Starting phenix.real_space_refine on Wed Mar 5 22:52:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7b_38097/03_2025/8x7b_38097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7b_38097/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x7b_38097/03_2025/8x7b_38097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7b_38097/03_2025/8x7b_38097.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7b_38097/03_2025/8x7b_38097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7b_38097/03_2025/8x7b_38097.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.89, per 1000 atoms: 0.72 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: 0.96 Conformation dependent library (CDL) restraints added in 471.5 milliseconds 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: 0.52 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: 0.86 Time building geometry restraints manager: 1.14 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: 0.03 Found NCS groups: 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 'A' selection = chain 'I' } 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.750 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- 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= 1.032 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 : 30.43 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 (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: -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 HIS 0.003 0.001 HIS D 50 PHE 0.016 0.008 PHE B 94 *********************** 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 : 0.392 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: 1.2298 time to fit residues: 123.0407 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 : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- 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 = 0.4553 r_free = 0.4553 target = 0.160707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.108662 restraints weight = 4346.911| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.23 r_work: 0.3660 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4392 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= 0.278 Angle : 0.684 5.881 5494 Z= 0.355 Chirality : 0.053 0.166 670 Planarity : 0.003 0.012 676 Dihedral : 14.280 66.771 588 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.16 % Allowed : 18.68 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.44 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 50 PHE 0.007 0.002 PHE F 94 *********************** 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 61 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.436 Fit side-chains REVERT: A 61 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7401 (tt0) REVERT: A 83 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7675 (mp0) REVERT: B 72 THR cc_start: 0.9299 (m) cc_final: 0.9080 (m) REVERT: B 83 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7968 (mp0) REVERT: C 61 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7453 (tt0) REVERT: C 83 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7801 (mp0) REVERT: D 83 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8014 (mp0) REVERT: E 61 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7452 (tm-30) REVERT: E 83 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8006 (mm-30) REVERT: F 61 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7830 (tm-30) REVERT: F 97 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7779 (mttt) REVERT: G 61 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7509 (tm-30) REVERT: G 83 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7803 (mp0) REVERT: H 61 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8061 (tt0) REVERT: I 61 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7923 (tt0) REVERT: J 61 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7808 (tt0) REVERT: J 83 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: J 99 GLN cc_start: 0.5944 (tp40) cc_final: 0.5709 (tm-30) outliers start: 12 outliers final: 6 residues processed: 57 average time/residue: 1.7065 time to fit residues: 99.7882 Evaluate side-chains 46 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 I residue 49 VAL 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 6 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.1980 chunk 39 optimal weight: 0.0070 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.0060 overall best weight: 0.8418 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.159064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.106540 restraints weight = 4263.800| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.06 r_work: 0.3635 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4054 Z= 0.206 Angle : 0.582 4.741 5494 Z= 0.303 Chirality : 0.051 0.160 670 Planarity : 0.002 0.012 676 Dihedral : 13.606 73.830 588 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.63 % Allowed : 21.32 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.29 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 50 PHE 0.006 0.001 PHE D 94 *********************** 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 39 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.427 Fit side-chains REVERT: A 83 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7724 (mp0) REVERT: B 96 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7405 (mtpm) REVERT: C 83 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7773 (mp0) REVERT: D 83 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7978 (mp0) REVERT: F 61 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7766 (tm-30) REVERT: H 61 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7952 (tt0) REVERT: I 61 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7921 (tt0) REVERT: J 61 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7727 (tm-30) REVERT: J 99 GLN cc_start: 0.6240 (tp40) cc_final: 0.5777 (tm-30) outliers start: 10 outliers final: 3 residues processed: 35 average time/residue: 1.6420 time to fit residues: 59.2272 Evaluate side-chains 28 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 24 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 99 GLN Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 16 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.155886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.102340 restraints weight = 4183.263| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.05 r_work: 0.3602 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.6123 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= 0.228 Angle : 0.565 4.551 5494 Z= 0.294 Chirality : 0.050 0.153 670 Planarity : 0.002 0.012 676 Dihedral : 12.734 74.298 588 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.32 % Allowed : 15.53 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.24 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.006 0.001 PHE C 94 *********************** 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 58 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 34 time to evaluate : 0.463 Fit side-chains REVERT: A 83 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7736 (mp0) REVERT: C 99 GLN cc_start: 0.6077 (mt0) cc_final: 0.5654 (tm-30) REVERT: D 83 GLU cc_start: 0.8433 (mt-10) cc_final: 0.7961 (mp0) REVERT: E 99 GLN cc_start: 0.6102 (mt0) cc_final: 0.5706 (tm-30) REVERT: G 83 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: G 99 GLN cc_start: 0.6218 (OUTLIER) cc_final: 0.5844 (tm-30) REVERT: H 61 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7851 (tt0) REVERT: J 61 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7455 (tm-30) REVERT: J 83 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: J 99 GLN cc_start: 0.6355 (tp40) cc_final: 0.5977 (tm-30) outliers start: 24 outliers final: 6 residues processed: 50 average time/residue: 1.7652 time to fit residues: 90.5451 Evaluate side-chains 36 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 6 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 1 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 F 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.154506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.099374 restraints weight = 4317.840| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.10 r_work: 0.3570 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4054 Z= 0.275 Angle : 0.576 4.469 5494 Z= 0.300 Chirality : 0.052 0.156 670 Planarity : 0.002 0.012 676 Dihedral : 13.126 77.009 588 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.74 % Allowed : 17.11 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.37 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.005 0.001 PHE C 94 *********************** 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 61 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.389 Fit side-chains REVERT: A 83 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7777 (mp0) REVERT: B 83 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7949 (mp0) REVERT: C 98 ASP cc_start: 0.7682 (m-30) cc_final: 0.7439 (m-30) REVERT: C 99 GLN cc_start: 0.6268 (mt0) cc_final: 0.5921 (tm-30) REVERT: D 61 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7464 (tt0) REVERT: D 83 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7987 (mp0) REVERT: E 99 GLN cc_start: 0.6390 (mt0) cc_final: 0.6018 (tm-30) REVERT: F 83 GLU cc_start: 0.8385 (mp0) cc_final: 0.7869 (mp0) REVERT: G 83 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: G 99 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.6105 (tm-30) REVERT: H 61 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7793 (tt0) REVERT: I 83 GLU cc_start: 0.7812 (mp0) cc_final: 0.7379 (mp0) REVERT: J 61 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7519 (tm-30) REVERT: J 98 ASP cc_start: 0.7603 (m-30) cc_final: 0.7330 (m-30) REVERT: J 99 GLN cc_start: 0.6435 (tp40) cc_final: 0.6115 (tm-30) outliers start: 18 outliers final: 6 residues processed: 54 average time/residue: 1.5149 time to fit residues: 84.1644 Evaluate side-chains 44 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL 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 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 44 optimal weight: 0.0470 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 I 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.162589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.108836 restraints weight = 4078.197| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.96 r_work: 0.3650 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.7010 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= 0.225 Angle : 0.534 4.311 5494 Z= 0.277 Chirality : 0.051 0.151 670 Planarity : 0.002 0.015 676 Dihedral : 12.701 76.998 588 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.47 % Allowed : 17.63 % 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 (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: -3.31 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 50 PHE 0.004 0.001 PHE C 94 *********************** 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 55 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.388 Fit side-chains REVERT: A 83 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7877 (mp0) REVERT: A 97 LYS cc_start: 0.8555 (mttm) cc_final: 0.8326 (mtpm) REVERT: C 83 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7734 (mp0) REVERT: C 98 ASP cc_start: 0.7701 (m-30) cc_final: 0.7456 (m-30) REVERT: C 99 GLN cc_start: 0.6446 (mt0) cc_final: 0.6095 (tm-30) REVERT: D 61 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7432 (tt0) REVERT: D 83 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7908 (mp0) REVERT: E 83 