Starting phenix.real_space_refine on Fri Dec 27 09:44:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7b_38097/12_2024/8x7b_38097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7b_38097/12_2024/8x7b_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_38097/12_2024/8x7b_38097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7b_38097/12_2024/8x7b_38097.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7b_38097/12_2024/8x7b_38097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7b_38097/12_2024/8x7b_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-5532/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: 0.99 Conformation dependent library (CDL) restraints added in 494.3 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: 0.57 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: 0.94 Time building geometry restraints manager: 1.15 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 45 through 99) selection = chain 'B' selection = (chain 'C' and resid 45 through 99) selection = chain 'D' selection = (chain 'E' and resid 45 through 99) selection = (chain 'F' and resid 45 through 99) selection = chain 'G' selection = chain 'H' selection = (chain 'I' and resid 45 through 99) selection = (chain 'J' and resid 45 through 99) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.690 Find NCS groups from input model: 0.190 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:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 27.340 ------------------------------------------------------------------------------- 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 : 0.417 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: 1.2315 time to fit residues: 123.2556 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 : 0.389 ------------------------------------------------------------------------------- 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: 5.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5182 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 : 0.418 Fit side-chains REVERT: A 61 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6367 (tt0) REVERT: A 83 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6638 (mp0) REVERT: B 72 THR cc_start: 0.8617 (m) cc_final: 0.8399 (m) REVERT: B 83 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7454 (mp0) REVERT: C 61 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6261 (tt0) REVERT: C 83 GLU cc_start: 0.7459 (mm-30) cc_final: 0.6783 (mp0) REVERT: D 83 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7301 (mp0) REVERT: E 61 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6209 (tm-30) REVERT: E 83 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6854 (mm-30) REVERT: F 61 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6565 (tm-30) REVERT: F 83 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: G 61 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6286 (tm-30) REVERT: G 83 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6859 (mp0) REVERT: H 61 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6918 (tt0) REVERT: I 61 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6804 (tt0) REVERT: I 83 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7075 (mp0) REVERT: J 61 GLU cc_start: 0.7477 (mt-10) cc_final: 0.6622 (tt0) REVERT: J 83 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6688 (mp0) outliers start: 12 outliers final: 6 residues processed: 57 average time/residue: 1.6750 time to fit residues: 97.9996 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 : 0.419 ------------------------------------------------------------------------------- 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 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 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 25 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4054 Z= 0.425 Angle : 0.719 5.061 5494 Z= 0.379 Chirality : 0.054 0.174 670 Planarity : 0.003 0.012 676 Dihedral : 15.070 81.078 588 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 6.05 % Allowed : 18.16 % 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 (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: -3.63 (0.29), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.22), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.008 0.002 PHE C 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 65 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 0.375 Fit side-chains REVERT: A 83 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6809 (mp0) REVERT: B 96 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6942 (mtpm) REVERT: C 61 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6056 (tt0) REVERT: D 61 GLU cc_start: 0.7778 (mt-10) cc_final: 0.6878 (tt0) REVERT: D 83 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7312 (mp0) REVERT: G 83 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: J 61 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6350 (tm-30) REVERT: J 83 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7470 (mp0) outliers start: 23 outliers final: 9 residues processed: 55 average time/residue: 1.4466 time to fit residues: 81.9748 Evaluate side-chains 43 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 52 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN E 79 GLN H 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5287 moved from start: 0.6573 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= 0.198 Angle : 0.558 4.457 5494 Z= 0.288 Chirality : 0.051 0.152 670 Planarity : 0.002 0.011 676 Dihedral : 13.540 77.788 588 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.53 % Allowed : 18.68 % 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 (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: -3.40 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 50 PHE 0.005 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: 21 poor density : 37 time to evaluate : 0.418 Fit side-chains REVERT: A 83 GLU cc_start: 0.7425 (mt-10) cc_final: 0.6770 (mp0) REVERT: B 79 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: D 61 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7084 (tt0) REVERT: D 83 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7304 (mp0) REVERT: D 97 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7490 (mttm) REVERT: H 61 GLU cc_start: 0.7587 (mt-10) cc_final: 0.6843 (tt0) REVERT: J 61 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6413 (tm-30) outliers start: 21 outliers final: 4 residues processed: 52 average time/residue: 1.5743 time to fit residues: 84.1571 Evaluate side-chains 36 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain D residue 50 HIS Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 0.3980 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN F 79 GLN H 79 GLN I 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5275 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4054 Z= 0.171 Angle : 0.532 4.386 5494 Z= 0.275 Chirality : 0.051 0.148 670 Planarity : 0.002 0.013 676 Dihedral : 12.844 75.899 588 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.42 % Allowed : 20.26 % 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: -3.20 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.004 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 44 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.412 Fit side-chains REVERT: A 83 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6696 (mp0) REVERT: B 79 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8008 (mt0) REVERT: D 83 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7259 (mp0) REVERT: G 83 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7067 (mp0) REVERT: H 61 GLU cc_start: 0.7621 (mt-10) cc_final: 0.6865 (tt0) REVERT: I 83 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7515 (mt-10) REVERT: I 99 GLN cc_start: 0.5378 (tm-30) cc_final: 0.5087 (mp10) REVERT: J 61 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6422 (tm-30) outliers start: 13 outliers final: 4 residues processed: 41 average time/residue: 1.8435 time to fit residues: 77.5817 Evaluate side-chains 35 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain H residue 79 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 0.0970 chunk 40 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 4054 Z= 0.389 Angle : 0.663 4.815 5494 Z= 0.344 Chirality : 0.053 0.162 670 Planarity : 0.002 0.010 676 Dihedral : 13.922 81.682 588 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.00 % Allowed : 17.63 % 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: -3.51 (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 0.000 HIS B 50 PHE 0.006 0.001 PHE A 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 62 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.410 Fit side-chains REVERT: A 83 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7083 (mp0) REVERT: B 79 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: B 97 LYS cc_start: 0.7587 (mttm) cc_final: 0.7369 (mtmm) REVERT: D 61 GLU cc_start: 0.7780 (mt-10) cc_final: 0.6896 (tt0) REVERT: D 83 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7392 (mp0) REVERT: E 83 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7034 (mt-10) REVERT: F 83 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7365 (mp0) REVERT: G 83 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: J 61 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6341 (tt0) REVERT: J 83 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7292 (mp0) outliers start: 19 outliers final: 11 residues processed: 56 average time/residue: 1.4892 time to fit residues: 85.8392 Evaluate side-chains 53 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 GLN 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 G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL 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 Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.0040 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN F 99 GLN H 79 GLN I 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5309 moved from start: 0.7429 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= 0.268 Angle : 0.603 4.931 5494 Z= 0.311 Chirality : 0.052 0.156 670 Planarity : 0.002 0.017 676 Dihedral : 13.463 80.771 588 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.42 % Allowed : 20.26 % 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: -3.46 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 50 PHE 0.006 0.001 PHE A 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 56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.385 Fit side-chains REVERT: A 83 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6962 (mp0) REVERT: B 79 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7964 (mt0) REVERT: B 97 LYS cc_start: 0.7751 (mttm) cc_final: 0.7512 (mttp) REVERT: C 98 ASP cc_start: 0.6201 (m-30) cc_final: 0.5882 (p0) REVERT: D 61 GLU cc_start: 0.7789 (mt-10) cc_final: 0.6880 (tt0) REVERT: D 83 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7296 (mp0) REVERT: E 83 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6767 (mp0) REVERT: F 83 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: G 83 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7050 (mp0) REVERT: H 99 GLN cc_start: 0.5116 (tm-30) cc_final: 0.4728 (tp40) REVERT: I 58 LYS cc_start: 0.7147 (mmtp) cc_final: 0.6465 (tptp) REVERT: I 99 GLN cc_start: 0.5583 (tm-30) cc_final: 0.5146 (mp10) REVERT: J 61 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6418 (tm-30) REVERT: J 83 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7303 (mp0) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 1.5294 time to fit residues: 78.6945 Evaluate side-chains 52 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN 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 83 GLU Chi-restraints excluded: chain H 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 Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.0060 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 moved from start: 0.7539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4054 Z= 0.189 Angle : 0.553 5.463 5494 Z= 0.285 Chirality : 0.051 0.148 670 Planarity : 0.001 0.011 676 Dihedral : 12.673 79.250 588 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.37 % Allowed : 21.84 % 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 (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: -3.25 (0.31), 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 0.001 0.000 HIS J 50 PHE 0.003 0.001 PHE E 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 54 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.420 Fit side-chains REVERT: A 83 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6930 (mp0) REVERT: B 79 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: C 98 ASP cc_start: 0.6267 (m-30) cc_final: 0.6008 (p0) REVERT: C 99 GLN cc_start: 0.4708 (tm-30) cc_final: 0.4386 (tm-30) REVERT: D 83 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7238 (mp0) REVERT: E 83 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6768 (mp0) REVERT: F 61 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6346 (tm-30) REVERT: F 83 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7331 (mp0) REVERT: G 83 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7019 (mp0) REVERT: H 99 GLN cc_start: 0.4993 (tm-30) cc_final: 0.4726 (tp40) REVERT: I 58 LYS cc_start: 0.7315 (mmtp) cc_final: 0.6629 (tptp) REVERT: I 99 GLN cc_start: 0.5751 (tm-30) cc_final: 0.5184 (mp10) REVERT: J 61 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6416 (tm-30) REVERT: J 83 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7217 (mp0) outliers start: 9 outliers final: 5 residues processed: 52 average time/residue: 1.6365 time to fit residues: 87.4116 Evaluate side-chains 50 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5327 moved from start: 0.7672 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= 0.354 Angle : 0.648 5.420 5494 Z= 0.335 Chirality : 0.053 0.160 670 Planarity : 0.002 0.008 676 Dihedral : 13.507 83.160 588 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.95 % Allowed : 20.79 % Favored : 75.26 % 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: -3.42 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 50 PHE 0.005 0.001 PHE A 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 65 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.429 Fit side-chains REVERT: A 83 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7069 (mp0) REVERT: B 79 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: C 61 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6220 (tt0) REVERT: C 83 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7289 (mm-30) REVERT: C 99 GLN cc_start: 0.4853 (tm-30) cc_final: 0.4649 (tm-30) REVERT: D 61 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7142 (tt0) REVERT: D 83 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7384 (mp0) REVERT: E 83 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7045 (mt-10) REVERT: F 83 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: G 83 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: H 83 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7349 (mt-10) REVERT: I 58 LYS cc_start: 0.7122 (mmtp) cc_final: 0.6375 (mmtt) REVERT: I 98 ASP cc_start: 0.6827 (m-30) cc_final: 0.6197 (p0) REVERT: I 99 GLN cc_start: 0.5666 (tm-30) cc_final: 0.4946 (mp10) REVERT: J 61 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6324 (tt0) REVERT: J 83 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7284 (mp0) outliers start: 15 outliers final: 7 residues processed: 58 average time/residue: 1.4814 time to fit residues: 88.5015 Evaluate side-chains 59 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN 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 H residue 49 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 0.0170 chunk 5 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5315 moved from start: 0.7812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4054 Z= 0.245 Angle : 0.590 5.834 5494 Z= 0.303 Chirality : 0.052 0.151 670 Planarity : 0.001 0.007 676 Dihedral : 13.019 81.549 588 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.63 % Allowed : 22.89 % Favored : 74.47 % 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: -3.35 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS J 50 PHE 0.004 0.001 PHE G 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 56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.406 Fit side-chains REVERT: A 83 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6970 (mp0) REVERT: B 79 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: D 61 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7102 (tt0) REVERT: D 83 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7285 (mp0) REVERT: E 83 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6947 (mt-10) REVERT: F 50 HIS cc_start: 0.5261 (OUTLIER) cc_final: 0.4521 (m90) REVERT: F 83 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7223 (mp0) REVERT: G 83 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7096 (mp0) REVERT: H 83 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7262 (mt-10) REVERT: I 58 LYS cc_start: 0.7265 (mmtp) cc_final: 0.6550 (mmtt) REVERT: I 99 GLN cc_start: 0.5655 (tm-30) cc_final: 0.5251 (mp10) REVERT: J 61 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6371 (tm-30) REVERT: J 83 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7232 (mp0) outliers start: 10 outliers final: 5 residues processed: 53 average time/residue: 1.4269 time to fit residues: 77.9805 Evaluate side-chains 52 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G 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 40 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.161682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.105915 restraints weight = 4086.343| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.83 r_work: 0.3561 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.7925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4054 Z= 0.429 Angle : 0.704 5.757 5494 Z= 0.364 Chirality : 0.054 0.163 670 Planarity : 0.002 0.007 676 Dihedral : 14.000 85.342 588 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 3.42 % Allowed : 22.11 % Favored : 74.47 % 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: -3.54 (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 0.006 0.001 PHE A 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.42 seconds wall clock time: 37 minutes 57.49 seconds (2277.49 seconds total)