cc_final: 0.7545 (m-30) REVERT: C 99 GLN cc_start: 0.6752 (mt0) cc_final: 0.6378 (tm-30) REVERT: D 61 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7445 (tt0) REVERT: D 83 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7909 (mp0) REVERT: E 83 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7889 (mp0) REVERT: E 98 ASP cc_start: 0.7433 (m-30) cc_final: 0.7037 (p0) REVERT: E 99 GLN cc_start: 0.6690 (mt0) cc_final: 0.6047 (tm-30) REVERT: F 50 HIS cc_start: 0.6085 (OUTLIER) cc_final: 0.5288 (m90) REVERT: F 83 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: F 99 GLN cc_start: 0.6006 (tm-30) cc_final: 0.5397 (mp10) REVERT: G 83 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: G 99 GLN cc_start: 0.6908 (tt0) cc_final: 0.6571 (tm-30) REVERT: H 99 GLN cc_start: 0.5967 (tm-30) cc_final: 0.5612 (tp40) REVERT: I 58 LYS cc_start: 0.7877 (mmtp) cc_final: 0.7102 (mmtt) REVERT: I 99 GLN cc_start: 0.6032 (tm-30) cc_final: 0.5360 (mp10) REVERT: J 61 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7485 (tm-30) REVERT: J 99 GLN cc_start: 0.6373 (tm-30) cc_final: 0.6031 (tm-30) outliers start: 19 outliers final: 11 residues processed: 54 average time/residue: 0.7298 time to fit residues: 40.5344 Evaluate side-chains 54 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 0.0020 chunk 30 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN D 79 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.163647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.109770 restraints weight = 4114.024| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.98 r_work: 0.3783 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4054 Z= 0.121 Angle : 0.516 4.213 5494 Z= 0.265 Chirality : 0.051 0.149 670 Planarity : 0.001 0.007 676 Dihedral : 13.077 80.194 588 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.16 % Allowed : 21.05 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.39 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 94 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4054) covalent geometry : angle 0.51550 ( 5494) hydrogen bonds : bond 0.00686 ( 33) hydrogen bonds : angle 4.87565 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.147 Fit side-chains REVERT: A 83 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7815 (mp0) REVERT: A 98 ASP cc_start: 0.7473 (m-30) cc_final: 0.7144 (m-30) REVERT: C 98 ASP cc_start: 0.7529 (m-30) cc_final: 0.7011 (p0) REVERT: C 99 GLN cc_start: 0.6695 (mt0) cc_final: 0.6010 (tm-30) REVERT: D 83 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7942 (mp0) REVERT: E 83 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7869 (mp0) REVERT: E 98 ASP cc_start: 0.7400 (m-30) cc_final: 0.7127 (p0) REVERT: E 99 GLN cc_start: 0.6717 (mt0) cc_final: 0.6067 (tm-30) REVERT: F 61 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7462 (tt0) REVERT: F 83 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: G 83 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: G 99 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: H 99 GLN cc_start: 0.5911 (tm-30) cc_final: 0.5536 (tp40) REVERT: I 58 LYS cc_start: 0.7875 (mmtp) cc_final: 0.7169 (tptp) REVERT: I 97 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8673 (mttp) REVERT: I 99 GLN cc_start: 0.6021 (tm-30) cc_final: 0.5344 (mp10) REVERT: J 61 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7546 (tm-30) REVERT: J 99 GLN cc_start: 0.6356 (tm-30) cc_final: 0.5989 (tm-30) outliers start: 12 outliers final: 5 residues processed: 51 average time/residue: 0.7826 time to fit residues: 40.9644 Evaluate side-chains 54 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain J residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.0070 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN D 79 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.164666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.110696 restraints weight = 4190.455| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.96 r_work: 0.3685 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.7621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4054 Z= 0.116 Angle : 0.514 5.876 5494 Z= 0.264 Chirality : 0.051 0.147 670 Planarity : 0.001 0.007 676 Dihedral : 12.386 78.054 588 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.63 % Allowed : 21.84 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.23 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE C 94 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4054) covalent geometry : angle 0.51403 ( 5494) hydrogen bonds : bond 0.00655 ( 33) hydrogen bonds : angle 4.69475 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.149 Fit side-chains REVERT: A 83 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7817 (mp0) REVERT: A 98 ASP cc_start: 0.7593 (m-30) cc_final: 