Starting phenix.real_space_refine on Sun Mar 10 20:58:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/03_2024/6w4s_21539.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/03_2024/6w4s_21539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/03_2024/6w4s_21539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/03_2024/6w4s_21539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/03_2024/6w4s_21539.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w4s_21539/03_2024/6w4s_21539.pdb" } resolution = 3.2 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= -0.041 sd= 0.719 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 29 5.16 5 C 3240 2.51 5 N 814 2.21 5 O 903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ASP 84": "OD1" <-> "OD2" Residue "F ASP 166": "OD1" <-> "OD2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 296": "NH1" <-> "NH2" Residue "F ASP 297": "OD1" <-> "OD2" Residue "F ARG 371": "NH1" <-> "NH2" Residue "F ARG 466": "NH1" <-> "NH2" Residue "F ASP 473": "OD1" <-> "OD2" Residue "F ASP 504": "OD1" <-> "OD2" Residue "F GLU 518": "OE1" <-> "OE2" Residue "F PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 540": "NH1" <-> "NH2" Residue "H ASP 32": "OD1" <-> "OD2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 24": "NH1" <-> "NH2" Residue "L TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 74": "OD1" <-> "OD2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 96": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4986 Number of models: 1 Model: "" Number of chains: 3 Chain: "F" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3216 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 412} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 926 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 113} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.23, per 1000 atoms: 0.65 Number of scatterers: 4986 At special positions: 0 Unit cell: (100.158, 98.4608, 92.5192, 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 29 16.00 O 903 8.00 N 814 7.00 C 3240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.03 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: 1.66 Conformation dependent library (CDL) restraints added in 850.2 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1194 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 8 sheets defined 60.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 25 through 55 Processing helix chain 'F' and resid 57 through 86 removed outlier: 5.183A pdb=" N ALA F 77 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN F 86 " --> pdb=" O TRP F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 116 removed outlier: 3.649A pdb=" N ILE F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 123 Processing helix chain 'F' and resid 125 through 157 removed outlier: 4.326A pdb=" N LEU F 129 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 162 removed outlier: 3.507A pdb=" N VAL F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 198 removed outlier: 4.236A pdb=" N LEU F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 186 " --> pdb=" O GLN F 182 " (cutoff:3.500A) Proline residue: F 189 - end of helix Processing helix chain 'F' and resid 200 through 230 removed outlier: 3.694A pdb=" N GLY F 206 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER F 209 " --> pdb=" O CYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 231 through 234 removed outlier: 3.622A pdb=" N ALA F 234 " --> pdb=" O PRO F 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 231 through 234' Processing helix chain 'F' and resid 292 through 304 removed outlier: 3.694A pdb=" N ASN F 304 " --> pdb=" O VAL F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 317 removed outlier: 3.560A pdb=" N LEU F 317 " --> pdb=" O GLY F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 335 Processing helix chain 'F' and resid 338 through 367 Processing helix chain 'F' and resid 370 through 393 removed outlier: 3.903A pdb=" N LEU F 374 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 386 " --> pdb=" O SER F 382 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL F 391 " --> pdb=" O CYS F 387 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE F 392 " --> pdb=" O VAL F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 484 removed outlier: 4.547A pdb=" N ILE F 467 " --> pdb=" O ILE F 463 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN F 483 " --> pdb=" O LEU F 479 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 484 " --> pdb=" O LEU F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 514 Processing helix chain 'F' and