Starting phenix.real_space_refine on Thu Dec 7 22:14:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/12_2023/7zky_14771.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/12_2023/7zky_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/12_2023/7zky_14771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/12_2023/7zky_14771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/12_2023/7zky_14771.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zky_14771/12_2023/7zky_14771.pdb" } 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 Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 26": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 19": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H GLU 26": "OE1" <-> "OE2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H ARG 47": "NH1" <-> "NH2" Residue "H PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G ARG 19": "NH1" <-> "NH2" Residue "J ARG 15": "NH1" <-> "NH2" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J ARG 39": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 15": "NH1" <-> "NH2" Residue "I ARG 19": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "L GLU 26": "OE1" <-> "OE2" Residue "L ARG 39": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 15": "NH1" <-> "NH2" Residue "K ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5238 Number of models: 1 Model: "" Number of chains: 12 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} Chain: "D" 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: "C" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "F" 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: "E" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "H" 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: "G" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "J" 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: "I" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "L" 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: "K" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 323 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Time building chain proxies: 3.06, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 914.4 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: 0.52 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: 1.02 Time building geometry restraints manager: 2.06 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: 100.83 - 107.56: 295 107.56 - 114.30: 2217 114.30 - 121.03: 2835 121.03 - 127.77: 1817 127.77 - 134.50: 54 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 2.520 nonbonded pdb=" OD2 ASP F 33 " pdb=" N SER I 2 " model vdw 2.509 2.520 nonbonded pdb=" OD2 ASP B 33 " pdb=" N SER E 2 " model vdw 2.509 2.520 nonbonded pdb=" OD2 ASP D 33 " pdb=" N SER G 2 " model vdw 2.509 2.520 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 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: 0.710 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: 3.580 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.200 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 0.611 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 1.2279 time to fit residues: 300.3548 Evaluate side-chains 174 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7416 ------------------------------------------------------------------------------- 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: 0.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5246 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 5394 Z= 0.144 Angle : 0.546 6.712 7218 Z= 0.306 Chirality : 0.038 0.138 618 Planarity : 0.003 0.032 972 Dihedral : 4.422 12.804 738 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.33 % Allowed : 21.88 % Favored : 74.79 % 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 (0.27), 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 0.017 0.002 TRP K 18 HIS 0.005 0.001 HIS G 37 PHE 0.025 0.002 PHE E 36 TYR 0.018 0.002 TYR F 42 ARG 0.007 0.000 ARG I 25 *********************** 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 177 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 0.612 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 168 average time/residue: 1.3735 time to fit residues: 238.6704 Evaluate side-chains 146 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.1355 time to fit residues: 1.6553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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** ** F 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5393 moved from start: 0.6167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5394 Z= 0.328 Angle : 0.658 8.361 7218 Z= 0.369 Chirality : 0.041 0.137 618 Planarity : 0.004 0.043 972 Dihedral : 5.607 18.887 738 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.58 % Allowed : 22.71 % 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 (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: -3.31 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 18 HIS 0.003 0.001 HIS G 37 PHE 0.025 0.003 PHE F 6 TYR 0.013 0.002 TYR E 21 ARG 0.006 0.001 ARG F 67 *********************** 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 183 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 174 average time/residue: 1.4847 time to fit residues: 266.4551 Evaluate side-chains 163 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.5225 time to fit residues: 2.9397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 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 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** K 37 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5405 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5394 Z= 0.405 Angle : 0.685 8.122 7218 Z= 0.387 Chirality : 0.042 0.159 618 Planarity : 0.004 0.036 972 Dihedral : 5.977 21.545 738 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.42 % Allowed : 23.54 % Favored : 71.04 % 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: -3.46 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 18 HIS 0.003 0.001 HIS G 37 PHE 0.031 0.003 PHE D 3 TYR 0.016 0.002 TYR K 29 ARG 0.006 0.001 ARG J 67 *********************** 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 195 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 0.600 Fit side-chains outliers start: 26 outliers final: 13 residues processed: 180 average time/residue: 1.5185 time to fit residues: 281.8525 Evaluate side-chains 176 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 163 time to evaluate : 0.577 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.6696 time to fit residues: 5.0542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5370 moved from start: 0.6720 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= 0.194 Angle : 0.564 8.032 7218 Z= 0.308 Chirality : 0.038 0.126 618 Planarity : 0.003 0.033 972 Dihedral : 5.120 18.749 738 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.38 % Allowed : 25.83 % Favored : 69.79 % 