0.7118 (m-30) REVERT: A 99 GLN cc_start: 0.6571 (mt0) cc_final: 0.5888 (tm-30) REVERT: C 98 ASP cc_start: 0.7514 (m-30) cc_final: 0.7069 (p0) REVERT: C 99 GLN cc_start: 0.6723 (mt0) cc_final: 0.6067 (tm-30) REVERT: D 83 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7900 (mp0) REVERT: E 83 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7890 (mp0) REVERT: E 99 GLN cc_start: 0.6726 (mt0) cc_final: 0.6137 (tm-30) REVERT: F 61 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7549 (tm-30) REVERT: F 83 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: F 99 GLN cc_start: 0.5987 (tm-30) cc_final: 0.5419 (mp10) REVERT: G 83 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: G 99 GLN cc_start: 0.7069 (tt0) cc_final: 0.6845 (tm-30) REVERT: H 99 GLN cc_start: 0.5984 (tm-30) cc_final: 0.5570 (tp40) REVERT: I 58 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7297 (tptp) REVERT: I 97 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8663 (mttp) REVERT: I 99 GLN cc_start: 0.6096 (tm-30) cc_final: 0.5390 (mp10) REVERT: J 61 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7604 (tm-30) REVERT: J 99 GLN cc_start: 0.6348 (tm-30) cc_final: 0.6031 (tm-30) outliers start: 10 outliers final: 4 residues processed: 54 average time/residue: 0.7924 time to fit residues: 43.8269 Evaluate side-chains 54 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain J residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.0570 chunk 35 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN D 79 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.160931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.105874 restraints weight = 4151.162| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.98 r_work: 0.3731 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.7719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4054 Z= 0.196 Angle : 0.593 5.033 5494 Z= 0.307 Chirality : 0.052 0.155 670 Planarity : 0.002 0.007 676 Dihedral : 12.846 80.216 588 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 2.63 % Allowed : 21.84 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.29 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE C 94 HIS 0.001 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 4054) covalent geometry : angle 0.59252 ( 5494) hydrogen bonds : bond 0.00790 ( 33) hydrogen bonds : angle 5.10971 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.148 Fit side-chains REVERT: A 83 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7917 (mp0) REVERT: A 99 GLN cc_start: 0.6479 (mt0) cc_final: 0.6068 (tm-30) REVERT: C 99 GLN cc_start: 0.6795 (mt0) cc_final: 0.6440 (tm-30) REVERT: D 61 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7432 (tt0) REVERT: D 83 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8036 (mp0) REVERT: E 83 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8060 (mt-10) REVERT: F 83 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: G 83 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: G 99 GLN cc_start: 0.7100 (tt0) cc_final: 0.6898 (tm-30) REVERT: H 99 GLN cc_start: 0.6112 (tm-30) cc_final: 0.5896 (tm-30) REVERT: I 58 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7231 (mmtt) REVERT: I 97 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8634 (mttp) REVERT: I 99 GLN cc_start: 0.6123 (tm-30) cc_final: 0.5405 (mp10) REVERT: J 61 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7506 (tm-30) REVERT: J 99 GLN cc_start: 0.6431 (tm-30) cc_final: 0.6066 (tm-30) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.8309 time to fit residues: 44.3187 Evaluate side-chains 54 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 97 LYS Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 5 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** H 62 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 = 0.4551 r_free = 0.4551 target = 0.160949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.105701 restraints weight = 4226.749| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.99 r_work: 0.3722 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.7819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4054 Z= 0.199 Angle : 0.620 6.043 5494 Z= 0.320 Chirality : 0.052 0.156 670 Planarity : 0.002 0.007 676 Dihedral : 13.016 80.213 588 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.16 % Allowed : 22.11 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.37 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 94 HIS 0.001 0.000 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 4054) covalent geometry : angle 0.62029 ( 5494) hydrogen bonds : bond 0.00752 ( 33) hydrogen bonds : angle 5.14764 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.01 seconds wall clock time: 28 minutes 6.45 seconds (1686.45 seconds total)