resid 516 through 546 removed outlier: 4.133A pdb=" N LEU F 525 " --> pdb=" O GLY F 521 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.863A pdb=" N GLN H 66 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.628A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.389A pdb=" N VAL H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.772A pdb=" N CYS L 23 " --> pdb=" O PHE L 75 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE L 75 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.736A pdb=" N VAL L 13 " --> pdb=" O GLU L 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 30 through 31 Processing sheet with id=AA7, first strand: chain 'L' and resid 49 through 52 removed outlier: 6.855A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR L 101 " --> pdb=" O HIS L 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 49 through 52 removed outlier: 6.855A pdb=" N TRP L 39 " --> pdb=" O LEU L 51 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1068 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: 1.38 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1539 1.34 - 1.46: 1053 1.46 - 1.58: 2463 1.58 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 5101 Sorted by residual: bond pdb=" CA ASP L 86 " pdb=" C ASP L 86 " ideal model delta sigma weight residual 1.523 1.499 0.025 1.80e-02 3.09e+03 1.86e+00 bond pdb=" CG1 ILE H 37 " pdb=" CD1 ILE H 37 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.70e-01 bond pdb=" N VAL L 62 " pdb=" CA VAL L 62 " ideal model delta sigma weight residual 1.468 1.460 0.009 1.05e-02 9.07e+03 6.89e-01 bond pdb=" CB ASP F 473 " pdb=" CG ASP F 473 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.26e-01 bond pdb=" CB ASN L 95 " pdb=" CG ASN L 95 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.09e-01 ... (remaining 5096 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.77: 125 106.77 - 113.58: 2912 113.58 - 120.39: 1887 120.39 - 127.20: 1976 127.20 - 134.02: 52 Bond angle restraints: 6952 Sorted by residual: angle pdb=" N ILE F 186 " pdb=" CA ILE F 186 " pdb=" C ILE F 186 " ideal model delta sigma weight residual 113.42 110.12 3.30 1.17e+00 7.31e-01 7.93e+00 angle pdb=" C GLY F 55 " pdb=" N ASN F 56 " pdb=" CA ASN F 56 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.75e+00 angle pdb=" C PHE F 472 " pdb=" N ASP F 473 " pdb=" CA ASP F 473 " ideal model delta sigma weight residual 120.31 116.82 3.49 1.52e+00 4.33e-01 5.28e+00 angle pdb=" N PRO L 50 " pdb=" CA PRO L 50 " pdb=" C PRO L 50 " ideal model delta sigma weight residual 110.21 113.76 -3.55 1.64e+00 3.72e-01 4.68e+00 angle pdb=" C LEU L 54 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.67e+00 ... (remaining 6947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 2640 16.75 - 33.50: 250 33.50 - 50.25: 46 50.25 - 66.99: 16 66.99 - 83.74: 5 Dihedral angle restraints: 2957 sinusoidal: 1085 harmonic: 1872 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 136.54 -43.54 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" CA TYR H 50 " pdb=" C TYR H 50 " pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA LEU L 54 " pdb=" C LEU L 54 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 2954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 475 0.027 - 0.053: 211 0.053 - 0.080: 89 0.080 - 0.107: 37 0.107 - 0.133: 12 Chirality restraints: 824 Sorted by residual: chirality pdb=" CA ILE L 52 " pdb=" N ILE L 52 " pdb=" C ILE L 52 " pdb=" CB ILE L 52 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ASN F 56 " pdb=" N ASN F 56 " pdb=" C ASN F 56 " pdb=" CB ASN F 56 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE H 37 " pdb=" N ILE H 37 " pdb=" C ILE H 37 " pdb=" CB ILE H 37 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 821 not shown) Planarity restraints: 849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 516 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO F 517 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 517 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 517 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 47 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO L 48 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 48 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 48 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 40 " -0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO H 41 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.019 5.00e-02 4.00e+02 ... (remaining 846 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 267 2.72 - 3.27: 5211 3.27 - 3.81: 7917 3.81 - 4.36: 9283 4.36 - 4.90: 16708 Nonbonded