Starting phenix.real_space_refine on Thu Mar 6 06:09:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zky_14771/03_2025/7zky_14771.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zky_14771/03_2025/7zky_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_2025/7zky_14771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zky_14771/03_2025/7zky_14771.map" model { file = "/net/cci-nas-00/data/ceres_data/7zky_14771/03_2025/7zky_14771.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zky_14771/03_2025/7zky_14771.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, E, G, I, K, D, F, H, J, L Time building chain proxies: 2.85, per 1000 atoms: 0.54 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: 2.22 Conformation dependent library (CDL) restraints added in 636.7 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: 0.59 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: 1.56 Time building geometry restraints manager: 2.47 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 59.340 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 21.720 Find NCS groups from input model: 0.110 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:17.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.830 ------------------------------------------------------------------------------- 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= 0.837 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (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 TRP 0.023 0.005 TRP A 18 HIS 0.002 0.001 HIS G 37 PHE 0.021 0.003 PHE K 36 TYR 0.009 0.003 TYR C 21 ARG 0.003 0.001 ARG J 62 *********************** 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 : 0.687 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: 0.6374 (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: 1.4998 time to fit residues: 366.7434 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 : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.155427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.133494 restraints weight = 6423.908| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.14 r_work: 0.3877 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3756 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5394 Z= 0.157 Angle : 0.548 6.513 7218 Z= 0.309 Chirality : 0.039 0.143 618 Planarity : 0.003 0.030 972 Dihedral : 4.495 13.127 738 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.25 % Allowed : 19.58 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 18 HIS 0.005 0.001 HIS G 37 PHE 0.024 0.002 PHE E 36 TYR 0.016 0.002 TYR F 42 ARG 0.005 0.000 ARG H 39 *********************** 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 173 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 167 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: B 67 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7411 (ttt90) REVERT: A 17 MET cc_start: 0.8097 (ttp) cc_final: 0.7810 (ttp) REVERT: D 67 ARG cc_start: 0.7901 (mtt180) cc_final: 0.7000 (tmt90) REVERT: F 58 ILE cc_start: 0.8480 (mt) cc_final: 0.8260 (mp) REVERT: F 67 ARG cc_start: 0.7795 (mtt180) cc_final: 0.6955 (ttt90) REVERT: H 46 LYS cc_start: 0.7939 (mttt) cc_final: 0.7610 (mtpm) REVERT: H 67 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7036 (ttt90) REVERT: G 21 TYR cc_start: 0.7413 (m-80) cc_final: 0.7010 (m-80) REVERT: J 58 ILE cc_start: 0.8594 (mt) cc_final: 0.8316 (mp) REVERT: J 67 ARG cc_start: 0.7897 (mtt180) cc_final: 0.7100 (tmt90) REVERT: L 67 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7207 (tmt90) REVERT: K 34 LYS cc_start: 0.8354 (tttt) cc_final: 0.7778 (tptp) outliers start: 6 outliers final: 3 residues processed: 172 average time/residue: 1.4536 time to fit residues: 258.5451 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 : 0.557 ------------------------------------------------------------------------------- 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 9 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 46 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 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4009 r_free = 0.4009 target = 0.132597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.111392 restraints weight = 6379.745| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.06 r_work: 0.3564 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.6057 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= 0.580 Angle : 0.781 8.150 7218 Z= 0.447 Chirality : 0.045 0.147 618 Planarity : 0.006 0.059 972 Dihedral : 6.609 23.083 738 