Starting phenix.real_space_refine on Wed Mar 4 14:31:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n2p_9332/03_2026/6n2p_9332.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n2p_9332/03_2026/6n2p_9332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n2p_9332/03_2026/6n2p_9332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n2p_9332/03_2026/6n2p_9332.map" model { file = "/net/cci-nas-00/data/ceres_data/6n2p_9332/03_2026/6n2p_9332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n2p_9332/03_2026/6n2p_9332.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.004 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 4630 2.51 5 N 1210 2.21 5 O 1330 1.98 5 H 7380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14570 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "B" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "C" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "D" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "E" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "F" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "G" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "H" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "I" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "J" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1457 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Time building chain proxies: 2.66, per 1000 atoms: 0.18 Number of scatterers: 14570 At special positions: 0 Unit cell: (91.14, 91.14, 87.885, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 1330 8.00 N 1210 7.00 C 4630 6.00 H 7380 1.00 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: 1.10 Conformation dependent library (CDL) restraints added in 438.8 milliseconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Proline residue: A 32 - end of helix Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 87 Processing helix chain 'A' and resid 87 through 95 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 18 through 25 Processing helix chain 'B' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Proline residue: B 32 - end of helix Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Proline residue: C 32 - end of helix Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 57 through 70 removed outlier: 3.658A pdb=" N VAL C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 87 Processing helix chain 'C' and resid 87 through 95 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 18 through 25 Processing helix chain 'D' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Proline residue: D 32 - end of helix Processing helix chain 'D' and resid 41 through 50 Processing helix chain 'D' and resid 57 through 70 removed outlier: 3.658A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 87 Processing helix chain 'D' and resid 87 through 95 Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 18 through 25 Processing helix chain 'E' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) Proline residue: E 32 - end of helix Processing helix chain 'E' and resid 41 through 50 Processing helix chain 'E' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL E 61 " --> pdb=" O ARG E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 87 Processing helix chain 'E' and resid 87 through 95 Processing helix chain 'F' and resid 10 through 15 Processing helix chain 'F' and resid 18 through 25 Processing helix chain 'F' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Proline residue: F 32 - end of helix Processing helix chain 'F' and resid 41 through 50 Processing helix chain 'F' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 87 Processing helix chain 'F' and resid 87 through 95 Processing helix chain 'G' and resid 10 through 15 Processing helix chain 'G' and resid 18 through 25 Processing helix chain 'G' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) Proline residue: G 32 - end of helix Processing helix chain 'G' and resid 41 through 50 Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 87 Processing helix chain 'G' and resid 87 through 95 Processing helix chain 'H' and resid 10 through 15 Processing helix chain 'H' and resid 18 through 25 Processing helix chain 'H' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE H 30 " --> pdb=" O ASP H 26 " (cutoff:3.500A) Proline residue: H 32 - end of helix Processing helix chain 'H' and resid 41 through 50 Processing helix chain 'H' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 87 Processing helix chain 'H' and resid 87 through 95 Processing helix chain 'I' and resid 10 through 15 Processing helix chain 'I' and resid 18 through 25 Processing helix chain 'I' and resid 26 through 37 removed outlier: 4.070A pdb=" N ILE I 30 " --> pdb=" O ASP I 26 " (cutoff:3.500A) Proline residue: I 32 - end of helix Processing helix chain 'I' and resid 41 through 50 Processing helix chain 'I' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL I 61 " --> pdb=" O ARG I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 