Starting phenix.real_space_refine on Tue Mar 3 13:26:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zky_14771/03_2026/7zky_14771.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zky_14771/03_2026/7zky_14771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zky_14771/03_2026/7zky_14771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zky_14771/03_2026/7zky_14771.map" model { file = "/net/cci-nas-00/data/ceres_data/7zky_14771/03_2026/7zky_14771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zky_14771/03_2026/7zky_14771.cif" } resolution = 2.56 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= 0.006 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 24 5.16 5 C 3324 2.51 5 N 930 2.21 5 O 960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.00s 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: 5238 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 550 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "A" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Restraints were copied for chains: D, F, H, J, L, C, E, G, I, K Time building chain proxies: 0.63, per 1000 atoms: 0.12 Number of scatterers: 5238 At special positions: 0 Unit cell: (71.76, 109.2, 50.96, 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 24 16.00 O 960 8.00 N 930 7.00 C 3324 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: 0.41 Conformation dependent library (CDL) restraints added in 254.6 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.981A pdb=" N TYR B 42 " --> pdb=" O ASP D 43 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR D 42 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR F 42 " --> pdb=" O ASP H 43 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR H 42 " --> pdb=" O ASP J 43 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR J 42 " --> pdb=" O ASP L 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 55 through 58 removed outlier: 6.813A pdb=" N ALA B 55 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE D 58 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 57 " --> pdb=" O ILE D 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA D 55 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE F 58 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA D 57 " --> pdb=" O ILE F 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA F 55 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE H 58 " --> pdb=" O ALA F 55 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA F 57 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA H 55 " --> pdb=" O GLU J 56 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE J 58 " --> pdb=" O ALA H 55 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA H 57 " --> pdb=" O ILE J 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA J 55 " --> pdb=" O GLU L 56 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ILE L 58 " --> pdb=" O ALA J 55 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA J 57 " --> pdb=" O ILE L 58 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 68 Processing sheet with id=AA4, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.687A pdb=" N TYR A 35 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR C 35 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR E 35 " --> pdb=" O PHE G 36 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR G 35 " --> pdb=" O PHE I 36 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR I 35 " --> pdb=" O PHE K 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 25 hydrogen bonds defined for protein. 