Starting phenix.real_space_refine on Fri Apr 5 20:53:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/04_2024/7ura_26707_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/04_2024/7ura_26707.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/04_2024/7ura_26707_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/04_2024/7ura_26707_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/04_2024/7ura_26707_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/04_2024/7ura_26707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/04_2024/7ura_26707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/04_2024/7ura_26707_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ura_26707/04_2024/7ura_26707_updated.pdb" } resolution = 3.11 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= 0.007 sd= 0.122 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3 5.49 5 S 32 5.16 5 C 3550 2.51 5 N 869 2.21 5 O 945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 27": "OD1" <-> "OD2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 103": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5400 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3449 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 196 Unusual residues: {' ZN': 1, 'AJP': 1, 'CLR': 2, 'OH6': 1, 'OLA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 14 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2833 SG CYS A 370 54.449 29.304 19.614 1.00100.07 S ATOM 2880 SG CYS A 376 53.464 29.646 22.508 1.00107.56 S ATOM 2908 SG CYS A 380 56.441 28.777 22.619 1.00114.72 S Time building chain proxies: 4.07, per 1000 atoms: 0.75 Number of scatterers: 5400 At special positions: 0 Unit cell: (97.11, 68.89, 93.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 3 15.00 O 945 8.00 N 869 7.00 C 3550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 380 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 376 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 370 " Number of angles added : 3 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 7 sheets defined 48.0% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 6 through 16 removed outlier: 4.505A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 44 removed outlier: 5.127A pdb=" N LEU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LEU A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 67 Processing helix chain 'A' and resid 71 through 88 removed outlier: 4.218A pdb=" N LEU A 81 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 88 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 111 Processing helix chain 'A' and resid 117 through 143 removed outlier: 3.577A pdb=" N HIS A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N GLY A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 187 through 209 Processing helix chain 'A' and resid 236 through 262 Processing helix chain 'A' and resid 284 through 287 No H-bonds generated for 'chain 'A' and resid 284 through 287' Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 302 through 319 removed outlier: 5.912A pdb=" N ARG A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 335 Processing helix chain 'A' and resid 343 through 367 Processing helix chain 'A' and resid 389 through 411 removed outlier: 4.977A pdb=" N LEU A 411 " --> pdb=" O TYR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 436 Processing helix chain 'A' and resid 440 through 455 Processing helix chain 'L' and resid 100 through 102 No H-bonds generated for 'chain 'L' and resid 100 through 102' Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 81 through 83 No H-bonds generated for 'chain 'H' and resid 81 through 83' Processing helix chain 'H' and resid 107 through 109 No H-bonds generated for 'chain 'H' and resid 107 through 109' Processing sheet with id= A, first strand: chain 'L' and resid 24 through 27 removed outlier: 3.604A pdb=" N GLN L 90 " --> pdb=" O SER L 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 30 through 33 removed outlier: 5.847A pdb=" N LYS L 123 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA L 33 " --> pdb=" O LYS L 123 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU L 125 " --> pdb=" O ALA L 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'L' and resid 105 through 110 removed outlier: 6.434A pdb=" N GLN L 57 " --> pdb=" O LEU L 66 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU L 66 " --> pdb=" O GLN L 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 22 through 25 Processing sheet with id= E, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.275A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 36 through 38 Processing sheet with id= G, first strand: chain 'H' and resid 116 through 118 removed outlier: 3.715A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 274 hydrogen bonds defined for protein. 