Starting phenix.real_space_refine on Mon Jan 13 20:31:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x7b_38097/01_2025/8x7b_38097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x7b_38097/01_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_38097/01_2025/8x7b_38097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x7b_38097/01_2025/8x7b_38097.map" model { file = "/net/cci-nas-00/data/ceres_data/8x7b_38097/01_2025/8x7b_38097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x7b_38097/01_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-5571/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: 2.94, per 1000 atoms: 0.73 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: 0.93 Conformation dependent library (CDL) restraints added in 529.2 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: 0.87 Time building geometry restraints manager: 1.09 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.430 Find NCS groups from input model: 0.080 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.890 ------------------------------------------------------------------------------- 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 : 0.435 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: 1.2316 time to fit residues: 123.2392 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 : 0.410 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.160706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.108659 restraints weight = 4346.913| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.23 r_work: 0.3661 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- 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 : 0.434 Fit side-chains REVERT: A 61 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7402 (tt0) REVERT: A 83 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7676 (mp0) REVERT: B 72 THR cc_start: 0.9300 (m) cc_final: 0.9080 (m) REVERT: B 83 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7968 (mp0) REVERT: C 61 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7454 (tt0) REVERT: C 83 GLU cc_start: 0.8201 (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: 0.8221 (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: 0.8389 (mt-10) cc_final: 0.7829 (tm-30) REVERT: F 97 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7778 (mttt) REVERT: G 61 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7510 (tm-30) REVERT: G 83 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: H 61 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8060 (tt0) REVERT: I 61 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7922 (tt0) REVERT: J 61 GLU cc_start: 0.8391 (mt-10) cc_final: 0.7809 (tt0) REVERT: J 83 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: J 99 GLN cc_start: 0.5947 (tp40) cc_final: 0.5712 (tm-30) outliers start: 12 outliers final: 6 residues processed: 57 average time/residue: 1.7128 time to fit residues: 100.1666 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 : 0.423 ------------------------------------------------------------------------------- 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: 3.9990 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 14 optimal weight: 0.0980 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4504 r_free = 0.4504 target = 0.157957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.105262 restraints weight = 4217.912| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.03 r_work: 0.3645 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5543 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= 0.228 Angle : 0.593 4.537 5494 Z= 0.311 Chirality : 0.052 0.163 670 Planarity : 0.002 0.011 676 Dihedral : 13.713 76.215 588 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.89 % Allowed : 21.05 % 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: -3.33 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 50 PHE 0.008 0.002 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 44 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.417 Fit side-chains REVERT: A 83 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7751 (mp0) REVERT: B 96 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7449 (mtpp) REVERT: C 83 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7656 (mp0) REVERT: C 99 GLN cc_start: 0.5820 (mt0) cc_final: 0.5321 (tm-30) REVERT: D 83 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7921 (mp0) REVERT: H 61 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7780 (tt0) REVERT: J 61 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7507 (tm-30) REVERT: J 99 GLN cc_start: 0.6263 (tp40) cc_final: 0.5824 (tm-30) outliers start: 11 outliers final: 1 residues processed: 39 average time/residue: 1.5587 time to fit residues: 62.6692 Evaluate side-chains 28 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 LYS 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: 3.