75 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: 0.62 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 868 1.32 - 1.44: 1874 1.44 - 1.56: 2604 1.56 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 5394 Sorted by residual: bond pdb=" CA SER E 32 " pdb=" CB SER E 32 " ideal model delta sigma weight residual 1.526 1.475 0.051 1.26e-02 6.30e+03 1.61e+01 bond pdb=" CA SER K 32 " pdb=" CB SER K 32 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.26e-02 6.30e+03 1.58e+01 bond pdb=" CA SER A 32 " pdb=" CB SER A 32 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.26e-02 6.30e+03 1.58e+01 bond pdb=" CA SER I 32 " pdb=" CB SER I 32 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.26e-02 6.30e+03 1.58e+01 bond pdb=" CA SER G 32 " pdb=" CB SER G 32 " ideal model delta sigma weight residual 1.526 1.476 0.050 1.26e-02 6.30e+03 1.57e+01 ... (remaining 5389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 4606 1.47 - 2.94: 1411 2.94 - 4.41: 888 4.41 - 5.88: 271 5.88 - 7.35: 42 Bond angle restraints: 7218 Sorted by residual: angle pdb=" N ARG H 62 " pdb=" CA ARG H 62 " pdb=" C ARG H 62 " ideal model delta sigma weight residual 112.90 105.55 7.35 1.31e+00 5.83e-01 3.15e+01 angle pdb=" N ARG B 62 " pdb=" CA ARG B 62 " pdb=" C ARG B 62 " ideal model delta sigma weight residual 112.90 105.58 7.32 1.31e+00 5.83e-01 3.12e+01 angle pdb=" N ARG L 62 " pdb=" CA ARG L 62 " pdb=" C ARG L 62 " ideal model delta sigma weight residual 112.90 105.58 7.32 1.31e+00 5.83e-01 3.12e+01 angle pdb=" N ARG J 62 " pdb=" CA ARG J 62 " pdb=" C ARG J 62 " ideal model delta sigma weight residual 112.90 105.58 7.32 1.31e+00 5.83e-01 3.12e+01 angle pdb=" N ARG D 62 " pdb=" CA ARG D 62 " pdb=" C ARG D 62 " ideal model delta sigma weight residual 112.90 105.61 7.29 1.31e+00 5.83e-01 3.10e+01 ... (remaining 7213 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.55: 2737 17.55 - 35.10: 215 35.10 - 52.65: 54 52.65 - 70.20: 12 70.20 - 87.75: 12 Dihedral angle restraints: 3030 sinusoidal: 1206 harmonic: 1824 Sorted by residual: dihedral pdb=" CA ASP L 60 " pdb=" CB ASP L 60 " pdb=" CG ASP L 60 " pdb=" OD1 ASP L 60 " ideal model delta sinusoidal sigma weight residual -30.00 -87.95 57.95 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP F 60 " pdb=" CB ASP F 60 " pdb=" CG ASP F 60 " pdb=" OD1 ASP F 60 " ideal model delta sinusoidal sigma weight residual -30.00 -87.94 57.94 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP D 60 " pdb=" CB ASP D 60 " pdb=" CG ASP D 60 " pdb=" OD1 ASP D 60 " ideal model delta sinusoidal sigma weight residual -30.00 -87.94 57.94 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 3027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 209 0.050 - 0.101: 202 0.101 - 0.151: 129 0.151 - 0.201: 54 0.201 - 0.252: 24 Chirality restraints: 618 Sorted by residual: chirality pdb=" CA GLU L 9 " pdb=" N GLU L 9 " pdb=" C GLU L 9 " pdb=" CB GLU L 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA GLU F 9 " pdb=" N GLU F 9 " pdb=" C GLU F 9 " pdb=" CB GLU F 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA GLU H 9 " pdb=" N GLU H 9 " pdb=" C GLU H 9 " pdb=" CB GLU H 9 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 615 not shown) Planarity restraints: 972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 10 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.85e+00 pdb=" C ALA B 10 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA B 10 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE B 11 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 10 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C ALA D 10 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA D 10 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE D 11 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 10 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C ALA J 10 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA J 10 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE J 11 " -0.018 2.00e-02 2.50e+03 ... (remaining 969 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2588 2.99 - 3.47: 4931 3.47 - 3.94: 9219 3.94 - 4.42: 10402 4.42 - 4.90: 19642 Nonbonded interactions: 46782 Sorted by model distance: nonbonded pdb=" OD2 ASP H 33 " pdb=" N SER K 2 " model vdw 2.509 3.120 nonbonded pdb=" OD2 ASP F 33 " pdb=" N SER I 2 " model vdw 2.509 3.120 nonbonded pdb=" OD2 ASP B 33 " pdb=" N SER E 2 " model vdw 2.509 3.120 nonbonded pdb=" OD2 ASP D 33 " pdb=" N SER G 2 " model vdw 2.509 3.120 nonbonded pdb=" N PHE A 36 " pdb=" O PHE A 36 " model vdw 2.526 2.496 ... (remaining 46777 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 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5134 