interactions: 39386 Sorted by model distance: nonbonded pdb=" OG1 THR F 122 " pdb=" O ARG L 96 " model vdw 2.176 2.440 nonbonded pdb=" NE2 GLN L 93 " pdb=" OD1 ASN L 95 " model vdw 2.210 2.520 nonbonded pdb=" OD1 ASN H 60 " pdb=" OG SER H 62 " model vdw 2.240 2.440 nonbonded pdb=" O VAL F 67 " pdb=" OG SER F 71 " model vdw 2.247 2.440 nonbonded pdb=" OE2 GLU F 119 " pdb=" OH TYR H 33 " model vdw 2.260 2.440 ... (remaining 39381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 6.040 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 16.900 Find NCS groups from input model: 0.120 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 0.004 0.034 5101 Z= 0.276 Angle : 0.571 5.823 6952 Z= 0.331 Chirality : 0.039 0.133 824 Planarity : 0.004 0.049 849 Dihedral : 14.378 83.741 1757 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.45 % Allowed : 11.87 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: -1.13 (0.33), residues: 640 helix: 0.50 (0.27), residues: 371 sheet: -0.84 (0.53), residues: 100 loop : -3.49 (0.37), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 470 HIS 0.004 0.001 HIS F 507 PHE 0.018 0.001 PHE F 295 TYR 0.019 0.002 TYR H 78 ARG 0.002 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 0.587 Fit side-chains REVERT: F 42 TRP cc_start: 0.8779 (OUTLIER) cc_final: 0.8337 (t-100) REVERT: F 112 MET cc_start: 0.7755 (mmm) cc_final: 0.7532 (mmm) REVERT: F 167 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7886 (mmt-90) REVERT: F 385 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8752 (tt) REVERT: F 482 GLU cc_start: 0.7658 (tt0) cc_final: 0.7205 (tt0) REVERT: F 486 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7573 (tm-30) REVERT: F 540 ARG cc_start: 0.6969 (mtm180) cc_final: 0.6696 (ttt90) REVERT: L 24 ARG cc_start: 0.7906 (mpp-170) cc_final: 0.7693 (ptt90) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.1679 time to fit residues: 27.0407 Evaluate side-chains 111 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 42 TRP Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 477 THR Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 527 SER Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 28 SER Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 79 TYR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 79 ILE Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN F 99 GLN F 141 ASN F 174 ASN F 304 ASN F 481 GLN F 496 GLN F 516 ASN H 16 GLN H 76 ASN H 77 HIS L 38 HIS L 78 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5101 Z= 0.159 Angle : 0.509 5.807 6952 Z= 0.278 Chirality : 0.039 0.201 824 Planarity : 0.004 0.039 849 Dihedral : 6.844 57.126 731 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.34 % Allowed : 18.37 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.68 (0.35), residues: 640 helix: 1.95 (0.29), residues: 370 sheet: -0.03 (0.56), residues: 101 loop : -2.78 (0.39), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 34 HIS 0.002 0.001 HIS F 116 PHE 0.010 0.001 PHE F 295 TYR 0.015 0.001 TYR H 78 ARG 0.002 0.000 ARG F 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 0.569 Fit side-chains REVERT: F 112 MET cc_start: 0.7561 (mmm) cc_final: 0.7357 (mmm) REVERT: F 385 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8625 (tt) outliers start: 18 outliers final: 12 residues processed: 119 average time/residue: 0.1746 time to fit residues: 26.4039 Evaluate side-chains 105 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 62 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5101 Z= 0.178 Angle : 0.508 6.019 6952 Z= 0.275 Chirality : 0.039 0.141 824 Planarity : 0.004 0.039 849 Dihedral : 5.728 56.291 709 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.82 % Allowed : 17.81 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.18 (0.35), residues: 640 helix: 2.37 (0.28), residues: 369 sheet: -0.18 (0.54), residues: 104 loop : -2.37 (0.41), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 42 HIS 0.003 0.001 HIS F 507 PHE 0.013 0.001 PHE F 295 TYR 0.017 0.001 TYR H 78 ARG 0.002 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.624 Fit side-chains REVERT: F 112 MET cc_start: 0.7583 (mmm) cc_final: 0.7380 (mmm) REVERT: F 124 TYR cc_start: 0.7685 (m-10) cc_final: 0.7481 (m-10) REVERT: F 385 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8539 (tt) REVERT: F 386 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7846 (tt) outliers start: 26 outliers final: 19 residues processed: 124 average time/residue: 0.1552 time to fit residues: 25.1252 Evaluate side-chains 116 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 82 