87 Processing helix chain 'I' and resid 87 through 95 Processing helix chain 'J' and resid 10 through 15 Processing helix chain 'J' and resid 18 through 25 Processing helix chain 'J' and resid 26 through 37 removed outlier: 4.069A pdb=" N ILE J 30 " --> pdb=" O ASP J 26 " (cutoff:3.500A) Proline residue: J 32 - end of helix Processing helix chain 'J' and resid 41 through 50 Processing helix chain 'J' and resid 57 through 70 removed outlier: 3.657A pdb=" N VAL J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 87 Processing helix chain 'J' and resid 87 through 95 420 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7360 1.03 - 1.23: 20 1.23 - 1.42: 2950 1.42 - 1.62: 4360 1.62 - 1.81: 20 Bond restraints: 14710 Sorted by residual: bond pdb=" CG LEU H 65 " pdb=" CD1 LEU H 65 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CG LEU J 65 " pdb=" CD1 LEU J 65 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CG LEU G 65 " pdb=" CD1 LEU G 65 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CG LEU E 65 " pdb=" CD1 LEU E 65 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00 bond pdb=" CG LEU I 65 " pdb=" CD1 LEU I 65 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.57e+00 ... (remaining 14705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 24237 1.27 - 2.53: 2236 2.53 - 3.80: 217 3.80 - 5.07: 20 5.07 - 6.34: 30 Bond angle restraints: 26740 Sorted by residual: angle pdb=" C GLN C 36 " pdb=" N CYS C 37 " pdb=" CA CYS C 37 " ideal model delta sigma weight residual 122.31 116.66 5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" C GLN F 36 " pdb=" N CYS F 37 " pdb=" CA CYS F 37 " ideal model delta sigma weight residual 122.31 116.66 5.65 2.00e+00 2.50e-01 7.97e+00 angle pdb=" C GLN E 36 " pdb=" N CYS E 37 " pdb=" CA CYS E 37 " ideal model delta sigma weight residual 122.31 116.67 5.64 2.00e+00 2.50e-01 7.95e+00 angle pdb=" C GLN A 36 " pdb=" N CYS A 37 " pdb=" CA CYS A 37 " ideal model delta sigma weight residual 122.31 116.67 5.64 2.00e+00 2.50e-01 7.95e+00 angle pdb=" C GLN B 36 " pdb=" N CYS B 37 " pdb=" CA CYS B 37 " ideal model delta sigma weight residual 122.31 116.69 5.62 2.00e+00 2.50e-01 7.91e+00 ... (remaining 26735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.88: 6381 11.88 - 23.77: 259 23.77 - 35.65: 100 35.65 - 47.53: 70 47.53 - 59.41: 30 Dihedral angle restraints: 6840 sinusoidal: 3850 harmonic: 2990 Sorted by residual: dihedral pdb=" CA LEU E 54 " pdb=" C LEU E 54 " pdb=" N VAL E 55 " pdb=" CA VAL E 55 " ideal model delta harmonic sigma weight residual -180.00 -163.91 -16.09 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA LEU F 54 " pdb=" C LEU F 54 " pdb=" N VAL F 55 " pdb=" CA VAL F 55 " ideal model delta harmonic sigma weight residual -180.00 -163.95 -16.05 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA LEU J 54 " pdb=" C LEU J 54 " pdb=" N VAL J 55 " pdb=" CA VAL J 55 " ideal model delta harmonic sigma weight residual -180.00 -163.96 -16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 6837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 529 0.025 - 0.050: 353 0.050 - 0.075: 192 0.075 - 0.100: 46 0.100 - 0.125: 40 Chirality restraints: 1160 Sorted by residual: chirality pdb=" CA PRO J 32 " pdb=" N PRO J 32 " pdb=" C PRO J 32 " pdb=" CB PRO J 32 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.89e-01 chirality pdb=" CA PRO C 52 " pdb=" N PRO C 52 " pdb=" C PRO C 52 " pdb=" CB PRO C 52 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA PRO E 32 " pdb=" N PRO E 32 " pdb=" C PRO E 32 " pdb=" CB PRO E 32 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1157 not shown) Planarity restraints: 2070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 51 " -0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 52 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 51 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO D 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 52 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 51 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO I 52 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO I 52 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO I 52 " -0.030 5.00e-02 4.00e+02 ... (remaining 2067 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 817 2.19 - 2.79: 30538 2.79 - 3.39: 36506 3.39 - 4.00: 45180 4.00 - 4.60: 72363 Nonbonded interactions: 185404 Sorted by model distance: nonbonded pdb="HD22 ASN D 53 " pdb=" O PRO E 52 " model vdw 1.586 2.450 nonbonded pdb=" OE2 GLU B 15 " pdb=" HE ARG E 35 " model vdw 1.589 2.450 nonbonded pdb=" OE2 GLU C 15 " pdb=" HE ARG F 35 " model vdw 1.596 2.450 nonbonded pdb=" HE ARG B 35 " pdb=" OE2 GLU H 15 " model vdw 1.601 2.450 nonbonded pdb="HD22 ASN E 53 " pdb=" O PRO F 52 " model vdw 1.621 2.450 ... (remaining 185399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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 group one per residue 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.630 Find