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 : 0.013 0.051 5394 Z= 0.941 Angle : 1.999 7.348 7218 Z= 1.464 Chirality : 0.100 0.252 618 Planarity : 0.010 0.030 972 Dihedral : 15.174 87.747 1878 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % 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: -3.47 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 62 TYR 0.009 0.003 TYR C 21 PHE 0.021 0.003 PHE K 36 TRP 0.023 0.005 TRP A 18 HIS 0.002 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.01264 ( 5394) covalent geometry : angle 1.99915 ( 7218) hydrogen bonds : bond 0.18047 ( 25) hydrogen bonds : angle 7.96415 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.116 Fit side-chains REVERT: B 3 PHE cc_start: 0.6667 (m-10) cc_final: 0.6453 (m-80) REVERT: B 24 MET cc_start: 0.7434 (mmm) cc_final: 0.6930 (mtm) REVERT: B 39 ARG cc_start: 0.6256 (ttt180) cc_final: 0.5382 (ttt90) REVERT: B 56 GLU cc_start: 0.7174 (tt0) cc_final: 0.6770 (mt-10) REVERT: B 58 ILE cc_start: 0.7441 (mt) cc_final: 0.7124 (mp) REVERT: B 67 ARG cc_start: 0.7076 (mtt180) cc_final: 0.5907 (ttt-90) REVERT: A 12 ASP cc_start: 0.7747 (t70) cc_final: 0.7159 (m-30) REVERT: A 19 ARG cc_start: 0.7297 (mtt180) cc_final: 0.6914 (ttm110) REVERT: A 26 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6543 (mt-10) REVERT: A 33 ASP cc_start: 0.6762 (m-30) cc_final: 0.6500 (m-30) REVERT: D 19 ARG cc_start: 0.6184 (mtt180) cc_final: 0.5875 (mtt90) REVERT: D 67 ARG cc_start: 0.5640 (mtt180) cc_final: 0.4634 (tmt90) REVERT: C 18 TRP cc_start: 0.6658 (t60) cc_final: 0.6105 (t60) REVERT: C 19 ARG cc_start: 0.6388 (mtt180) cc_final: 0.5566 (ttm-80) REVERT: C 24 MET cc_start: 0.6708 (mtt) cc_final: 0.6393 (mmm) REVERT: F 56 GLU cc_start: 0.6344 (tt0) cc_final: 0.5659 (mt-10) REVERT: F 58 ILE cc_start: 0.5875 (mt) cc_final: 0.5612 (mp) REVERT: F 67 ARG cc_start: 0.5810 (mtt180) cc_final: 0.4816 (tmt90) REVERT: E 19 ARG cc_start: 0.6107 (mtt180) cc_final: 0.5839 (ttm170) REVERT: E 24 MET cc_start: 0.6857 (mtt) cc_final: 0.6599 (mtp) REVERT: E 32 SER cc_start: 0.6455 (p) cc_final: 0.6221 (m) REVERT: H 26 GLU cc_start: 0.5532 (mt-10) cc_final: 0.5211 (mt-10) REVERT: H 63 GLU cc_start: 0.6532 (tt0) cc_final: 0.6315 (tt0) REVERT: H 67 ARG cc_start: 0.5664 (mtt180) cc_final: 0.4591 (tmt90) REVERT: G 24 MET cc_start: 0.6749 (mtt) cc_final: 0.6336 (mmm) REVERT: G 26 GLU cc_start: 0.5505 (mt-10) cc_final: 0.5302 (mt-10) REVERT: G 32 SER cc_start: 0.6653 (p) cc_final: 0.6398 (m) REVERT: J 26 GLU cc_start: 0.5319 (mt-10) cc_final: 0.5023 (mt-10) REVERT: J 56 GLU cc_start: 0.6375 (tt0) cc_final: 0.5732 (mt-10) REVERT: J 58 ILE cc_start: 0.6028 (mt) cc_final: 0.5717 (mp) REVERT: J 67 ARG cc_start: 0.5572 (mtt180) cc_final: 0.4321 (tmt90) REVERT: I 12 ASP cc_start: 0.6837 (t70) cc_final: 0.6189 (m-30) REVERT: I 19 ARG cc_start: 0.6062 (mtt180) cc_final: 0.5739 (ttm110) REVERT: I 25 ARG cc_start: 0.5714 (mtt180) cc_final: 0.5456 (mtm-85) REVERT: I 26 GLU cc_start: 0.5572 (mt-10) cc_final: 0.5259 (mt-10) REVERT: L 9 GLU cc_start: 0.6021 (mt-10) cc_final: 0.5568 (tt0) REVERT: L 23 ASP cc_start: 0.7195 (t0) cc_final: 0.6976 (t0) REVERT: L 39 ARG cc_start: 0.6916 (ttt180) cc_final: 0.6507 (ttp-170) REVERT: L 63 GLU cc_start: 0.6438 (tt0) cc_final: 0.6135 (tt0) REVERT: L 67 ARG cc_start: 0.6131 (mtt180) cc_final: 0.5120 (ttt90) REVERT: K 12 ASP cc_start: 0.7078 (t70) cc_final: 0.6431 (m-30) REVERT: K 22 SER cc_start: 0.7753 (p) cc_final: 0.7337 (t) REVERT: K 23 ASP cc_start: 0.6222 (t0) cc_final: 0.4794 (t0) REVERT: K 24 MET cc_start: 0.7613 (mtt) cc_final: 0.6947 (mmm) REVERT: K 25 ARG cc_start: 0.6168 (mtt180) cc_final: 0.5112 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.5903 time to fit residues: 143.9357 Evaluate side-chains 178 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 HIS ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 41 ASN K 37 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.152998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.131078 restraints weight = 6440.005| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.14 r_work: 0.3837 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5394 