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5101 Z= 0.188 Angle : 0.515 7.794 6952 Z= 0.275 Chirality : 0.039 0.144 824 Planarity : 0.004 0.040 849 Dihedral : 5.640 53.347 708 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.19 % Allowed : 18.37 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.37 (0.35), residues: 640 helix: 2.35 (0.28), residues: 375 sheet: -0.15 (0.54), residues: 104 loop : -1.94 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 470 HIS 0.003 0.001 HIS F 507 PHE 0.012 0.001 PHE F 295 TYR 0.016 0.001 TYR H 78 ARG 0.001 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 0.606 Fit side-chains REVERT: F 385 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8453 (tt) REVERT: F 474 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7715 (mp) REVERT: L 17 GLN cc_start: 0.7812 (tt0) cc_final: 0.7104 (tt0) REVERT: L 37 MET cc_start: 0.7681 (tpt) cc_final: 0.7200 (tpt) outliers start: 28 outliers final: 20 residues processed: 116 average time/residue: 0.1428 time to fit residues: 22.0007 Evaluate side-chains 111 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 122 THR Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5101 Z= 0.234 Angle : 0.540 6.437 6952 Z= 0.290 Chirality : 0.039 0.139 824 Planarity : 0.004 0.039 849 Dihedral : 5.436 56.184 706 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.82 % Allowed : 19.67 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.36 (0.35), residues: 640 helix: 2.29 (0.27), residues: 374 sheet: 0.17 (0.55), residues: 102 loop : -2.00 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 42 HIS 0.005 0.001 HIS F 507 PHE 0.015 0.001 PHE F 295 TYR 0.018 0.002 TYR H 78 ARG 0.003 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 94 time to evaluate : 0.587 Fit side-chains REVERT: F 474 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7807 (mp) REVERT: L 17 GLN cc_start: 0.7873 (tt0) cc_final: 0.7311 (tt0) outliers start: 26 outliers final: 20 residues processed: 114 average time/residue: 0.1414 time to fit residues: 21.5718 Evaluate side-chains 111 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5101 Z= 0.195 Angle : 0.525 6.173 6952 Z= 0.282 Chirality : 0.039 0.147 824 Planarity : 0.004 0.039 849 Dihedral : 4.924 51.793 704 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.82 % Allowed : 20.41 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.53 (0.35), residues: 640 helix: 2.37 (0.27), residues: 375 sheet: 0.11 (0.54), residues: 105 loop : -1.74 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 42 HIS 0.003 0.001 HIS F 507 PHE 0.012 0.001 PHE F 295 TYR 0.016 0.001 TYR H 78 ARG 0.006 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 0.588 Fit side-chains REVERT: F 474 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7818 (mp) REVERT: H 100 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8960 (mp) REVERT: L 17 GLN cc_start: 0.7803 (tt0) cc_final: 0.7540 (tt0) outliers start: 26 outliers final: 19 residues processed: 116 average time/residue: 0.1604 time to fit residues: 25.0439 Evaluate side-chains 111 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 86 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5101 Z= 0.219 Angle : 0.570 9.272 6952 Z= 0.298 Chirality : 0.040 0.288 824 Planarity : 0.004 0.040 849 Dihedral : 5.004 51.066 704 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.27 % Allowed : 21.34 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.52 (0.35), residues: 640 helix: 2.31 (0.27), residues: 375 sheet: 0.18 (0.54), residues: 105 loop : -1.66 (0.47), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 42 HIS 0.004 0.001 HIS F 507 PHE 0.013 0.001 PHE F 295 TYR 0.017 0.001 TYR H 78 ARG 0.007 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 0.518 Fit side-chains REVERT: F 385 ILE cc_start: 0.8034 (tp) cc_final: 0.7683 (pt) REVERT: F 474 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7807 (mp) REVERT: H 100 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8954 (mp) REVERT: L 17 GLN cc_start: 0.7825 (tt0) cc_final: 0.7193 (tt0) REVERT: L 37 MET cc_start: 0.7805 (tpt) cc_final: 0.7519 (tpt) outliers start: 23 outliers final: 19 residues processed: 114 average time/residue: 0.1468 time to fit residues: 22.2822 Evaluate side-chains 112 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 333 TYR Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 522 LEU Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 0.1980 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 ASN F 212 ASN H 35 ASN L 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 5101 Z= 0.437 Angle : 0.692 