759 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: 1.39 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.19: 3 1.19 - 1.39: 2276 1.39 - 1.59: 3198 1.59 - 1.79: 45 1.79 - 1.99: 42 Bond restraints: 5564 Sorted by residual: bond pdb=" C07 AJP A 505 " pdb=" C08 AJP A 505 " ideal model delta sigma weight residual 1.550 1.986 -0.436 2.00e-02 2.50e+03 4.76e+02 bond pdb=" C01 AJP A 505 " pdb=" C02 AJP A 505 " ideal model delta sigma weight residual 1.521 1.954 -0.433 2.00e-02 2.50e+03 4.69e+02 bond pdb=" C08 AJP A 505 " pdb=" O09 AJP A 505 " ideal model delta sigma weight residual 1.410 0.994 0.416 2.00e-02 2.50e+03 4.32e+02 bond pdb=" C05 AJP A 505 " pdb=" O09 AJP A 505 " ideal model delta sigma weight residual 1.407 1.798 -0.391 2.00e-02 2.50e+03 3.81e+02 bond pdb=" C02 AJP A 505 " pdb=" C03 AJP A 505 " ideal model delta sigma weight residual 1.525 1.138 0.387 2.00e-02 2.50e+03 3.74e+02 ... (remaining 5559 not shown) Histogram of bond angle deviations from ideal: 97.60 - 105.26: 105 105.26 - 112.92: 3090 112.92 - 120.57: 2411 120.57 - 128.23: 1909 128.23 - 135.89: 69 Bond angle restraints: 7584 Sorted by residual: angle pdb=" N54 OH6 A 501 " pdb=" C53 OH6 A 501 " pdb=" N58 OH6 A 501 " ideal model delta sigma weight residual 80.10 121.69 -41.59 3.00e+00 1.11e-01 1.92e+02 angle pdb=" C07 OH6 A 501 " pdb=" C08 OH6 A 501 " pdb=" C09 OH6 A 501 " ideal model delta sigma weight residual 152.67 121.20 31.47 3.00e+00 1.11e-01 1.10e+02 angle pdb=" C52 OH6 A 501 " pdb=" C53 OH6 A 501 " pdb=" N58 OH6 A 501 " ideal model delta sigma weight residual 144.25 119.33 24.92 3.00e+00 1.11e-01 6.90e+01 angle pdb=" N SER A 381 " pdb=" CA SER A 381 " pdb=" C SER A 381 " ideal model delta sigma weight residual 113.17 104.12 9.05 1.26e+00 6.30e-01 5.16e+01 angle pdb=" N HIS A 382 " pdb=" CA HIS A 382 " pdb=" C HIS A 382 " ideal model delta sigma weight residual 109.96 118.89 -8.93 1.50e+00 4.44e-01 3.55e+01 ... (remaining 7579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 3225 35.76 - 71.53: 81 71.53 - 107.29: 36 107.29 - 143.05: 35 143.05 - 178.81: 9 Dihedral angle restraints: 3386 sinusoidal: 1479 harmonic: 1907 Sorted by residual: dihedral pdb=" CA TYR H 74 " pdb=" C TYR H 74 " pdb=" N VAL H 75 " pdb=" CA VAL H 75 " ideal model delta harmonic sigma weight residual 180.00 -153.98 -26.02 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" C06 AJP A 505 " pdb=" C07 AJP A 505 " pdb=" C12 AJP A 505 " pdb=" C13 AJP A 505 " ideal model delta sinusoidal sigma weight residual 109.15 -69.66 178.81 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C12 AJP A 505 " pdb=" C10 AJP A 505 " pdb=" C11 AJP A 505 " pdb=" O82 AJP A 505 " ideal model delta sinusoidal sigma weight residual -72.62 101.75 -174.37 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.101: 831 1.101 - 2.203: 0 2.203 - 3.304: 0 3.304 - 4.405: 2 4.405 - 5.507: 19 Chirality restraints: 852 Sorted by residual: chirality pdb=" C20 AJP A 505 " pdb=" C15 AJP A 505 " pdb=" C19 AJP A 505 " pdb=" C21 AJP A 505 " both_signs ideal model delta sigma weight residual False 2.96 -2.55 5.51 2.00e-01 2.50e+01 7.58e+02 chirality pdb=" C16 AJP A 505 " pdb=" C11 AJP A 505 " pdb=" C15 AJP A 505 " pdb=" C17 AJP A 505 " both_signs ideal model delta sigma weight residual False -2.70 2.74 -5.44 2.00e-01 2.50e+01 7.40e+02 chirality pdb=" C15 AJP A 505 " pdb=" C14 AJP A 505 " pdb=" C16 AJP A 505 " pdb=" C20 AJP A 505 " both_signs ideal model delta sigma weight residual False -2.42 2.93 -5.35 2.00e-01 2.50e+01 7.14e+02 ... (remaining 849 not shown) Planarity restraints: 900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 310 " -0.014 2.00e-02 2.50e+03 2.71e-02 7.36e+00 pdb=" C ASN A 310 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN A 310 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR A 311 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 309 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C ASN A 309 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN A 309 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN A 310 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 377 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 378 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.029 5.00e-02 4.00e+02 ... (remaining 897 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 52 2.62 - 3.19: 4722 3.19 - 3.76: 8268 3.76 - 4.33: 11987 4.33 - 4.90: 20015 Nonbonded interactions: 45044 Sorted by model distance: nonbonded pdb=" O33 AJP A 505 " pdb=" O40 AJP A 505 " model vdw 2.051 2.440 nonbonded pdb=" O PHE A 340 " pdb=" ND1 HIS A 341 " model vdw 2.136 2.520 nonbonded pdb=" O VAL A 76 " pdb=" OG SER A 79 " model vdw 2.258 2.440 nonbonded pdb=" O GLY L 119 " pdb=" OG SER H 63 " model vdw 2.272 2.440 nonbonded pdb=" O42 AJP A 505 " pdb=" O43 AJP A 505 " model vdw 2.282 2.440 ... (remaining 45039 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: 1.250 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: 4.820 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.660 Find NCS groups from input model: 0.150 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.020 0.436 5564 Z= 1.297 Angle : 1.120 41.594 7584 Z= 0.472 Chirality : 0.781 5.507 852 Planarity : 0.005 0.053 900 Dihedral : 26.535 178.815 2159 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -2.18 (0.29), residues: 648 helix: -0.48 (0.26), residues: 330 sheet: -1.36 (0.41), residues: 119 loop : -3.00 (0.36), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.005 0.001 HIS L 111 PHE 0.015 0.001 PHE A 403 TYR 0.019 0.002 TYR A 311 ARG 0.006 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7223 (mtt180) cc_final: 0.7015 (mtp85) REVERT: L 94 LYS cc_start: 0.8366 (ttpt) cc_final: 0.7702 (tttm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3187 time to fit residues: 29.9797 Evaluate side-chains 68 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 91 HIS A 113 HIS A 174 HIS A 315 ASN L 57 GLN L 111 HIS H 52 ASN H 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5564 Z= 0.247 Angle : 1.136 36.184 7584 Z= 0.429 Chirality : 0.122 2.384 852 Planarity : 0.004 0.045 900 Dihedral : 22.745 176.542 1036 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.54 % Allowed : 9.30 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: -0.87 (0.32), residues: 648 helix: 0.76 (0.28), residues: 325 sheet: -0.83 (0.43), residues: 119 loop : -2.59 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.006 0.001 HIS A 341 PHE 0.015 0.001 PHE A 403 TYR 0.019 0.001 TYR A 311 ARG 0.003 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7223 (mtt180) cc_final: 0.7005 (mtp85) REVERT: L 81 ARG cc_start: 0.8655 (ptt-90) cc_final: 0.8390 (ptt-90) REVERT: H 39 MET cc_start: 0.8689 (mtm) cc_final: 0.8479 (mtm) outliers start: 3 outliers final: 3 residues processed: 67 average time/residue: 0.2600 time to fit residues: 21.3302 Evaluate side-chains 64 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 48 optimal weight: 0.0370 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS L 57 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5564 Z= 0.156 Angle : 1.093 34.809 7584 Z= 0.405 Chirality : 0.119 2.228 852 Planarity : 0.004 0.043 900 Dihedral : 22.418 178.731 1036 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.07 % Allowed : 11.27 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.05 (0.33), residues: 648 helix: 1.49 (0.29), residues: 325 sheet: -0.13 (0.48), residues: 110 loop : -2.24 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 128 HIS 0.005 0.001 HIS A 341 PHE 0.013 0.001 PHE A 403 TYR 0.014 0.001 TYR H 74 ARG 0.002 0.000 ARG L 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 67 average time/residue: 0.2964 time to fit residues: 24.2167 Evaluate side-chains 62 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain L residue 80 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.0000 chunk 43 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 51 optimal weight: 0.7980 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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: 0.8054 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5564 Z= 0.149 Angle : 1.086 34.107 7584 Z= 0.400 Chirality : 0.118 2.186 852 Planarity : 0.004 0.042 900 Dihedral : 22.153 179.229 1036 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.25 % Allowed : 11.45 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.46 (0.34), residues: 648 helix: 1.77 (0.29), residues: 325 sheet: -0.02 (0.47), residues: 119 loop : -1.96 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 66 HIS 0.004 0.001 HIS A 341 PHE 0.013 0.001 PHE A 403 TYR 0.014 0.001 TYR A 311 ARG 0.003 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: L 44 ARG cc_start: 0.7491 (mtt-85) cc_final: 0.7224 (mtt-85) outliers start: 7 outliers final: 3 residues processed: 67 average time/residue: 0.2611 time to fit residues: 21.6245 Evaluate side-chains 63 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain L residue 80 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 113 HIS A 336 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5564 Z= 0.378 Angle : 1.145 33.818 7584 Z= 0.440 Chirality : 0.120 2.210 852 Planarity : 0.004 0.044 900 Dihedral : 22.513 179.942 1036 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.43 % Allowed : 13.77 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.17 (0.33), residues: 648 helix: 1.35 (0.29), residues: 327 sheet: -0.08 (0.46), residues: 119 loop : -1.83 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 66 HIS 0.006 0.001 HIS A 94 PHE 0.020 0.002 PHE A 403 TYR 0.025 0.002 TYR A 311 ARG 0.004 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8790 (mttt) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.2600 time to fit residues: 22.3395 Evaluate side-chains 69 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 39 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain L residue 80 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 7.9990 chunk 15 optimal weight: 0.1980 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5564 Z= 0.164 Angle : 1.089 33.388 7584 Z= 0.403 Chirality : 0.118 2.150 852 Planarity : 0.004 0.046 900 Dihedral : 22.137 179.917 1036 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.25 % Allowed : 15.03 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.56 (0.34), residues: 648 helix: 1.76 (0.29), residues: 325 sheet: 0.02 (0.47), residues: 119 loop : -1.74 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 30 