Z= 0.119 Angle : 0.557 6.738 7218 Z= 0.315 Chirality : 0.038 0.136 618 Planarity : 0.003 0.028 972 Dihedral : 4.611 13.029 738 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.04 % Allowed : 20.00 % Favored : 78.96 % 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: -3.11 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 39 TYR 0.017 0.002 TYR F 42 PHE 0.025 0.002 PHE E 36 TRP 0.016 0.002 TRP I 18 HIS 0.005 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5394) covalent geometry : angle 0.55746 ( 7218) hydrogen bonds : bond 0.02765 ( 25) hydrogen bonds : angle 4.81058 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 0.157 Fit side-chains REVERT: B 39 ARG cc_start: 0.8059 (ttt180) cc_final: 0.7382 (ttt90) REVERT: B 46 LYS cc_start: 0.8149 (mttt) cc_final: 0.7932 (mtpm) REVERT: B 67 ARG cc_start: 0.8359 (mtt180) cc_final: 0.7505 (ttt90) REVERT: A 17 MET cc_start: 0.8061 (ttp) cc_final: 0.7784 (ttp) REVERT: D 19 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8187 (mtt90) REVERT: D 67 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7028 (tmt90) REVERT: F 56 GLU cc_start: 0.8099 (tt0) cc_final: 0.7858 (mt-10) REVERT: F 58 ILE cc_start: 0.8529 (mt) cc_final: 0.8306 (mp) REVERT: F 67 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7044 (ttt90) REVERT: H 46 LYS cc_start: 0.7997 (mttt) cc_final: 0.7654 (mtpm) REVERT: H 67 ARG cc_start: 0.7789 (mtt180) cc_final: 0.7052 (ttt90) REVERT: G 21 TYR cc_start: 0.7563 (m-80) cc_final: 0.7203 (m-80) REVERT: J 58 ILE cc_start: 0.8610 (mt) cc_final: 0.8325 (mp) REVERT: L 67 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7298 (ttt90) REVERT: K 23 ASP cc_start: 0.8461 (t0) cc_final: 0.8227 (t0) REVERT: K 25 ARG cc_start: 0.8134 (mtt180) cc_final: 0.7519 (mmt180) REVERT: K 34 LYS cc_start: 0.8389 (tttt) cc_final: 0.7807 (tptp) outliers start: 5 outliers final: 3 residues processed: 164 average time/residue: 0.6549 time to fit residues: 110.7876 Evaluate side-chains 143 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain K residue 32 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 39 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.132054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.110854 restraints weight = 6368.611| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.06 r_work: 0.3550 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 5394 Z= 0.417 Angle : 0.775 8.317 7218 Z= 0.444 Chirality : 0.045 0.142 618 Planarity : 0.006 0.038 972 Dihedral : 6.582 22.718 738 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.58 % Allowed : 20.42 % Favored : 75.00 % 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: -3.38 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 25 TYR 0.022 0.003 TYR K 29 PHE 0.040 0.004 PHE F 6 TRP 0.015 0.003 TRP E 18 HIS 0.004 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00909 ( 5394) covalent geometry : angle 0.77498 ( 7218) hydrogen bonds : bond 0.03711 ( 25) hydrogen bonds : angle 4.82679 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8447 (m-80) cc_final: 0.8001 (m-80) REVERT: D 3 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: F 47 ARG cc_start: 0.8039 (tpp-160) cc_final: 0.7676 (mmt180) REVERT: H 47 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7251 (mtm-85) REVERT: H 60 ASP cc_start: 0.7970 (t0) cc_final: 0.7735 (t70) REVERT: G 34 LYS cc_start: 0.8215 (tttt) cc_final: 0.7559 (mttt) REVERT: J 46 LYS cc_start: 0.8630 (mttt) cc_final: 0.8358 (ttmt) REVERT: I 12 ASP cc_start: 0.8202 (t70) cc_final: 0.7830 (m-30) REVERT: L 47 ARG cc_start: 0.8330 (mpt180) cc_final: 0.7945 (tpt170) REVERT: K 9 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7690 (mm-30) REVERT: K 12 ASP cc_start: 0.8348 (t0) cc_final: 0.7741 (m-30) REVERT: K 26 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8429 (mt-10) REVERT: K 34 LYS cc_start: 0.8511 (tttt) cc_final: 0.7899 (tmtt) outliers start: 22 outliers final: 8 residues processed: 190 average time/residue: 0.6205 time to fit residues: 121.6454 Evaluate side-chains 175 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.141765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.121298 