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: -3.38 (0.26), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.20), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 18 HIS 0.002 0.001 HIS G 37 PHE 0.021 0.002 PHE H 3 TYR 0.012 0.001 TYR F 42 ARG 0.008 0.000 ARG J 67 *********************** 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 181 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 0.589 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 171 average time/residue: 1.4606 time to fit residues: 257.7086 Evaluate side-chains 169 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 0.593 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.1482 time to fit residues: 1.4997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- 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 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** K 37 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 5394 Z= 0.521 Angle : 0.769 8.796 7218 Z= 0.432 Chirality : 0.044 0.170 618 Planarity : 0.005 0.052 972 Dihedral : 6.337 23.507 738 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 5.42 % Allowed : 26.67 % Favored : 67.92 % 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 0.002 TRP I 18 HIS 0.007 0.002 HIS G 37 PHE 0.031 0.004 PHE H 3 TYR 0.014 0.002 TYR C 29 ARG 0.014 0.001 ARG J 67 *********************** 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 201 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 0.560 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 186 average time/residue: 1.4081 time to fit residues: 270.7433 Evaluate side-chains 182 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 0.612 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 7 residues processed: 7 average time/residue: 0.8324 time to fit residues: 6.9328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5384 moved from start: 0.7129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5394 Z= 0.175 Angle : 0.575 8.500 7218 Z= 0.308 Chirality : 0.038 0.129 618 Planarity : 0.002 0.019 972 Dihedral : 5.023 17.229 738 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.71 % Allowed : 28.96 % 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 (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: -3.53 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.19), 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 0.020 0.002 PHE H 3 TYR 0.011 0.001 TYR A 21 ARG 0.006 0.000 ARG J 67 *********************** 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 fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 169 average time/residue: 1.5107 time to fit residues: 263.3824 Evaluate side-chains 169 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 158 time to evaluate : 0.567 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.1983 time to fit residues: 1.4855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 48 optimal weight: 0.0870 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5415 moved from start: 0.7253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5394 Z= 0.322 Angle : 0.675 9.095 7218 Z= 0.366 Chirality : 0.041 0.139 618 Planarity : 0.004 0.073 972 Dihedral : 5.645 20.257 738 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 3.33 % Allowed : 29.58 % Favored : 67.08 % 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: -3.66 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 18 HIS 0.004 0.001 HIS G 37 PHE 0.032 0.003 PHE H 3 TYR 0.012 0.001 TYR H 42 ARG 0.018 0.001 ARG L 67 *********************** 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 fitting. rotamer outliers: 16 poor density : 168 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 175 average time/residue: 1.4567 time to fit residues: 263.1069 Evaluate side-chains 176 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 0.511 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.4640 time to fit residues: 2.6842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5392 moved from start: 0.7262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5394 Z= 0.200 Angle : 0.605 8.793 7218 Z= 0.321 Chirality : 0.039 0.130 618 Planarity : 0.003 0.037 972 Dihedral : 5.038 16.835 738 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.71 % Allowed : 30.00 % Favored : 67.29 % 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: -3.62 (0.25), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 18 HIS 0.003 0.001 HIS G 37 PHE 0.021 0.002 PHE H 3 TYR 0.012 0.001 TYR F 42 ARG 0.008 0.000 ARG J 67 *********************** 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 168 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 163 average time/residue: 1.5340 time to fit residues: 257.7935 Evaluate side-chains 162 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 0.617 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1917 time to fit residues: 1.2429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5427 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 5394 Z= 0.428 Angle : 0.742 9.541 7218 Z= 0.403 Chirality : 0.043 0.153 618 Planarity : 0.004 0.035 972 Dihedral : 5.928 22.774 738 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 2.08 % Allowed : 29.79 % Favored : 68.12 % 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: -3.80 (0.24), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.19), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 18 HIS 0.005 0.001 HIS G 37 PHE 0.037 0.003 PHE H 3 TYR 0.013 0.002 TYR B 35 ARG 0.009 0.001 ARG J 67 ********************** 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 175 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 172 average time/residue: 1.4444 time to fit residues: 256.3632 Evaluate side-chains 171 residues out of total 480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.1933 time to fit residues: 1.2483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 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 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 = 0.4043 r_free = 0.4043 target = 0.131910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.112079 restraints weight = 6278.343| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.03 r_work: 0.3605 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.7468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 5394 Z= 0.382 Angle : 0.714 9.365 7218 Z= 0.387 Chirality : 0.042 0.132 618 Planarity : 0.004 0.035 972 Dihedral : 5.771 21.089 738 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.50 % Allowed : 30.42 % Favored : 67.08 % 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: -3.83 (0.24), residues: 618 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.18), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 18 HIS 0.005 0.001 HIS G 37 PHE 0.033 0.003 PHE H 3 TYR 0.015 0.002 TYR J 35 ARG 0.008 0.001 ARG J 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3929.23 seconds wall clock time: 69 minutes 33.67 seconds (4173.67 seconds total)