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.4491 r_free = 0.4491 target = 0.155137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.101358 restraints weight = 4234.426| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.06 r_work: 0.3606 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.6182 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= 0.215 Angle : 0.552 4.470 5494 Z= 0.288 Chirality : 0.050 0.155 670 Planarity : 0.002 0.012 676 Dihedral : 12.689 73.911 588 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.79 % Allowed : 16.58 % 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: -3.21 (0.30), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 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 56 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 0.432 Fit side-chains REVERT: A 83 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7684 (mp0) REVERT: B 79 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8769 (mt0) REVERT: C 83 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7609 (mp0) REVERT: C 99 GLN cc_start: 0.6112 (mt0) cc_final: 0.5694 (tm-30) REVERT: D 83 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7895 (mp0) REVERT: E 99 GLN cc_start: 0.6132 (mt0) cc_final: 0.5714 (tm-30) REVERT: H 61 GLU cc_start: 0.8346 (mt-10) cc_final: 0.7880 (tt0) REVERT: I 97 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8472 (mttt) REVERT: J 61 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7484 (tm-30) REVERT: J 83 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: J 99 GLN cc_start: 0.6434 (tp40) cc_final: 0.6013 (tm-30) outliers start: 22 outliers final: 5 residues processed: 49 average time/residue: 1.7041 time to fit residues: 85.7711 Evaluate side-chains 37 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 97 LYS 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: 1.9990 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 F 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.158970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.104082 restraints weight = 4251.246| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.99 r_work: 0.3692 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.6790 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= 0.369 Angle : 0.631 4.705 5494 Z= 0.329 Chirality : 0.053 0.162 670 Planarity : 0.002 0.012 676 Dihedral : 13.874 80.345 588 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.53 % Allowed : 17.37 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 5.56 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.30), 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 0.001 HIS C 50 PHE 0.006 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 62 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 0.417 Fit side-chains REVERT: A 83 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7964 (mp0) REVERT: B 79 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8721 (mt0) REVERT: C 98 ASP cc_start: 0.7746 (m-30) cc_final: 0.7491 (m-30) REVERT: C 99 GLN cc_start: 0.6442 (mt0) cc_final: 0.6075 (tm-30) REVERT: D 61 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7428 (tt0) REVERT: D 83 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8060 (mp0) REVERT: E 83 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8160 (mt-10) REVERT: E 99 GLN cc_start: 0.6517 (mt0) cc_final: 0.6185 (tm-30) REVERT: F 83 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: G 83 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: G 99 GLN cc_start: 0.6365 (mt0) cc_final: 0.5856 (tm-30) REVERT: I 83 GLU cc_start: 0.7880 (mp0) cc_final: 0.7426 (mp0) REVERT: J 61 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7540 (tm-30) REVERT: J 83 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: J 98 ASP cc_start: 0.7599 (m-30) cc_final: 0.7331 (m-30) REVERT: J 99 GLN cc_start: 0.6450 (tp40) cc_final: 0.6102 (tm-30) outliers start: 21 outliers final: 9 residues processed: 54 average time/residue: 1.5494 time to fit residues: 86.0307 Evaluate side-chains 49 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 E 79 GLN I 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.162337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.108819 restraints weight = 4076.654| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.90 r_work: 0.3660 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.7119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4054 Z= 0.227 Angle : 0.540 4.303 5494 Z= 0.279 Chirality : 0.051 0.153 670 Planarity : 0.002 0.016 676 Dihedral : 13.120 78.620 588 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.21 % Allowed : 19.21 % Favored : 76.58 % 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 0.002 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 53 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.386 Fit side-chains REVERT: A 83 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7806 (mp0) REVERT: C 83 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7695 (mp0) REVERT: C 98 ASP cc_start: 0.7790 (m-30) cc_final: 0.7227 (m-30) REVERT: C 99 GLN cc_start: 0.6508 (mt0) cc_final: 0.5841 (tm-30) REVERT: D 83 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7883 (mp0) REVERT: E 99 GLN cc_start: 0.6583 (mt0) cc_final: 0.6281 (tm-30) REVERT: F 83 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: G 83 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: G 98 ASP cc_start: 0.7454 (m-30) cc_final: 0.6871 (p0) REVERT: J 61 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7566 (tm-30) REVERT: J 98 ASP cc_start: 0.7710 (m-30) cc_final: 0.7446 (m-30) REVERT: J 99 GLN cc_start: 0.6464 (tp40) cc_final: 0.6169 (tm-30) outliers start: 16 outliers final: 5 residues processed: 47 average time/residue: 1.6032 time to fit residues: 77.5273 Evaluate