restraints weight = 6336.382| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.06 r_work: 0.3737 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5394 Z= 0.104 Angle : 0.520 7.275 7218 Z= 0.286 Chirality : 0.038 0.138 618 Planarity : 0.003 0.026 972 Dihedral : 4.838 14.915 738 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.50 % Allowed : 21.67 % Favored : 75.83 % 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: -3.17 (0.27), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 19 TYR 0.013 0.001 TYR H 42 PHE 0.020 0.002 PHE E 36 TRP 0.012 0.001 TRP I 18 HIS 0.002 0.000 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 5394) covalent geometry : angle 0.52049 ( 7218) hydrogen bonds : bond 0.02156 ( 25) hydrogen bonds : angle 4.22822 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8269 (m-80) cc_final: 0.7983 (m-80) REVERT: D 63 GLU cc_start: 0.7852 (tt0) cc_final: 0.7398 (mt-10) REVERT: F 47 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7443 (mmt180) REVERT: F 56 GLU cc_start: 0.8256 (tt0) cc_final: 0.8052 (mt-10) REVERT: H 39 ARG cc_start: 0.8147 (ttt90) cc_final: 0.7937 (ttp-170) REVERT: H 47 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6924 (mtm-85) REVERT: H 60 ASP cc_start: 0.7960 (t0) cc_final: 0.7661 (t70) REVERT: H 63 GLU cc_start: 0.7888 (tt0) cc_final: 0.7491 (mt-10) REVERT: G 12 ASP cc_start: 0.8300 (t0) cc_final: 0.7684 (m-30) REVERT: J 46 LYS cc_start: 0.8543 (mttt) cc_final: 0.8337 (ttmt) REVERT: J 60 ASP cc_start: 0.7953 (t0) cc_final: 0.7705 (t70) REVERT: K 9 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: K 12 ASP cc_start: 0.8369 (t0) cc_final: 0.7795 (m-30) REVERT: K 25 ARG cc_start: 0.8996 (mtt90) cc_final: 0.7500 (mmt180) REVERT: K 34 LYS cc_start: 0.8566 (tttt) cc_final: 0.7822 (tptp) outliers start: 12 outliers final: 2 residues processed: 161 average time/residue: 0.6969 time to fit residues: 115.4767 Evaluate side-chains 150 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.132342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.111631 restraints weight = 6467.310| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.06 r_work: 0.3586 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5394 Z= 0.279 Angle : 0.655 8.604 7218 Z= 0.367 Chirality : 0.042 0.141 618 Planarity : 0.004 0.022 972 Dihedral : 5.841 19.741 738 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.00 % Allowed : 23.12 % Favored : 71.88 % 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: -3.40 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 19 TYR 0.015 0.002 TYR F 42 PHE 0.025 0.003 PHE F 6 TRP 0.011 0.002 TRP J 18 HIS 0.008 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 5394) covalent geometry : angle 0.65542 ( 7218) hydrogen bonds : bond 0.03049 ( 25) hydrogen bonds : angle 4.59387 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 PHE cc_start: 0.7421 (m-80) cc_final: 0.7179 (m-10) REVERT: A 21 TYR cc_start: 0.8330 (m-80) cc_final: 0.7964 (m-80) REVERT: D 3 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7781 (m-10) REVERT: D 63 GLU cc_start: 0.7844 (tt0) cc_final: 0.7492 (mt-10) REVERT: F 47 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7628 (mmt180) REVERT: H 3 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.7947 (m-10) REVERT: H 39 ARG cc_start: 0.8185 (ttt90) cc_final: 0.7974 (ttp-170) REVERT: H 47 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7261 (mtm-85) REVERT: H 60 ASP cc_start: 0.7882 (t0) cc_final: 0.7642 (t70) REVERT: H 63 GLU cc_start: 0.7949 (tt0) cc_final: 0.7557 (mt-10) REVERT: G 12 ASP cc_start: 0.8351 (t0) cc_final: 0.7703 (m-30) REVERT: G 34 LYS cc_start: 0.8089 (tttt) cc_final: 0.7498 (mttt) REVERT: I 12 ASP cc_start: 0.8357 (t0) cc_final: 0.7736 (m-30) REVERT: L 63 GLU cc_start: 0.7934 (tt0) cc_final: 0.7689 (mt-10) REVERT: K 9 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7581 (mm-30) REVERT: K 12 ASP cc_start: 0.8311 (t0) cc_final: 0.7749 (m-30) REVERT: K 25 ARG cc_start: 0.8986 (mtt90) cc_final: 0.7492 (mmt-90) outliers start: 24 outliers final: 8 residues processed: 183 