Starting phenix.real_space_refine on Sun Mar 10 23:58:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urf_26711/03_2024/7urf_26711_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urf_26711/03_2024/7urf_26711.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urf_26711/03_2024/7urf_26711_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urf_26711/03_2024/7urf_26711_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urf_26711/03_2024/7urf_26711_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urf_26711/03_2024/7urf_26711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urf_26711/03_2024/7urf_26711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urf_26711/03_2024/7urf_26711_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urf_26711/03_2024/7urf_26711_updated.pdb" } resolution = 2.8 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= 0.000 sd= 0.003 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 Fe 1 7.16 5 P 3 5.49 5 S 42 5.16 5 C 4072 2.51 5 N 957 2.21 5 O 1058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 35": "OE1" <-> "OE2" Residue "O PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 126": "OD1" <-> "OD2" Residue "P TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 78": "NH1" <-> "NH2" Residue "P PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 105": "OE1" <-> "OE2" Residue "P TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 6133 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 4031 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 16, 'TRANS': 474} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 47 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "O" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 914 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 282 Unusual residues: {'AJP': 5, 'HEM': 1, 'PKZ': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 676 Unresolved non-hydrogen chiralities: 126 Planarities with less than four sites: {'PKZ:plan-3': 1, 'PKZ:plan-2': 1, 'PKZ:plan-1': 1, 'PKZ:plan-5': 1, 'PKZ:plan-4': 1} Unresolved non-hydrogen planarities: 26 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2682 SG CYS A 324 44.053 47.482 32.785 1.00 36.62 S Time building chain proxies: 4.00, per 1000 atoms: 0.65 Number of scatterers: 6133 At special positions: 0 Unit cell: (74.938, 85.042, 118.722, 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) Fe 1 26.01 S 42 16.00 P 3 15.00 O 1058 8.00 N 957 7.00 C 4072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 115 " distance=2.03 Simple disulfide: pdb=" SG CYS P 42 " - pdb=" SG CYS P 112 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.1 seconds 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 5 sheets defined 53.7% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 4 through 31 Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 58 through 67 Processing helix chain 'A' and resid 71 through 88 Processing helix chain 'A' and resid 93 through 130 removed outlier: 7.887A pdb=" N THR A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix removed outlier: 4.659A pdb=" N PHE A 130 " --> pdb=" O CYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.837A pdb=" N LEU A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 165 through 189 removed outlier: 3.856A pdb=" N LEU A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.750A pdb=" N GLN A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 264 removed outlier: 3.738A pdb=" N CYS A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 282 through 314 removed outlier: 3.756A pdb=" N VAL A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 351 through 354 No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 360 through 379 Processing helix chain 'A' and resid 383 through 406 Processing helix chain 'A' and resid 409 through 418 Processing helix chain 'A' and resid 421 through 447 removed outlier: 4.029A pdb=" N MET A 438 " --> pdb=" O CYS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 468 through 489 removed outlier: 3.764A pdb=" N GLN A 488 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 50 No H-bonds generated for 'chain 'O' and resid 48 through 50' Processing sheet with id= A, first strand: chain 'O' and resid 22 through 25 Processing sheet with id= B, first strand: chain 'O' and resid 77 through 79 removed outlier: 6.793A pdb=" N TRP O 55 " --> pdb=" O MET O 67 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP O 69 " --> pdb=" O MET O 53 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N MET O 53 " --> pdb=" O TRP O 69 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR O 127 " --> pdb=" O ARG O 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'P' and resid 24 through 26 Processing sheet with id= D, first strand: chain 'P' and resid 29 through 32 removed outlier: 6.258A pdb=" N LYS P 127 " --> pdb=" O LEU P 30 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL P 32 " --> pdb=" O LYS P 127 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N