side-chains 42 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain 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 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 36 optimal weight: 0.0030 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.159631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.105117 restraints weight = 4180.203| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.92 r_work: 0.3715 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4054 Z= 0.339 Angle : 0.612 4.694 5494 Z= 0.317 Chirality : 0.053 0.161 670 Planarity : 0.002 0.007 676 Dihedral : 13.636 81.823 588 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 4.47 % Allowed : 17.89 % 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: -3.51 (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 61 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.425 Fit side-chains REVERT: A 83 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7935 (mp0) REVERT: A 98 ASP cc_start: 0.7829 (m-30) cc_final: 0.7511 (m-30) REVERT: B 83 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8073 (mp0) REVERT: B 97 LYS cc_start: 0.8171 (mttp) cc_final: 0.7800 (mttp) REVERT: C 98 ASP cc_start: 0.7909 (m-30) cc_final: 0.7643 (m-30) REVERT: C 99 GLN cc_start: 0.6655 (mt0) cc_final: 0.6345 (tm-30) REVERT: D 61 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7521 (tt0) REVERT: D 83 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8094 (mp0) REVERT: E 83 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8065 (mt-10) REVERT: E 98 ASP cc_start: 0.7789 (m-30) cc_final: 0.7455 (m-30) REVERT: E 99 GLN cc_start: 0.6751 (mt0) cc_final: 0.6424 (tm-30) REVERT: F 83 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: G 83 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: I 58 LYS cc_start: 0.7901 (mmtp) cc_final: 0.7163 (mmtt) REVERT: I 99 GLN cc_start: 0.6003 (tm-30) cc_final: 0.5315 (mp10) REVERT: J 61 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7524 (tt0) REVERT: J 99 GLN cc_start: 0.6567 (tp40) cc_final: 0.6284 (tm-30) outliers start: 17 outliers final: 10 residues processed: 55 average time/residue: 1.3689 time to fit residues: 77.7431 Evaluate side-chains 52 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 12 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 46 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4517 r_free = 0.4517 target = 0.161271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.106146 restraints weight = 4135.715| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 3.01 r_work: 0.3720 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.7495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4054 Z= 0.161 Angle : 0.508 5.625 5494 Z= 0.261 Chirality : 0.051 0.147 670 Planarity : 0.001 0.009 676 Dihedral : 12.601 78.342 588 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.63 % Allowed : 20.53 % Favored : 76.84 % 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 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (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 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 50 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.397 Fit side-chains REVERT: A 83 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7804 (mp0) REVERT: A 98 ASP cc_start: 0.7799 (m-30) cc_final: 0.7257 (m-30) REVERT: C 98 ASP cc_start: 0.7779 (m-30) cc_final: 0.6867 (p0) REVERT: C 99 GLN cc_start: 0.6568 (mt0) cc_final: 0.5826 (tm-30) REVERT: D 83 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7877 (mp0) REVERT: E 83 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7895 (mp0) REVERT: E 98 ASP cc_start: 0.7505 (m-30) cc_final: 0.6778 (p0) REVERT: E 99 GLN cc_start: 0.6681 (mt0) cc_final: 0.5976 (tm-30) REVERT: F 50 HIS cc_start: 0.6068 (OUTLIER) cc_final: 0.5381 (m90) REVERT: F 61 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7592 (tm-30) REVERT: F 83 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: G 83 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7971 (mp0) REVERT: G 98 ASP cc_start: 0.7489 (m-30) cc_final: 0.7039 (p0) REVERT: G 99 GLN cc_start: 0.6692 (mt0) cc_final: 0.5933 (tm-30) REVERT: I 58 LYS cc_start: 0.7992 (mmtp) cc_final: 0.7320 (tptp) REVERT: I 99 GLN cc_start: 0.6056 (tm-30) cc_final: 0.5400 (mp10) REVERT: J 61 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7660 (tm-30) REVERT: J 99 GLN cc_start: 0.6914 (tp40) cc_final: 0.6626 (tm-30) outliers start: 10 outliers final: 3 residues processed: 48 average time/residue: 1.5732 time to fit residues: 77.6038 Evaluate side-chains 45 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 83 GLU 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 23 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 0.0370 chunk 16 optimal weight: 0.0270 chunk 46 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 overall best weight: 1.0920 ------------------------------------------------------------------------------- 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 = 0.4596 r_free = 0.4596 target = 0.165138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.109973 restraints weight = 4018.929| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.81 r_work: 0.3636 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.7570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4054 Z= 0.259 