average time/residue: 0.6764 time to fit residues: 127.6073 Evaluate side-chains 173 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 32 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.134235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.113422 restraints weight = 6314.044| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.04 r_work: 0.3617 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5394 Z= 0.207 Angle : 0.614 8.444 7218 Z= 0.339 Chirality : 0.041 0.131 618 Planarity : 0.003 0.027 972 Dihedral : 5.577 17.841 738 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.96 % Allowed : 23.33 % Favored : 72.71 % 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: -3.48 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 19 TYR 0.014 0.002 TYR H 42 PHE 0.020 0.002 PHE E 36 TRP 0.009 0.002 TRP I 18 HIS 0.004 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 5394) covalent geometry : angle 0.61424 ( 7218) hydrogen bonds : bond 0.02933 ( 25) hydrogen bonds : angle 4.58608 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8293 (m-80) cc_final: 0.7959 (m-80) REVERT: D 3 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7833 (m-10) REVERT: D 63 GLU cc_start: 0.7885 (tt0) cc_final: 0.7525 (mt-10) REVERT: H 3 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: H 47 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7238 (mtm-85) REVERT: H 60 ASP cc_start: 0.7973 (t0) cc_final: 0.7738 (t70) REVERT: H 63 GLU cc_start: 0.7925 (tt0) cc_final: 0.7573 (mt-10) REVERT: G 12 ASP cc_start: 0.8315 (t0) cc_final: 0.7693 (m-30) REVERT: G 34 LYS cc_start: 0.8084 (tttt) cc_final: 0.7499 (mttt) REVERT: J 63 GLU cc_start: 0.7892 (tt0) cc_final: 0.7434 (mt-10) REVERT: I 12 ASP cc_start: 0.8451 (t0) cc_final: 0.8225 (t0) REVERT: L 63 GLU cc_start: 0.7907 (tt0) cc_final: 0.7697 (mt-10) REVERT: K 9 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: K 12 ASP cc_start: 0.8358 (t0) cc_final: 0.7808 (m-30) REVERT: K 25 ARG cc_start: 0.8985 (mtt90) cc_final: 0.7498 (mmt-90) REVERT: K 34 LYS cc_start: 0.8374 (tttt) cc_final: 0.7713 (mttt) outliers start: 19 outliers final: 8 residues processed: 174 average time/residue: 0.7033 time to fit residues: 126.0155 Evaluate side-chains 171 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 32 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.136051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.115188 restraints weight = 6302.871| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.06 r_work: 0.3641 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5394 Z= 0.167 Angle : 0.590 8.470 7218 Z= 0.320 Chirality : 0.040 0.131 618 Planarity : 0.003 0.019 972 Dihedral : 5.282 16.797 738 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.54 % Allowed : 23.75 % Favored : 72.71 % 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: -3.50 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.014 0.001 TYR F 42 PHE 0.018 0.002 PHE I 36 TRP 0.009 0.001 TRP I 18 HIS 0.003 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5394) covalent geometry : angle 0.58986 ( 7218) hydrogen bonds : bond 0.02667 ( 25) hydrogen bonds : angle 4.48897 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8312 (m-80) cc_final: 0.7977 (m-80) REVERT: D 63 GLU cc_start: 0.7827 (tt0) cc_final: 0.7492 (mt-10) REVERT: F 63 GLU cc_start: 0.7511 (tt0) cc_final: 0.7163 (mt-10) REVERT: H 47 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7179 (mtm-85) REVERT: H 60 ASP cc_start: 0.7956 (t0) cc_final: 0.7732 (t70) REVERT: H 63 GLU cc_start: 0.7866 (tt0) cc_final: 0.7525 (mt-10) REVERT: G 12 ASP cc_start: 0.8301 (t0) cc_final: 0.8087 (t0) REVERT: G 34 LYS cc_start: 0.8073 (tttt) cc_final: 0.7534 (mttt) REVERT: J 63 GLU cc_start: 0.7858 (tt0) cc_final: 0.7496 (mt-10) REVERT: L 63 GLU cc_start: 0.7896 (tt0) cc_final: 0.7633 (mt-10) REVERT: K 9 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: K 12 ASP cc_start: 0.8459 (t0) cc_final: 0.8229 (t0) REVERT: K 34 LYS cc_start: 0.8341 (tttt) cc_final: 0.7678 (mttt) outliers start: 17 outliers final: 6 residues processed: 166 average time/residue: 0.7113 time to fit