NCS groups from input model: 0.180 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 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 : 0.009 0.046 7330 Z= 0.360 Angle : 0.872 6.337 9950 Z= 0.466 Chirality : 0.043 0.125 1160 Planarity : 0.007 0.055 1250 Dihedral : 7.864 35.860 2810 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.67 (0.22), residues: 860 helix: -2.30 (0.16), residues: 670 sheet: None (None), residues: 0 loop : -5.46 (0.22), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 18 TYR 0.004 0.001 TYR D 87 PHE 0.013 0.004 PHE J 79 TRP 0.002 0.001 TRP B 11 HIS 0.004 0.003 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00945 ( 7330) covalent geometry : angle 0.87163 ( 9950) hydrogen bonds : bond 0.08360 ( 420) hydrogen bonds : angle 4.97738 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3730 time to fit residues: 51.4790 Evaluate side-chains 56 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.0070 overall best weight: 2.4006 ------------------------------------------------------------------------------- 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 = 0.3032 r_free = 0.3032 target = 0.044177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.039048 restraints weight = 233034.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.040204 restraints weight = 111969.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040978 restraints weight = 68895.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.041497 restraints weight = 48062.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.041873 restraints weight = 36457.599| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7330 Z= 0.129 Angle : 0.613 4.770 9950 Z= 0.319 Chirality : 0.036 0.103 1160 Planarity : 0.006 0.045 1250 Dihedral : 4.966 14.528 980 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.12 % Allowed : 8.31 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.27), residues: 860 helix: -0.38 (0.19), residues: 670 sheet: None (None), residues: 0 loop : -5.17 (0.27), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.010 0.001 TYR F 87 PHE 0.007 0.000 PHE E 17 TRP 0.004 0.000 TRP E 11 HIS 0.000 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7330) covalent geometry : angle 0.61302 ( 9950) hydrogen bonds : bond 0.03076 ( 420) hydrogen bonds : angle 3.87936 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9494 (tm-30) cc_final: 0.9290 (tm-30) REVERT: A 46 GLU cc_start: 0.9257 (pt0) cc_final: 0.8854 (pp20) REVERT: B 43 ASP cc_start: 0.9299 (p0) cc_final: 0.8745 (p0) REVERT: B 46 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.9117 (pp20) REVERT: B 56 ILE cc_start: 0.9470 (mt) cc_final: 0.9205 (mm) REVERT: C 43 ASP cc_start: 0.9050 (p0) cc_final: 0.8834 (p0) REVERT: C 47 GLN cc_start: 0.9700 (tt0) cc_final: 0.9188 (tm-30) REVERT: C 56 ILE cc_start: 0.9398 (mt) cc_final: 0.9089 (mm) REVERT: F 45 GLU cc_start: 0.9607 (tt0) cc_final: 0.9248 (mt-10) REVERT: F 46 GLU cc_start: 0.8210 (pt0) cc_final: 0.7883 (pp20) REVERT: F 47 GLN cc_start: 0.9627 (tt0) cc_final: 0.9151 (tm-30) REVERT: G 43 ASP cc_start: 0.8929 (p0) cc_final: 0.8312 (p0) REVERT: G 46 GLU cc_start: 0.9357 (pt0) cc_final: 0.9078 (pp20) REVERT: G 56 ILE cc_start: 0.9523 (mt) cc_final: 0.9111 (mm) REVERT: H 43 ASP cc_start: 0.8838 (p0) cc_final: 0.8288 (p0) REVERT: H 46 GLU cc_start: 0.9382 (pt0) cc_final: 0.9015 (pp20) REVERT: I 43 ASP cc_start: 0.9349 (m-30) cc_final: 0.9121 (p0) REVERT: I 56 ILE cc_start: 0.9723 (mt) cc_final: 0.9250 (mm) outliers start: 1 outliers final: 0 residues processed: 66 average time/residue: 0.2095 time to fit residues: 18.5129 Evaluate side-chains 56 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 2 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.3208 r_free = 0.3208 target = 0.051052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.047325 restraints weight = 269356.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.048248 restraints weight = 110923.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.048816 restraints weight = 62400.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.049191 restraints weight = 40917.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.049441 restraints weight = 30230.007| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 7330 Z= 0.267 Angle : 0.641 4.659 9950 Z= 0.345 Chirality : 0.035 0.105 1160 Planarity : 0.005 0.033 1250 Dihedral : 4.998 14.864 980 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.48 % Allowed : 8.07 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.28), residues: 860 helix: 0.01 (0.19), residues: 680 sheet: None (None), residues: 0 loop : -4.59 (0.36), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 35 TYR 0.011 0.002 TYR D 87 PHE 0.005 0.001 PHE G 17 TRP 0.010 0.001 TRP E 11 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00540 ( 7330) covalent geometry : angle 0.64071 ( 9950) hydrogen bonds : bond 0.03694 ( 420) hydrogen bonds : angle 4.35326 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.9387 (tm-30) cc_final: 0.9144 (tm-30) REVERT: B 43 ASP cc_start: 0.9235 (p0) cc_final: 0.8722 (p0) REVERT: B 46 GLU cc_start: 0.9282 (pt0) cc_final: 0.8980 (pp20) REVERT: C 46 GLU cc_start: 0.9308 (pt0) cc_final: 0.8978 (pp20) REVERT: D 56 ILE cc_start: 0.9341 (mt) cc_final: 0.9124 (mm) REVERT: F 47 GLN cc_start: 0.9634 (tt0) cc_final: 0.9275 (tm-30) outliers start: 4 outliers final: 4 residues processed: 47 average time/residue: 0.2488 time to fit residues: 15.2457 Evaluate side-chains 36 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain G residue 44 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 = 0.3258 r_free = 0.3258 target = 0.052825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.049076 restraints weight = 258470.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.050014 restraints weight = 105277.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.050578 restraints weight = 58527.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.050952 restraints weight = 38104.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.051246 restraints weight = 27763.982| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7330 Z= 0.107 Angle : 0.537 4.818 9950 Z= 0.274 Chirality : 0.035 0.106 1160 Planarity : 0.004 0.032 1250 Dihedral : 4.425 14.811 980 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.12 % Allowed : 9.04 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.29), residues: 860 helix: 0.85 (0.20), residues: 670 sheet: None (None), residues: 0 loop : -4.31 (0.33), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 35 TYR 0.006 0.001 TYR G 86 PHE 0.004 0.001 PHE E 17 TRP 0.006 0.001 TRP D 11 HIS 0.002 0.001 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7330) covalent geometry : angle 0.53665 ( 9950) hydrogen bonds : bond 0.02791 ( 420) hydrogen bonds : angle 3.63796 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9178 (pt0) cc_final: 0.8840 (pp20) REVERT: B 43 ASP cc_start: 0.9274 (p0) cc_final: 0.8713 (p0) REVERT: B 46 GLU cc_start: 0.9358 (pt0) cc_final: 0.9155 (pp20) REVERT: F 45 GLU cc_start: 0.9569 (tt0) cc_final: 0.9242 (mt-10) REVERT: F 47 GLN cc_start: 0.9644 (tt0) cc_final: 0.9259 (tm-30) REVERT: F 53 ASN cc_start: 0.9559 (m-40) cc_final: 0.9359 (m110) REVERT: G 43 ASP cc_start: 0.8931 (p0) cc_final: 0.8477 (p0) REVERT: G 46 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.8986 (pp20) outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.1338 time to fit residues: 8.2658 Evaluate side-chains 31 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 46 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 28 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.051728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.048052 restraints weight = 264245.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.048992 restraints weight = 107810.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.049555 restraints weight = 60090.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049930 restraints weight = 39076.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.050191 restraints weight = 28585.990| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7330 Z= 0.145 Angle : 0.527 4.605 9950 Z= 0.274 Chirality : 0.034 0.102 1160 Planarity : 0.004 0.031 1250 Dihedral : 4.383 14.164 980 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.12 % Allowed : 9.52 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.29), residues: 860 helix: 0.93 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.25 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 35 TYR 0.007 0.001 TYR D 87 PHE 0.002 0.001 PHE G 17 TRP 0.005 0.001 TRP D 11 HIS 0.001 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7330) covalent geometry : angle 0.52749 ( 9950) hydrogen bonds : bond 0.02809 ( 420) hydrogen bonds : angle 3.70029 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9177 (pt0) cc_final: 0.8791 (pp20) REVERT: B 43 ASP cc_start: 0.9282 (p0) cc_final: 0.8727 (p0) REVERT: B 46 GLU cc_start: 0.9275 (pt0) cc_final: 0.9012 (pp20) REVERT: F 47 GLN cc_start: 0.9639 (tt0) cc_final: 0.9235 (tm-30) REVERT: F 53 ASN cc_start: 0.9548 (m-40) cc_final: 0.9342 (m110) REVERT: G 46 GLU cc_start: 0.9259 (pt0) cc_final: 0.9039 (pp20) outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.1436 time to fit residues: 7.0867 Evaluate side-chains 27 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 13 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.052508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.048841 restraints weight = 260698.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.049786 restraints weight = 105209.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.050344 restraints weight = 58384.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.050711 restraints weight = 37993.