GLU P 129 " --> pdb=" O VAL P 32 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'P' and resid 109 through 114 removed outlier: 3.626A pdb=" N ILE P 72 " --> pdb=" O TRP P 59 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU P 61 " --> pdb=" O LEU P 70 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU P 70 " --> pdb=" O LEU P 61 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 918 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: 1.75 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 2479 1.38 - 1.55: 3734 1.55 - 1.71: 67 1.71 - 1.88: 68 1.88 - 2.04: 6 Bond restraints: 6354 Sorted by residual: bond pdb=" C1B PKZ A 602 " pdb=" C2B PKZ A 602 " ideal model delta sigma weight residual 1.333 1.670 -0.337 2.00e-02 2.50e+03 2.83e+02 bond pdb=" C2B PKZ A 602 " pdb=" C3B PKZ A 602 " ideal model delta sigma weight residual 1.547 1.294 0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" C3B PKZ A 602 " pdb=" O3B PKZ A 602 " ideal model delta sigma weight residual 1.350 1.549 -0.199 2.00e-02 2.50e+03 9.86e+01 bond pdb=" C3B PKZ A 602 " pdb=" C4B PKZ A 602 " ideal model delta sigma weight residual 1.583 1.749 -0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" C2B PKZ A 602 " pdb=" O2B PKZ A 602 " ideal model delta sigma weight residual 1.477 1.589 -0.112 2.00e-02 2.50e+03 3.11e+01 ... (remaining 6349 not shown) Histogram of bond angle deviations from ideal: 89.19 - 107.25: 285 107.25 - 125.30: 8209 125.30 - 143.36: 219 143.36 - 161.42: 0 161.42 - 179.47: 2 Bond angle restraints: 8715 Sorted by residual: angle pdb=" N ILE P 48 " pdb=" CA ILE P 48 " pdb=" C ILE P 48 " ideal model delta sigma weight residual 112.29 108.53 3.76 9.40e-01 1.13e+00 1.60e+01 angle pdb=" N1A PKZ A 602 " pdb=" C6A PKZ A 602 " pdb=" N6A PKZ A 602 " ideal model delta sigma weight residual 108.45 120.15 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C5A PKZ A 602 " pdb=" C6A PKZ A 602 " pdb=" N6A PKZ A 602 " ideal model delta sigma weight residual 130.49 120.03 10.46 3.00e+00 1.11e-01 1.21e+01 angle pdb=" C LYS O 106 " pdb=" N ASP O 107 " pdb=" CA ASP O 107 " ideal model delta sigma weight residual 122.08 128.40 -6.32 1.84e+00 2.95e-01 1.18e+01 angle pdb=" C5P PKZ A 602 " pdb=" C6P PKZ A 602 " pdb=" C7P PKZ A 602 " ideal model delta sigma weight residual 109.47 118.14 -8.67 3.00e+00 1.11e-01 8.36e+00 ... (remaining 8710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 3543 35.59 - 71.19: 168 71.19 - 106.78: 83 106.78 - 142.38: 120 142.38 - 177.97: 30 Dihedral angle restraints: 3944 sinusoidal: 1856 harmonic: 2088 Sorted by residual: dihedral pdb=" C08 AJP A 607 " pdb=" C07 AJP A 607 " pdb=" C12 AJP A 607 " pdb=" C81 AJP A 607 " ideal model delta sinusoidal sigma weight residual 101.32 -76.65 177.97 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C22 AJP A 606 " pdb=" C20 AJP A 606 " pdb=" C21 AJP A 606 " pdb=" C80 AJP A 606 " ideal model delta sinusoidal sigma weight residual 65.75 -112.15 177.90 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C08 AJP A 606 " pdb=" C07 AJP A 606 " pdb=" C12 AJP A 606 " pdb=" C81 AJP A 606 " ideal model delta sinusoidal sigma weight residual 101.32 -75.49 176.81 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 3941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.215: 899 1.215 - 2.430: 0 2.430 - 3.644: 0 3.644 - 4.859: 16 4.859 - 6.074: 38 Chirality restraints: 953 Sorted by residual: chirality pdb=" C12 AJP A 604 " pdb=" C07 AJP A 604 " pdb=" C11 AJP A 604 " pdb=" C13 AJP A 604 " both_signs ideal model delta sigma weight residual False 3.01 -3.07 6.07 2.00e-01 2.50e+01 9.22e+02 chirality pdb=" C12 AJP A 606 " pdb=" C07 AJP A 606 " pdb=" C11 AJP A 606 " pdb=" C13 AJP A 606 " both_signs ideal model delta sigma weight residual False 3.01 -3.06 6.07 2.00e-01 2.50e+01 9.20e+02 chirality pdb=" C12 AJP A 607 " pdb=" C07 AJP A 607 " pdb=" C11 AJP A 607 " pdb=" C13 AJP A 607 " both_signs ideal model delta sigma weight residual False 3.01 -3.04 6.05 2.00e-01 2.50e+01 9.14e+02 ... (remaining 950 not shown) Planarity restraints: 1014 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P 82 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO P 83 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO P 83 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO P 83 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 201 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO A 202 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 2 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 3 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 3 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 3 " 0.019 5.00e-02 4.00e+02 ... (remaining 1011 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 115 2.70 - 3.25: 5776 3.25 - 3.80: 9847 3.80 - 4.35: 12786 4.35 - 4.90: 21516 Nonbonded interactions: 50040 Sorted by model distance: nonbonded pdb=" O MET A 328 " pdb=" OH TYR A 479 " model vdw 2.148 2.440 nonbonded