residues: 121.3380 Evaluate side-chains 161 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 32 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 0.1980 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.131378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.110576 restraints weight = 6259.473| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.02 r_work: 0.3575 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 5394 Z= 0.322 Angle : 0.708 9.117 7218 Z= 0.395 Chirality : 0.044 0.150 618 Planarity : 0.004 0.026 972 Dihedral : 6.122 21.549 738 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.75 % Allowed : 25.00 % Favored : 71.25 % 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: -3.68 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 39 TYR 0.017 0.002 TYR J 35 PHE 0.025 0.003 PHE B 6 TRP 0.009 0.002 TRP A 18 HIS 0.005 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00697 ( 5394) covalent geometry : angle 0.70835 ( 7218) hydrogen bonds : bond 0.03401 ( 25) hydrogen bonds : angle 4.98279 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 12 ASP cc_start: 0.8527 (t70) cc_final: 0.8213 (m-30) REVERT: A 21 TYR cc_start: 0.8315 (m-80) cc_final: 0.8002 (m-80) REVERT: D 3 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7701 (m-80) REVERT: D 39 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7771 (ttp80) REVERT: D 63 GLU cc_start: 0.7905 (tt0) cc_final: 0.7566 (mt-10) REVERT: F 47 ARG cc_start: 0.8131 (mpt180) cc_final: 0.7851 (mmt180) REVERT: F 63 GLU cc_start: 0.7595 (tt0) cc_final: 0.7166 (mt-10) REVERT: H 3 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: H 47 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7274 (mtm-85) REVERT: H 63 GLU cc_start: 0.7932 (tt0) cc_final: 0.7594 (mt-10) REVERT: G 12 ASP cc_start: 0.8336 (t0) cc_final: 0.8128 (t0) REVERT: G 34 LYS cc_start: 0.8189 (tttt) cc_final: 0.7568 (mttt) REVERT: J 63 GLU cc_start: 0.7883 (tt0) cc_final: 0.7503 (mt-10) REVERT: I 26 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8282 (mt-10) REVERT: L 63 GLU cc_start: 0.7870 (tt0) cc_final: 0.7650 (mt-10) REVERT: K 9 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: K 34 LYS cc_start: 0.8315 (tttt) cc_final: 0.7657 (mttt) outliers start: 18 outliers final: 8 residues processed: 175 average time/residue: 0.8033 time to fit residues: 144.5280 Evaluate side-chains 175 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.134696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.113874 restraints weight = 6260.039| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.04 r_work: 0.3623 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3496 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5394 Z= 0.193 Angle : 0.632 9.082 7218 Z= 0.344 Chirality : 0.041 0.135 618 Planarity : 0.003 0.027 972 Dihedral : 5.570 17.170 738 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 4.17 % Allowed : 25.83 % Favored : 70.00 % 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: -3.67 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 25 TYR 0.015 0.001 TYR F 42 PHE 0.018 0.002 PHE E 36 TRP 0.009 0.001 TRP I 18 HIS 0.004 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5394) covalent geometry : angle 0.63210 ( 7218) hydrogen bonds : bond 0.02838 ( 25) hydrogen bonds : angle 4.76254 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8295 (m-80) cc_final: 0.7977 (m-80) REVERT: D 3 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7841 (m-10) REVERT: D 39 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7788 (ttp80) REVERT: D 63 GLU cc_start: 0.7961 (tt0) cc_final: 0.7615 (mt-10) REVERT: F 63 GLU cc_start: 0.7668 (tt0) cc_final: 0.7229 (mt-10) REVERT: H 3 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: H 47 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7201 (mtm-85) REVERT: H 63 GLU cc_start: 0.7839 (tt0) cc_final: 0.7588 (mt-10) REVERT: G 12 ASP cc_start: 0.8309 (t0) cc_final: 0.8108 (t0) REVERT: G 34 LYS cc_start: 0.8140 (tttt) cc_final: 0.7540 (mttt) REVERT: J 63 GLU cc_start: 0.7874 (tt0) cc_final: 0.7508 (mt-10) REVERT: I 26 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8295 (mt-10) REVERT: L 63 GLU cc_start: 0.7885 (tt0) cc_final: 0.7651 (mt-10) REVERT: K 9 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: K 12 ASP cc_start: 0.8452 (t0) cc_final: 0.8234 (t0) REVERT: K 25 ARG cc_start: 0.8990 (mtt90) cc_final: 0.7481 (mmt-90) REVERT: K 34 LYS cc_start: 0.8334 (tttt) cc_final: 0.7659 (mttt) outliers start: 20 outliers final: 6 residues processed: 172 average time/residue: 0.7949 time to fit residues: 140.5696 Evaluate side-chains 168 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.0570 chunk 11 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.134303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.113481 restraints weight = 6314.990| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.05 r_work: 0.3618 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.6764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5394 Z= 0.204 Angle : 0.648 9.704 7218 Z= 0.351 Chirality : 0.041 0.134 618 Planarity : 0.003 0.029 972 Dihedral : 5.615 17.186 738 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.92 % Allowed : 28.54 % Favored : 68.54 % 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: -3.73 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.013 0.001 TYR J 35 PHE 0.019 0.002 PHE E 36 TRP 0.010 0.002 TRP I 18 HIS 0.004 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 5394) covalent geometry : angle 0.64815 ( 7218) hydrogen bonds : bond 0.02879 ( 25) hydrogen bonds : angle 4.82569 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8270 (m-80) cc_final: 0.7946 (m-80) REVERT: D 3 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7861 (m-10) REVERT: D 39 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7735 (ttp80) REVERT: D 63 GLU cc_start: 0.7940 (tt0) cc_final: 0.7616 (mt-10) REVERT: F 63 GLU cc_start: 0.7668 (tt0) cc_final: 0.7252 (mt-10) REVERT: H 3 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: H 47 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7218 (mtm-85) REVERT: H 63 GLU cc_start: 0.7763 (tt0) cc_final: 0.7541 (mt-10) REVERT: G 12 ASP cc_start: 0.8302 (t0) cc_final: 0.8096 (t0) REVERT: G 34 LYS cc_start: 0.8132 (tttt) cc_final: 0.7526 (mttt) REVERT: J 63 GLU cc_start: 0.7870 (tt0) cc_final: 0.7536 (mt-10) REVERT: L 63 GLU cc_start: 0.7861 (tt0) cc_final: 0.7635 (mt-10) REVERT: K 9 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: K 12 ASP cc_start: 0.8485 (t0) cc_final: 0.8230 (t0) REVERT: K 25 ARG cc_start: 0.8964 (mtt90) cc_final: 0.7371 (mmt-90) REVERT: K 34 LYS cc_start: 0.8320 (tttt) cc_final: 0.7650 (mttt) outliers start: 14 outliers final: 7 residues processed: 161 average time/residue: 0.7885 time to fit residues: 130.6347 Evaluate side-chains 164 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain D residue 3 PHE Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain C residue 5 SER Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain F residue 3 PHE Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain G residue 24 MET Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 5 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.136192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115350 restraints weight = 6313.889| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.06 r_work: 0.3656 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.6754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5394 Z= 0.156 Angle : 0.602 9.590 7218 Z= 0.326 Chirality : 0.040 0.132 618 Planarity : 0.003 0.034 972 Dihedral : 5.289 17.478 738 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.50 % Allowed : 29.17 % Favored : 68.33 % 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: -3.71 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 25 TYR 0.017 0.001 TYR F 42 PHE 0.018 0.002 PHE I 36 TRP 0.010 0.001 TRP I 18 HIS 0.003 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5394) covalent geometry : angle 0.60245 ( 7218) hydrogen bonds : bond 0.02585 ( 25) hydrogen bonds : angle 4.71819 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2743.52 seconds wall clock time: 47 minutes 15.13 seconds (2835.13 seconds total)