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.00 % Allowed : 20.83 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 18 HIS 0.005 0.001 HIS L 37 PHE 0.041 0.004 PHE B 6 TYR 0.023 0.003 TYR K 29 ARG 0.006 0.001 ARG D 19 *********************** 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 203 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8397 (m-80) cc_final: 0.8056 (m-80) REVERT: D 3 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.7748 (m-10) REVERT: C 12 ASP cc_start: 0.8290 (t0) cc_final: 0.7987 (t0) REVERT: F 47 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7717 (mmt180) REVERT: H 17 MET cc_start: 0.8868 (mmp) cc_final: 0.8655 (mmp) REVERT: H 39 ARG cc_start: 0.8210 (ttt90) cc_final: 0.7946 (ttp-170) REVERT: H 47 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7255 (mtm-85) REVERT: H 60 ASP cc_start: 0.7992 (t0) cc_final: 0.7780 (t70) REVERT: G 12 ASP cc_start: 0.8392 (t70) cc_final: 0.7684 (m-30) REVERT: G 34 LYS cc_start: 0.8191 (tttt) cc_final: 0.7547 (mttt) REVERT: J 46 LYS cc_start: 0.8621 (mttt) cc_final: 0.8384 (ttmt) REVERT: I 12 ASP cc_start: 0.8193 (t70) cc_final: 0.7827 (m-30) REVERT: L 47 ARG cc_start: 0.8373 (mpt180) cc_final: 0.8130 (mpt90) REVERT: K 9 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7713 (mm-30) REVERT: K 12 ASP cc_start: 0.8356 (t0) cc_final: 0.7742 (m-30) REVERT: K 26 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8430 (mt-10) REVERT: K 34 LYS cc_start: 0.8522 (tttt) cc_final: 0.7916 (tmtt) outliers start: 24 outliers final: 8 residues processed: 191 average time/residue: 1.9117 time to fit residues: 377.5951 Evaluate side-chains 179 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain K residue 32 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** 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** K 37 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.140494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.119848 restraints weight = 6466.450| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.07 r_work: 0.3714 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.6001 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= 0.157 Angle : 0.534 7.195 7218 Z= 0.293 Chirality : 0.038 0.128 618 Planarity : 0.003 0.039 972 Dihedral : 5.013 15.526 738 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.71 % Allowed : 22.92 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (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 TRP 0.011 0.001 TRP I 18 HIS 0.002 0.001 HIS G 37 PHE 0.020 0.002 PHE E 36 TYR 0.015 0.001 TYR H 42 ARG 0.004 0.000 ARG E 25 *********************** 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 170 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8333 (m-80) cc_final: 0.8017 (m-80) REVERT: F 16 ASP cc_start: 0.7299 (t0) cc_final: 0.6823 (t0) REVERT: F 47 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7431 (mmt180) REVERT: F 56 GLU cc_start: 0.8300 (tt0) cc_final: 0.8099 (tt0) REVERT: H 39 ARG cc_start: 0.8231 (ttt90) cc_final: 0.7982 (ttp-170) REVERT: H 47 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7016 (mtm-85) REVERT: H 60 ASP cc_start: 0.7950 (t0) cc_final: 0.7640 (t70) REVERT: J 60 ASP cc_start: 0.7970 (t0) cc_final: 0.7720 (t70) REVERT: K 9 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: K 12 ASP cc_start: 0.8297 (t0) cc_final: 0.7734 (m-30) REVERT: K 34 LYS cc_start: 0.8564 (tttt) cc_final: 0.7805 (tptp) outliers start: 13 outliers final: 2 residues processed: 164 average time/residue: 1.4756 time to fit residues: 249.5327 Evaluate side-chains 153 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain F residue 47 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 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** 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 = 0.4019 r_free = 0.4019 target = 0.131776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.111049 restraints weight = 6318.430| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.03 r_work: 0.3577 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 5394 Z= 0.464 Angle : 0.705 8.430 7218 Z= 0.396 Chirality : 0.043 0.158 618 Planarity : 0.004 0.022 972 Dihedral : 6.198 22.208 738 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 4.79 % Allowed : 23.12 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 18 HIS 0.008 0.001 HIS G 37 PHE 0.027 0.003 PHE F 6 TYR 0.014 0.002 TYR F 42 ARG 0.006 0.001 ARG D 19 *********************** 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 193 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.8477 (t70) cc_final: 0.8179 (m-30) REVERT: A 21 TYR cc_start: 0.8323 (m-80) cc_final: 0.7998 (m-80) REVERT: D 3 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: D 63 GLU cc_start: 0.7897 (tt0) cc_final: 0.7552 (mt-10) REVERT: F 47 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7652 (mmt180) REVERT: F 56 GLU cc_start: 0.8283 (tt0) cc_final: 0.8064 (tt0) REVERT: H 3 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.7961 (m-10) REVERT: H 47 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7286 (mtm-85) REVERT: H 60 ASP cc_start: 0.7882 (t0) cc_final: 0.7680 (t70) REVERT: H 63 GLU cc_start: 0.7954 (tt0) cc_final: 0.7555 (mt-10) REVERT: G 12 ASP cc_start: 0.8377 (t0) cc_final: 0.7715 (m-30) REVERT: G 34 LYS cc_start: 0.8137 (tttt) cc_final: 0.7537 (mttt) REVERT: I 12 ASP cc_start: 0.8388 (t0) cc_final: 0.7789 (m-30) REVERT: L 63 GLU cc_start: 0.7903 (tt0) cc_final: 0.7420 (mt-10) REVERT: K 9 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7625 (mm-30) REVERT: K 12 ASP cc_start: 0.8296 (t0) cc_final: 0.7761 (m-30) REVERT: K 34 LYS cc_start: 0.8450 (tttt) cc_final: 0.7863 (tmtt) outliers start: 23 outliers final: 9 residues processed: 185 average time/residue: 1.8842 time to fit residues: 360.8890 Evaluate side-chains 177 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 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 J residue 46 LYS Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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** ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.139581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.118883 restraints weight = 6322.079| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.06 r_work: 0.3708 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.6453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5394 Z= 0.161 Angle : 0.549 8.213 7218 Z= 0.296 Chirality : 0.038 0.128 618 Planarity : 0.002 0.017 972 Dihedral : 4.973 16.108 738 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.33 % Allowed : 23.54 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 18 HIS 0.003 0.001 HIS G 37 PHE 0.019 0.002 PHE I 36 TYR 0.015 0.001 TYR H 42 ARG 0.003 0.000 ARG D 19 *********************** 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 171 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8261 (m-80) cc_final: 0.7897 (m-80) REVERT: D 16 ASP cc_start: 0.8154 (m-30) cc_final: 0.7920 (m-30) REVERT: D 60 ASP cc_start: 0.7765 (t0) cc_final: 0.7556 (t70) REVERT: D 63 GLU cc_start: 0.7823 (tt0) cc_final: 0.7512 (mt-10) REVERT: F 63 GLU cc_start: 0.7409 (tt0) cc_final: 0.7094 (mt-10) REVERT: H 3 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: H 47 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7076 (mtm-85) REVERT: H 60 ASP cc_start: 0.7866 (t0) cc_final: 0.7614 (t70) REVERT: H 63 GLU cc_start: 0.7764 (tt0) cc_final: 0.7495 (mt-10) REVERT: G 12 ASP cc_start: 0.8312 (t0) cc_final: 0.7658 (m-30) REVERT: J 63 GLU cc_start: 0.7836 (tt0) cc_final: 0.7410 (mt-10) REVERT: L 63 GLU cc_start: 0.7818 (tt0) cc_final: 0.7481 (mt-10) REVERT: K 9 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7441 (mm-30) REVERT: K 34 LYS cc_start: 0.8503 (tttt) cc_final: 0.7802 (tptp) outliers start: 16 outliers final: 4 residues processed: 163 average time/residue: 1.4734 time to fit residues: 247.7792 Evaluate side-chains 157 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain D residue 39 ARG Chi-restraints excluded: chain H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 28 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** K 37 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.134831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.114011 restraints weight = 6232.035| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.04 r_work: 0.3631 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.6667 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= 0.280 Angle : 0.622 8.567 7218 Z= 0.340 Chirality : 0.040 0.125 618 Planarity : 0.003 0.022 972 Dihedral : 5.426 17.690 738 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 2.71 % Allowed : 25.62 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (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 TRP 0.008 0.002 TRP I 18 HIS 0.004 0.001 HIS G 37 PHE 0.019 0.002 PHE I 36 TYR 0.012 0.001 TYR J 42 ARG 0.005 0.000 ARG A 25 *********************** 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: 13 poor density : 160 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8377 (m-80) cc_final: 0.7912 (m-80) REVERT: D 39 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: D 63 GLU cc_start: 0.7819 (tt0) cc_final: 0.7496 (mt-10) REVERT: F 63 GLU cc_start: 0.7486 (tt0) cc_final: 0.7103 (mt-10) REVERT: H 3 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: H 47 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7194 (mtm-85) REVERT: H 60 ASP cc_start: 0.7963 (t0) cc_final: 0.7739 (t70) REVERT: H 63 GLU cc_start: 0.7866 (tt0) cc_final: 0.7548 (mt-10) REVERT: G 12 ASP cc_start: 0.8329 (t0) cc_final: 0.7690 (m-30) REVERT: G 34 LYS cc_start: 0.8122 (tttt) cc_final: 0.7528 (mttt) REVERT: J 63 GLU cc_start: 0.7832 (tt0) cc_final: 0.7469 (mt-10) REVERT: I 12 ASP cc_start: 0.8399 (t0) cc_final: 0.7772 (m-30) REVERT: L 63 GLU cc_start: 0.7893 (tt0) cc_final: 0.7526 (mt-10) REVERT: K 9 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: K 12 ASP cc_start: 0.8387 (t0) cc_final: 0.7770 (m-30) REVERT: K 34 LYS cc_start: 0.8413 (tttt) cc_final: 0.7719 (mttt) outliers start: 13 outliers final: 3 residues processed: 167 average time/residue: 1.4867 time to fit residues: 255.9582 Evaluate side-chains 164 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 157 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain D residue 39 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 46 LYS Chi-restraints excluded: chain K residue 9 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 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** H 28 ASN ** 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 37 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.130221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109498 restraints weight = 6367.872| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.03 r_work: 0.3561 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 5394 Z= 0.542 Angle : 0.773 8.985 7218 Z= 0.432 Chirality : 0.046 0.153 618 Planarity : 0.005 0.028 972 Dihedral : 6.357 21.161 738 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.58 % Allowed : 23.33 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.24), 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 TRP 0.011 0.002 TRP A 18 HIS 0.005 0.001 HIS G 37 PHE 0.029 0.004 PHE B 6 TYR 0.018 0.002 TYR J 35 ARG 0.005 0.001 ARG A 25 *********************** 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 191 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8405 (m-80) cc_final: 0.8015 (m-80) REVERT: D 3 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.7751 (m-10) REVERT: D 39 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7702 (ttp80) REVERT: D 56 GLU cc_start: 0.8494 (tt0) cc_final: 0.8285 (tt0) REVERT: D 63 GLU cc_start: 0.7944 (tt0) cc_final: 0.7584 (mt-10) REVERT: F 34 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8436 (mttm) REVERT: F 47 ARG cc_start: 0.8173 (mpt180) cc_final: 0.7913 (mmt180) REVERT: H 3 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7559 (m-80) REVERT: H 47 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7335 (mtm-85) REVERT: H 63 GLU cc_start: 0.7942 (tt0) cc_final: 0.7597 (mt-10) REVERT: G 12 ASP cc_start: 0.8369 (t0) cc_final: 0.7728 (m-30) REVERT: G 34 LYS cc_start: 0.8169 (tttt) cc_final: 0.7576 (mttt) REVERT: J 26 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: J 63 GLU cc_start: 0.7871 (tt0) cc_final: 0.7448 (mt-10) REVERT: I 26 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8233 (mt-10) REVERT: L 63 GLU cc_start: 0.7902 (tt0) cc_final: 0.7465 (mt-10) REVERT: K 9 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: K 12 ASP cc_start: 0.8365 (t0) cc_final: 0.7797 (m-30) outliers start: 22 outliers final: 4 residues processed: 179 average time/residue: 1.6406 time to fit residues: 302.3107 Evaluate side-chains 178 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 F residue 3 PHE Chi-restraints excluded: chain F residue 34 LYS 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 J residue 26 GLU 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 7 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.137323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116587 restraints weight = 6215.829| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.05 r_work: 0.3665 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.6758 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= 0.197 Angle : 0.616 9.113 7218 Z= 0.327 Chirality : 0.039 0.133 618 Planarity : 0.003 0.019 972 Dihedral : 5.239 17.888 738 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.12 % Allowed : 26.67 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 