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.050983 restraints weight = 27610.805| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7330 Z= 0.103 Angle : 0.509 4.580 9950 Z= 0.260 Chirality : 0.035 0.106 1160 Planarity : 0.003 0.029 1250 Dihedral : 4.195 14.010 980 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 0.12 % Allowed : 9.40 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.30), residues: 860 helix: 1.31 (0.21), residues: 670 sheet: None (None), residues: 0 loop : -3.91 (0.35), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 35 TYR 0.004 0.001 TYR G 86 PHE 0.002 0.000 PHE F 17 TRP 0.004 0.000 TRP D 11 HIS 0.001 0.000 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7330) covalent geometry : angle 0.50917 ( 9950) hydrogen bonds : bond 0.02544 ( 420) hydrogen bonds : angle 3.48418 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9194 (pt0) cc_final: 0.8866 (pp20) REVERT: B 43 ASP cc_start: 0.9294 (p0) cc_final: 0.8772 (p0) REVERT: B 46 GLU cc_start: 0.9289 (pt0) cc_final: 0.9073 (pp20) REVERT: B 53 ASN cc_start: 0.9072 (m-40) cc_final: 0.8802 (m-40) REVERT: F 47 GLN cc_start: 0.9648 (tt0) cc_final: 0.9402 (tp40) REVERT: F 53 ASN cc_start: 0.9501 (m-40) cc_final: 0.9250 (m110) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.1136 time to fit residues: 5.7993 Evaluate side-chains 24 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 83 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 19 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.051758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.048080 restraints weight = 262557.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.049032 restraints weight = 107890.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.049592 restraints weight = 59828.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.049953 restraints weight = 38932.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.050219 restraints weight = 28113.015| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 7330 Z= 0.132 Angle : 0.513 4.559 9950 Z= 0.265 Chirality : 0.035 0.102 1160 Planarity : 0.003 0.027 1250 Dihedral : 4.244 13.942 980 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 0.12 % Allowed : 9.40 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.30), residues: 860 helix: 1.24 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -3.95 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 35 TYR 0.005 0.001 TYR D 87 PHE 0.002 0.000 PHE G 17 TRP 0.004 0.001 TRP D 11 HIS 0.001 0.000 HIS I 73 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7330) covalent geometry : angle 0.51288 ( 9950) hydrogen bonds : bond 0.02596 ( 420) hydrogen bonds : angle 3.58393 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9162 (pt0) cc_final: 0.8799 (pp20) REVERT: B 43 ASP cc_start: 0.9299 (p0) cc_final: 0.8917 (p0) REVERT: B 46 GLU cc_start: 0.9272 (pt0) cc_final: 0.9030 (pp20) REVERT: B 53 ASN cc_start: 0.9109 (m-40) cc_final: 0.8823 (m110) REVERT: F 47 GLN cc_start: 0.9645 (tt0) cc_final: 0.9416 (tp40) REVERT: F 53 ASN cc_start: 0.9487 (m-40) cc_final: 0.9199 (m110) outliers start: 1 outliers final: 0 residues processed: 25 average time/residue: 0.1058 time to fit residues: 4.5811 Evaluate side-chains 24 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.050583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.046905 restraints weight = 267148.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.047844 restraints weight = 110819.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.048413 restraints weight = 61882.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.048756 restraints weight = 40413.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.049028 restraints weight = 29390.255| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7330 Z= 0.182 Angle : 0.548 4.471 9950 Z= 0.289 Chirality : 0.035 0.107 1160 Planarity : 0.003 0.024 1250 Dihedral : 4.502 14.740 980 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.12 % Allowed : 9.64 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.29), residues: 860 helix: 1.15 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -3.93 (0.35), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 35 TYR 0.007 0.001 TYR D 87 PHE 0.004 0.001 PHE C 79 TRP 0.006 0.001 TRP D 11 HIS 0.001 0.000 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7330) covalent geometry : angle 0.54829 ( 9950) hydrogen bonds : bond 0.02911 ( 420) hydrogen bonds : angle 3.84690 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9151 (pt0) cc_final: 0.8832 (pp20) REVERT: B 43 ASP cc_start: 0.9314 (p0) cc_final: 0.8936 (p0) REVERT: B 53 ASN cc_start: 0.9075 (m-40) cc_final: 0.8776 (m110) REVERT: D 53 ASN cc_start: 0.9043 (m-40) cc_final: 0.8652 (m110) REVERT: E 53 ASN cc_start: 0.9190 (m-40) cc_final: 0.8781 (m110) REVERT: F 53 ASN cc_start: 0.9495 (m-40) cc_final: 0.9207 (m110) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.1121 time to fit residues: 4.9191 Evaluate side-chains 24 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 60 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.051720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.048056 restraints weight = 263387.