HIS 0.004 0.001 HIS A 341 PHE 0.013 0.001 PHE A 403 TYR 0.017 0.001 TYR H 74 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8777 (mttt) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.2682 time to fit residues: 20.8311 Evaluate side-chains 63 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain L residue 80 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5564 Z= 0.178 Angle : 1.087 33.169 7584 Z= 0.403 Chirality : 0.118 2.138 852 Planarity : 0.004 0.045 900 Dihedral : 22.028 179.873 1036 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.07 % Allowed : 16.10 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.74 (0.34), residues: 648 helix: 1.90 (0.29), residues: 324 sheet: 0.17 (0.48), residues: 119 loop : -1.67 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.004 0.001 HIS A 341 PHE 0.014 0.001 PHE A 403 TYR 0.016 0.001 TYR A 311 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8771 (mttt) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.2619 time to fit residues: 20.6911 Evaluate side-chains 64 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 39 CYS Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain L residue 80 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5564 Z= 0.190 Angle : 1.088 32.950 7584 Z= 0.404 Chirality : 0.118 2.127 852 Planarity : 0.004 0.044 900 Dihedral : 21.924 179.766 1036 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.25 % Allowed : 16.28 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.80 (0.34), residues: 648 helix: 1.94 (0.29), residues: 324 sheet: 0.45 (0.51), residues: 109 loop : -1.70 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.004 0.001 HIS A 341 PHE 0.013 0.001 PHE A 403 TYR 0.017 0.001 TYR H 74 ARG 0.002 0.000 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8768 (mttt) outliers start: 7 outliers final: 6 residues processed: 70 average time/residue: 0.2647 time to fit residues: 22.8416 Evaluate side-chains 70 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 64 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 CYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain L residue 80 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5564 Z= 0.176 Angle : 1.083 32.814 7584 Z= 0.401 Chirality : 0.118 2.118 852 Planarity : 0.004 0.044 900 Dihedral : 21.796 179.638 1036 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.79 % Allowed : 15.74 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.89 (0.34), residues: 648 helix: 2.00 (0.29), residues: 324 sheet: 0.55 (0.51), residues: 109 loop : -1.66 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 66 HIS 0.004 0.001 HIS A 341 PHE 0.013 0.001 PHE A 403 TYR 0.016 0.001 TYR A 311 ARG 0.002 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8767 (mttt) REVERT: H 74 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.6846 (p90) outliers start: 10 outliers final: 7 residues processed: 74 average time/residue: 0.2399 time to fit residues: 21.9349 Evaluate side-chains 73 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 CYS Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.0570 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5564 Z= 0.154 Angle : 1.079 32.716 7584 Z= 0.398 Chirality : 0.118 2.106 852 Planarity : 0.004 0.044 900 Dihedral : 21.639 179.538 1036 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.07 % Allowed : 16.64 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 0.99 (0.34), residues: 648 helix: 2.10 (0.29), residues: 324 sheet: 0.58 (0.52), residues: 109 loop : -1.63 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 236 HIS 0.004 0.001 HIS A 432 PHE 0.013 0.001 PHE A 403 TYR 0.015 0.001 TYR H 74 ARG 0.002 0.000 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 LYS cc_start: 0.9028 (mtpp) cc_final: 0.8757 (mttt) REVERT: H 74 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.6795 (p90) outliers start: 6 outliers final: 5 residues processed: 69 average time/residue: 0.2472 time to fit residues: 21.1099 Evaluate side-chains 69 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 CYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 58 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.143947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105708 restraints weight = 5691.442| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.88 r_work: 0.2847 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5564 Z= 0.160 Angle : 1.079 32.693 7584 Z= 0.399 Chirality : 0.118 2.104 852 Planarity : 0.004 0.044 900 Dihedral : 21.563 179.460 1036 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.25 % Allowed : 16.28 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % 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: 1.05 (0.34), residues: 648 helix: 2.10 (0.29), residues: 325 sheet: 0.65 (0.52), residues: 109 loop : -1.56 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 236 HIS 0.004 0.001 HIS A 432 PHE 0.017 0.001 PHE A 446 TYR 0.015 0.001 TYR A 311 ARG 0.002 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1642.20 seconds wall clock time: 30 minutes 36.07 seconds (1836.07 seconds total)