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7927 (mp0) REVERT: E 99 GLN cc_start: 0.6537 (mt0) cc_final: 0.6247 (tm-30) REVERT: F 83 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: G 83 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: G 99 GLN cc_start: 0.6594 (OUTLIER) cc_final: 0.6199 (tm-30) REVERT: H 61 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7854 (tt0) REVERT: I 83 GLU cc_start: 0.7827 (mp0) cc_final: 0.7328 (mp0) REVERT: I 99 GLN cc_start: 0.6287 (tm-30) cc_final: 0.5670 (mp10) REVERT: J 61 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7585 (tm-30) REVERT: J 98 ASP cc_start: 0.7654 (m-30) cc_final: 0.7382 (m-30) REVERT: J 99 GLN cc_start: 0.6468 (tp40) cc_final: 0.6197 (tm-30) outliers start: 17 outliers final: 9 residues processed: 47 average time/residue: 1.6178 time to fit residues: 78.1741 Evaluate side-chains 50 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 83 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 F 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.159145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.105058 restraints weight = 4198.238| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.95 r_work: 0.3703 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.7289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4054 Z= 0.367 Angle : 0.614 4.770 5494 Z= 0.319 Chirality : 0.053 0.164 670 Planarity : 0.002 0.017 676 Dihedral : 13.598 81.753 588 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 5.26 % Allowed : 16.84 % 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 (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: -3.51 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 50 PHE 0.005 0.001 PHE C 94 *********************** 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 63 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 43 time to evaluate : 0.458 Fit side-chains REVERT: A 83 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8016 (mp0) REVERT: A 98 ASP cc_start: 0.7832 (m-30) cc_final: 0.7521 (m-30) REVERT: B 83 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8216 (mt-10) REVERT: C 83 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8197 (mm-30) REVERT: C 98 ASP cc_start: 0.7827 (m-30) cc_final: 0.7297 (m-30) REVERT: C 99 GLN cc_start: 0.6615 (mt0) cc_final: 0.6000 (tm-30) REVERT: D 61 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7444 (tt0) REVERT: D 83 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8033 (mp0) REVERT: D 97 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8290 (mttm) REVERT: E 83 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8080 (mt-10) REVERT: E 99 GLN cc_start: 0.6646 (mt0) cc_final: 0.6295 (tm-30) REVERT: F 83 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: G 83 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: G 98 ASP cc_start: 0.7505 (m-30) cc_final: 0.7040 (p0) REVERT: G 99 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.5985 (tm-30) REVERT: I 58 LYS cc_start: 0.7873 (mmtp) cc_final: 0.7099 (mmtt) REVERT: J 61 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7493 (tm-30) REVERT: J 98 ASP cc_start: 0.7688 (m-30) cc_final: 0.7460 (m-30) REVERT: J 99 GLN cc_start: 0.6486 (tp40) cc_final: 0.6192 (tm-30) outliers start: 20 outliers final: 10 residues processed: 55 average time/residue: 1.4644 time to fit residues: 82.9339 Evaluate side-chains 55 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 83 GLU 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 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 12 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 I 99 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.162027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.108214 restraints weight = 4077.212| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.95 r_work: 0.3759 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.7397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4054 Z= 0.239 Angle : 0.545 4.797 5494 Z= 0.281 Chirality : 0.051 0.153 670 Planarity : 0.002 0.017 676 Dihedral : 13.037 80.059 588 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.95 % Allowed : 18.42 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.39 (0.31), 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 HIS 0.001 0.000 HIS J 50 PHE 0.004 0.001 PHE C 94 *********************** 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 58 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.392 Fit side-chains REVERT: A 83 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7841 (mp0) REVERT: A 98 ASP cc_start: 0.7750 (m-30) cc_final: 0.7384 (m-30) REVERT: A 99 GLN cc_start: 0.6641 (mt0) cc_final: 0.6148 (tm-30) REVERT: C 98 ASP cc_start: 0.7794 (m-30) cc_final: 0.7320 (m-30) REVERT: C 99 GLN cc_start: 0.6591 (mt0) cc_final: 0.6066 (tm-30) REVERT: D 83 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7906 (mp0) REVERT: D 97 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8344 (mttm) REVERT: E 83 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7888 (mp0) REVERT: E 99 GLN cc_start: 0.6675 (mt0) cc_final: 0.6331 (tm-30) REVERT: F 83 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: F 99 GLN cc_start: 0.5962 (tm-30) cc_final: 0.5437 (mp10) REVERT: G 83 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: G 98 ASP cc_start: 0.7480 (m-30) cc_final: 0.7098 (p0) REVERT: G 99 GLN cc_start: 0.6672 (OUTLIER) cc_final: 0.6115 (tm-30) REVERT: H 99 GLN cc_start: 0.5857 (tm-30) cc_final: 0.5461 (tp40) REVERT: I 58 LYS cc_start: 0.7890 (mmtp) cc_final: 0.7202 (tptp) REVERT: J 61 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7577 (tm-30) outliers start: 15 outliers final: 9 residues processed: 49 average time/residue: 1.3870 time to fit residues: 70.1043 Evaluate side-chains 55 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 48 VAL 