18 HIS 0.003 0.001 HIS G 37 PHE 0.018 0.002 PHE I 36 TYR 0.014 0.001 TYR F 42 ARG 0.004 0.000 ARG A 25 *********************** 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 172 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8383 (m-80) cc_final: 0.7943 (m-80) REVERT: D 3 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7970 (m-10) REVERT: D 39 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7789 (ttp80) REVERT: D 63 GLU cc_start: 0.7959 (tt0) cc_final: 0.7654 (mt-10) REVERT: F 63 GLU cc_start: 0.7638 (tt0) cc_final: 0.7258 (mt-10) REVERT: H 3 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: H 47 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7059 (mtm-85) REVERT: H 63 GLU cc_start: 0.7746 (tt0) cc_final: 0.7492 (mt-10) REVERT: G 12 ASP cc_start: 0.8323 (t0) cc_final: 0.7706 (m-30) REVERT: G 34 LYS cc_start: 0.8073 (tttt) cc_final: 0.7505 (mttt) REVERT: J 63 GLU cc_start: 0.7850 (tt0) cc_final: 0.7476 (mt-10) REVERT: L 63 GLU cc_start: 0.7843 (tt0) cc_final: 0.7515 (mt-10) REVERT: K 12 ASP cc_start: 0.8353 (t0) cc_final: 0.7761 (m-30) REVERT: K 34 LYS cc_start: 0.8384 (tttt) cc_final: 0.7684 (mttt) outliers start: 15 outliers final: 3 residues processed: 165 average time/residue: 1.5546 time to fit residues: 264.2981 Evaluate side-chains 162 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 3 PHE Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain J residue 3 PHE Chi-restraints excluded: chain J residue 46 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.132947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.112061 restraints weight = 6301.474| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.05 r_work: 0.3598 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 5394 Z= 0.361 Angle : 0.694 9.439 7218 Z= 0.378 Chirality : 0.042 0.148 618 Planarity : 0.004 0.027 972 Dihedral : 5.842 18.720 738 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.12 % Allowed : 27.29 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 18 HIS 0.005 0.001 HIS G 37 PHE 0.022 0.003 PHE J 6 TYR 0.016 0.002 TYR J 35 ARG 0.004 0.000 ARG A 25 ********************** 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 172 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8412 (m-80) cc_final: 0.7981 (m-80) REVERT: D 3 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7882 (m-10) REVERT: D 39 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7746 (ttp80) REVERT: D 63 GLU cc_start: 0.7924 (tt0) cc_final: 0.7620 (mt-10) REVERT: F 63 GLU cc_start: 0.7695 (tt0) cc_final: 0.7241 (mt-10) REVERT: H 3 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7457 (m-80) REVERT: H 47 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7243 (mtm-85) REVERT: H 63 GLU cc_start: 0.7837 (tt0) cc_final: 0.7557 (mt-10) REVERT: G 12 ASP cc_start: 0.8357 (t0) cc_final: 0.7736 (m-30) REVERT: G 34 LYS cc_start: 0.8127 (tttt) cc_final: 0.7532 (mttt) REVERT: J 63 GLU cc_start: 0.7879 (tt0) cc_final: 0.7492 (mt-10) REVERT: L 63 GLU cc_start: 0.7850 (tt0) cc_final: 0.7461 (mt-10) REVERT: K 9 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: K 12 ASP cc_start: 0.8351 (t0) cc_final: 0.7799 (m-30) REVERT: K 34 LYS cc_start: 0.8351 (tttt) cc_final: 0.7638 (mttt) outliers start: 15 outliers final: 7 residues processed: 165 average time/residue: 1.5751 time to fit residues: 267.7741 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 : 0.546 ------------------------------------------------------------------------------- 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 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 J residue 46 LYS Chi-restraints excluded: chain L 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 30 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.134689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.113887 restraints weight = 6265.301| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.05 r_work: 0.3623 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5394 Z= 0.302 Angle : 0.671 9.355 7218 Z= 0.362 Chirality : 0.041 0.134 618 Planarity : 0.003 0.023 972 Dihedral : 5.684 17.919 738 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.12 % Allowed : 27.71 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.24), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 18 HIS 0.004 0.001 HIS G 37 PHE 0.019 0.002 PHE E 36 TYR 0.015 0.002 TYR J 35 ARG 0.004 0.000 ARG A 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6204.67 seconds wall clock time: 109 minutes 1.13 seconds (6541.13 seconds total)