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.049000 restraints weight = 106826.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.049492 restraints weight = 59166.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.049855 restraints weight = 41363.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.050143 restraints weight = 29397.267| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7330 Z= 0.103 Angle : 0.507 5.265 9950 Z= 0.260 Chirality : 0.035 0.105 1160 Planarity : 0.003 0.026 1250 Dihedral : 4.234 14.359 980 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.24 % Allowed : 9.28 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.30), residues: 860 helix: 1.38 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -3.81 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 35 TYR 0.004 0.001 TYR I 86 PHE 0.003 0.000 PHE I 17 TRP 0.002 0.000 TRP A 11 HIS 0.001 0.000 HIS D 73 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7330) covalent geometry : angle 0.50714 ( 9950) hydrogen bonds : bond 0.02513 ( 420) hydrogen bonds : angle 3.47125 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9160 (pt0) cc_final: 0.8797 (pp20) REVERT: B 53 ASN cc_start: 0.9044 (m-40) cc_final: 0.8741 (m110) REVERT: D 53 ASN cc_start: 0.9039 (m-40) cc_final: 0.8666 (m110) REVERT: E 53 ASN cc_start: 0.9207 (m-40) cc_final: 0.8755 (m110) REVERT: F 53 ASN cc_start: 0.9463 (m-40) cc_final: 0.9158 (m110) REVERT: I 46 GLU cc_start: 0.9122 (pt0) cc_final: 0.8716 (pp20) outliers start: 2 outliers final: 2 residues processed: 29 average time/residue: 0.1593 time to fit residues: 7.0610 Evaluate side-chains 28 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain G residue 83 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 57 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3225 r_free = 0.3225 target = 0.051053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.047376 restraints weight = 264956.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.048310 restraints weight = 108706.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.048879 restraints weight = 60521.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.049226 restraints weight = 39287.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.049493 restraints weight = 28565.923| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7330 Z= 0.141 Angle : 0.521 5.864 9950 Z= 0.271 Chirality : 0.035 0.105 1160 Planarity : 0.003 0.024 1250 Dihedral : 4.335 14.391 980 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 0.12 % Allowed : 9.52 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.30), residues: 860 helix: 1.35 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -3.89 (0.34), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 35 TYR 0.005 0.001 TYR D 87 PHE 0.002 0.000 PHE C 79 TRP 0.003 0.001 TRP D 11 HIS 0.001 0.000 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7330) covalent geometry : angle 0.52090 ( 9950) hydrogen bonds : bond 0.02588 ( 420) hydrogen bonds : angle 3.61727 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.9157 (pt0) cc_final: 0.8818 (pp20) REVERT: B 53 ASN cc_start: 0.9067 (m-40) cc_final: 0.8744 (m110) REVERT: D 53 ASN cc_start: 0.9053 (m-40) cc_final: 0.8670 (m110) REVERT: E 53 ASN cc_start: 0.9245 (m-40) cc_final: 0.8804 (m-40) REVERT: F 53 ASN cc_start: 0.9454 (m-40) cc_final: 0.9148 (m110) outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.1586 time to fit residues: 6.7345 Evaluate side-chains 27 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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 = 0.3241 r_free = 0.3241 target = 0.051634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.048010 restraints weight = 261969.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.048936 restraints weight = 104937.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.049494 restraints weight = 58203.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.049836 restraints weight = 37754.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.050110 restraints weight = 27261.556| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7330 Z= 0.100 Angle : 0.504 5.455 9950 Z= 0.257 Chirality : 0.035 0.105 1160 Planarity : 0.003 0.023 1250 Dihedral : 4.209 14.028 980 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.24 % Allowed : 9.28 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.30), residues: 860 helix: 1.51 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -3.83 (0.33), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 35 TYR 0.004 0.001 TYR D 86 PHE 0.002 0.000 PHE A 17 TRP 0.002 0.001 TRP J 11 HIS 0.000 0.000 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7330) covalent geometry : angle 0.50441 ( 9950) hydrogen bonds : bond 0.02415 ( 420) hydrogen bonds : angle 3.41830 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1885.33 seconds wall clock time: 32 minutes 48.40 seconds (1968.40 seconds total)