Angle : 0.569 4.880 5494 Z= 0.294 Chirality : 0.051 0.154 670 Planarity : 0.002 0.007 676 Dihedral : 12.799 80.235 588 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.37 % Allowed : 21.05 % Favored : 76.58 % 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: -3.28 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (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 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 51 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.360 Fit side-chains REVERT: A 83 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8021 (mp0) REVERT: A 98 ASP cc_start: 0.7745 (m-30) cc_final: 0.7408 (m-30) REVERT: A 99 GLN cc_start: 0.6656 (mt0) cc_final: 0.6280 (tm-30) REVERT: C 98 ASP cc_start: 0.7905 (m-30) cc_final: 0.7445 (m-30) REVERT: C 99 GLN cc_start: 0.6588 (mt0) cc_final: 0.6067 (tm-30) REVERT: D 61 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7611 (tt0) REVERT: D 83 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8069 (mp0) REVERT: E 83 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8060 (mp0) REVERT: E 99 GLN cc_start: 0.6727 (mt0) cc_final: 0.6346 (tm-30) REVERT: F 50 HIS cc_start: 0.6230 (OUTLIER) cc_final: 0.5327 (m90) REVERT: F 83 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: G 83 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: G 98 ASP cc_start: 0.7632 (m-30) cc_final: 0.7119 (p0) REVERT: G 99 GLN cc_start: 0.6743 (mt0) cc_final: 0.5868 (tm-30) REVERT: H 83 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8215 (mt-10) REVERT: I 58 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7372 (tptp) REVERT: I 99 GLN cc_start: 0.5980 (tm-30) cc_final: 0.5215 (mp10) REVERT: J 61 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7739 (tt0) outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 1.5344 time to fit residues: 72.6540 Evaluate side-chains 49 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 50 HIS Chi-restraints excluded: chain F residue 83 GLU Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain I residue 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 19 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 18 optimal weight: 0.0970 chunk 45 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.163126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.107839 restraints weight = 4034.704| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.83 r_work: 0.3608 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.7704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 4054 Z= 0.332 Angle : 0.626 6.375 5494 Z= 0.324 Chirality : 0.052 0.158 670 Planarity : 0.002 0.014 676 Dihedral : 13.231 81.758 588 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.63 % Allowed : 20.79 % Favored : 76.58 % 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: -3.38 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (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 C 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 53 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.423 Fit side-chains REVERT: A 83 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8036 (mp0) REVERT: A 98 ASP cc_start: 0.7788 (m-30) cc_final: 0.7398 (m-30) REVERT: A 99 GLN cc_start: 0.6661 (mt0) cc_final: 0.6296 (tm-30) REVERT: C 98 ASP cc_start: 0.7942 (m-30) cc_final: 0.7682 (m-30) REVERT: C 99 GLN cc_start: 0.6618 (mt0) cc_final: 0.6363 (tm-30) REVERT: D 61 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7619 (tt0) REVERT: D 83 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8062 (mp0) REVERT: E 83 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8218 (mt-10) REVERT: E 99 GLN cc_start: 0.6695 (mt0) cc_final: 0.6076 (tm-30) REVERT: F 83 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7940 (mp0) REVERT: G 83 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: G 99 GLN cc_start: 0.6806 (mt0) cc_final: 0.6178 (tm-30) REVERT: I 58 LYS cc_start: 0.8058 (mmtp) cc_final: 0.7325 (mmtt) REVERT: I 99 GLN cc_start: 0.6041 (tm-30) cc_final: 0.5412 (mp10) REVERT: J 61 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7704 (tt0) outliers start: 10 outliers final: 7 residues processed: 48 average time/residue: 1.5507 time to fit residues: 76.6400 Evaluate side-chains 51 residues out of total 380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 83 GLU 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 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: 2.9990 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4597 r_free = 0.4597 target = 0.165567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.110328 restraints weight = 3975.491| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.84 r_work: 0.3659 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.7780 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= 0.239 Angle : 0.570 5.143 5494 Z= 0.294 Chirality : 0.051 0.152 670 Planarity : 0.001 0.007 676 Dihedral : 12.837 80.369 588 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.11 % Allowed : 22.11 % 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: -3.34 (0.31), residues: 530 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (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 C 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3041.67 seconds wall clock time: 54 minutes 30.61 seconds (3270.61 seconds total)