8.746 6952 Z= 0.362 Chirality : 0.046 0.483 824 Planarity : 0.005 0.041 849 Dihedral : 5.539 51.280 704 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.82 % Allowed : 21.71 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 0.97 (0.34), residues: 640 helix: 1.83 (0.27), residues: 375 sheet: 0.12 (0.54), residues: 102 loop : -1.84 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 42 HIS 0.009 0.002 HIS F 507 PHE 0.022 0.002 PHE F 295 TYR 0.025 0.003 TYR F 133 ARG 0.003 0.001 ARG F 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 90 time to evaluate : 0.580 Fit side-chains REVERT: F 385 ILE cc_start: 0.8300 (tp) cc_final: 0.7890 (pt) REVERT: F 474 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7719 (mp) REVERT: L 17 GLN cc_start: 0.7808 (tt0) cc_final: 0.7266 (tt0) REVERT: L 37 MET cc_start: 0.7855 (tpt) cc_final: 0.7285 (tpt) outliers start: 26 outliers final: 22 residues processed: 111 average time/residue: 0.1498 time to fit residues: 21.9859 Evaluate side-chains 109 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 86 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 131 SER Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 333 TYR Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 474 LEU Chi-restraints excluded: chain F residue 498 SER Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 35 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5101 Z= 0.188 Angle : 0.583 9.740 6952 Z= 0.301 Chirality : 0.042 0.337 824 Planarity : 0.004 0.040 849 Dihedral : 4.792 52.797 702 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.53 % Allowed : 23.56 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.44 (0.35), residues: 640 helix: 2.20 (0.28), residues: 375 sheet: 0.27 (0.56), residues: 101 loop : -1.63 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 42 HIS 0.003 0.001 HIS F 507 PHE 0.010 0.001 PHE F 295 TYR 0.019 0.001 TYR F 133 ARG 0.004 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.592 Fit side-chains REVERT: F 385 ILE cc_start: 0.8043 (tp) cc_final: 0.7787 (tt) outliers start: 19 outliers final: 16 residues processed: 106 average time/residue: 0.1491 time to fit residues: 21.0892 Evaluate side-chains 105 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.0980 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5101 Z= 0.187 Angle : 0.599 13.837 6952 Z= 0.305 Chirality : 0.041 0.351 824 Planarity : 0.004 0.041 849 Dihedral : 4.650 49.498 702 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.15 % Allowed : 23.93 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.60 (0.35), residues: 640 helix: 2.33 (0.28), residues: 375 sheet: 0.23 (0.55), residues: 101 loop : -1.48 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 42 HIS 0.003 0.001 HIS F 507 PHE 0.012 0.001 PHE F 295 TYR 0.016 0.001 TYR H 78 ARG 0.003 0.000 ARG L 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 0.588 Fit side-chains REVERT: F 325 ASP cc_start: 0.7036 (t70) cc_final: 0.6625 (t70) REVERT: L 17 GLN cc_start: 0.7630 (tt0) cc_final: 0.7066 (tt0) outliers start: 17 outliers final: 16 residues processed: 109 average time/residue: 0.1471 time to fit residues: 21.3007 Evaluate side-chains 107 residues out of total 550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain F residue 471 SER Chi-restraints excluded: chain F residue 545 THR Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 52 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 94 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 21 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN H 81 GLN ** H 98 GLN ** 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 = 0.3738 r_free = 0.3738 target = 0.137521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.114268 restraints weight = 7567.907| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.71 r_work: 0.3323 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5101 Z= 0.162 Angle : 0.562 10.303 6952 Z= 0.288 Chirality : 0.040 0.312 824 Planarity : 0.004 0.041 849 Dihedral : 4.470 48.659 702 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.60 % Allowed : 24.68 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.79 % 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: 1.72 (0.35), residues: 640 helix: 2.46 (0.27), residues: 377 sheet: 0.14 (0.56), residues: 99 loop : -1.44 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 42 HIS 0.003 0.001 HIS F 507 PHE 0.011 0.001 PHE F 295 TYR 0.025 0.001 TYR F 133 ARG 0.002 0.000 ARG L 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.81 seconds wall clock time: 27 minutes 49.02 seconds (1669.02 seconds total)