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 52 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4499 r_free = 0.4499 target = 0.157194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101943 restraints weight = 4224.138| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 2.98 r_work: 0.3660 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.7606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 4054 Z= 0.464 Angle : 0.689 5.537 5494 Z= 0.357 Chirality : 0.055 0.164 670 Planarity : 0.002 0.008 676 Dihedral : 14.339 85.446 588 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % 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 (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: -3.55 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 50 PHE 0.007 0.001 PHE C 94 *********************** 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 67 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.432 Fit side-chains REVERT: A 83 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8038 (mp0) REVERT: A 98 ASP cc_start: 0.7768 (m-30) cc_final: 0.7329 (m-30) REVERT: A 99 GLN cc_start: 0.6622 (mt0) cc_final: 0.6123 (tm-30) REVERT: B 83 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8184 (mt-10) REVERT: C 83 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8224 (mm-30) REVERT: C 98 ASP cc_start: 0.7970 (m-30) cc_final: 0.7687 (m-30) REVERT: C 99 GLN cc_start: 0.6645 (mt0) cc_final: 0.6343 (tm-30) REVERT: D 61 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7484 (tt0) REVERT: D 83 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8070 (mp0) REVERT: E 83 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8071 (mt-10) REVERT: E 99 GLN cc_start: 0.6806 (mt0) cc_final: 0.6388 (tm-30) REVERT: F 83 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: G 58 LYS cc_start: 0.7682 (mmtp) cc_final: 0.7098 (mmtp) REVERT: G 83 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: G 99 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.6410 (tm-30) REVERT: I 58 LYS cc_start: 0.7865 (mmtp) cc_final: 0.7154 (mmtt) REVERT: I 99 GLN cc_start: 0.5932 (tm-30) cc_final: 0.5259 (mp10) REVERT: J 61 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7468 (tt0) outliers start: 17 outliers final: 11 residues processed: 60 average time/residue: 1.4418 time to fit residues: 89.1645 Evaluate side-chains 62 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 48 VAL 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 52 VAL 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 19 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.4576 r_free = 0.4576 target = 0.163583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.110242 restraints weight = 4085.767| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.93 r_work: 0.3784 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.7752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4054 Z= 0.191 Angle : 0.552 6.180 5494 Z= 0.283 Chirality : 0.051 0.147 670 Planarity : 0.001 0.007 676 Dihedral : 13.096 80.706 588 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % 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 (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: -3.33 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 PHE 0.003 0.001 PHE J 94 ********************** 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 55 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.426 Fit side-chains REVERT: A 83 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7605 (mp0) REVERT: A 98 ASP cc_start: 0.7596 (m-30) cc_final: 0.7164 (m-30) REVERT: A 99 GLN cc_start: 0.6691 (mt0) cc_final: 0.5935 (tm-30) REVERT: C 98 ASP cc_start: 0.7651 (m-30) cc_final: 0.6779 (p0) REVERT: C 99 GLN cc_start: 0.6612 (mt0) cc_final: 0.5937 (tm-30) REVERT: D 61 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7396 (tt0) REVERT: D 83 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7825 (mp0) REVERT: E 83 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7824 (mp0) REVERT: E 98 ASP cc_start: 0.7383 (m-30) cc_final: 0.7037 (p0) REVERT: E 99 GLN cc_start: 0.6797 (mt0) cc_final: 0.6134 (tm-30) REVERT: F 61 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7504 (tt0) REVERT: F 83 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: F 99 GLN cc_start: 0.6069 (tm-30) cc_final: 0.5467 (mp10) REVERT: G 83 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7958 (mp0) REVERT: H 99 GLN cc_start: 0.5854 (tm-30) cc_final: 0.5550 (tp40) REVERT: I 58 LYS cc_start: 0.8025 (mmtp) cc_final: 0.7323 (tptp) REVERT: I 99 GLN cc_start: 0.5925 (tm-30) cc_final: 0.5289 (mp10) REVERT: J 61 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7587 (tm-30) outliers start: 10 outliers final: 5 residues processed: 50 average time/residue: 1.5495 time to fit residues: 79.7700 Evaluate side-chains 51 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL 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 41 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4571 r_free = 0.4571 target = 0.162969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.108291 restraints weight = 4074.819| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.97 r_work: 0.3762 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.7809 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= 0.233 Angle : 0.577 6.463 5494 Z= 0.297 Chirality : 0.051 0.150 670 Planarity : 0.001 0.013 676 Dihedral : 12.893 80.955 588 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.42 % Allowed : 20.53 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % 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: -3.26 (0.32), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 50 PHE 0.005 0.001 PHE C 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2994.84 seconds wall clock time: 52 minutes 3.15 seconds (3123.15 seconds total)