pdb=" OH TYR A 207 " pdb=" O LEU A 220 " model vdw 2.196 2.440 nonbonded pdb=" O GLY O 129 " pdb=" OG SER P 67 " model vdw 2.243 2.440 nonbonded pdb=" NH1 ARG P 85 " pdb=" OD2 ASP P 106 " model vdw 2.285 2.520 nonbonded pdb=" NH2 ARG A 176 " pdb=" O VAL A 213 " model vdw 2.310 2.520 ... (remaining 50035 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.140 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.240 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 : 0.009 0.337 6354 Z= 0.699 Angle : 0.779 11.697 8715 Z= 0.371 Chirality : 1.243 6.074 953 Planarity : 0.004 0.042 1014 Dihedral : 38.417 177.971 2610 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.96 (0.29), residues: 712 helix: 0.22 (0.24), residues: 406 sheet: -0.52 (0.48), residues: 120 loop : -2.47 (0.38), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 66 HIS 0.008 0.001 HIS A 428 PHE 0.018 0.001 PHE A 17 TYR 0.019 0.002 TYR P 73 ARG 0.002 0.000 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.687 Fit side-chains REVERT: A 68 LYS cc_start: 0.8360 (ptmm) cc_final: 0.7750 (mttt) REVERT: A 238 LYS cc_start: 0.7237 (tptt) cc_final: 0.6791 (tppt) REVERT: A 403 ARG cc_start: 0.7739 (ttp80) cc_final: 0.6869 (tpp-160) REVERT: O 110 MET cc_start: 0.7853 (mtp) cc_final: 0.7623 (mtm) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 1.4441 time to fit residues: 156.4001 Evaluate side-chains 74 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 0.0570 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 232 GLN A 234 HIS A 428 HIS A 443 ASN O 25 GLN O 103 ASN P 25 GLN P 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6354 Z= 0.179 Angle : 1.908 35.513 8715 Z= 0.661 Chirality : 0.183 1.772 953 Planarity : 0.004 0.037 1014 Dihedral : 35.221 179.289 1315 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.25 % Allowed : 8.68 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.59 (0.32), residues: 712 helix: 1.70 (0.26), residues: 404 sheet: -0.10 (0.49), residues: 121 loop : -2.22 (0.39), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 465 HIS 0.005 0.001 HIS A 428 PHE 0.027 0.001 PHE A 17 TYR 0.026 0.001 TYR A 180 ARG 0.002 0.000 ARG P 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.722 Fit side-chains REVERT: A 31 GLU cc_start: 0.7325 (tm-30) cc_final: 0.7045 (tm-30) REVERT: A 238 LYS cc_start: 0.7182 (tptt) cc_final: 0.6727 (tppt) REVERT: A 403 ARG cc_start: 0.7744 (ttp80) cc_final: 0.6849 (tpp-160) REVERT: O 110 MET cc_start: 0.7811 (mtp) cc_final: 0.7559 (mtm) REVERT: P 58 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8639 (mt-10) outliers start: 14 outliers final: 9 residues processed: 89 average time/residue: 1.2121 time to fit residues: 113.4501 Evaluate side-chains 84 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 106 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 0.0170 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 234 HIS A 443 ASN P 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6354 Z= 0.262 Angle : 1.915 35.175 8715 Z= 0.669 Chirality : 0.185 1.848 953 Planarity : 0.004 0.037 1014 Dihedral : 35.153 179.600 1315 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.54 % Allowed : 9.81 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.94 (0.32), residues: 712 helix: 1.93 (0.26), residues: 401 sheet: 0.10 (0.50), residues: 121 loop : -1.93 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 465 HIS 0.006 0.001 HIS A 120 PHE 0.031 0.002 PHE A 17 TYR 0.023 0.002 TYR A 300 ARG 0.002 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.676 Fit side-chains REVERT: A 31 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7017 (tm-30) REVERT: A 238 LYS cc_start: 0.7208 (tptt) cc_final: 0.6767 (tppt) REVERT: A 403 ARG cc_start: 0.7775 (ttp80) cc_final: 0.6880 (tpp-160) REVERT: O 110 MET cc_start: 0.7873 (mtp) cc_final: 0.7583 (mtm) REVERT: P 127 LYS cc_start: 0.8540 (tttp) cc_final: 0.7991 (tttp) outliers start: 22 outliers final: 13 residues processed: 92 average time/residue: 1.1922 time to fit residues: 115.2794 Evaluate side-chains 89 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 130 GLN Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 234 HIS ** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6354 Z= 0.313 Angle : 1.933 35.369 8715 Z= 0.678 Chirality : 0.184 1.843 953 Planarity : 0.004 0.038 1014 Dihedral : 35.133 179.478 1315 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.05 % Allowed : 12.86 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 0.98 (0.32), residues: 712 helix: 1.90 (0.26), residues: 401 sheet: 0.26 (0.50), residues: 121 loop : -1.86 (0.39), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 128 HIS 0.007 0.001 HIS A 120 PHE 0.033 0.002 PHE A 17 TYR 0.025 0.002 TYR P 73 ARG 0.003 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.734 Fit side-chains REVERT: A 238 LYS cc_start: 0.7317 (tptt) cc_final: 0.6870 (tppt) REVERT: A 403 ARG cc_start: 0.7788 (ttp80) cc_final: 0.6884 (tpp-160) REVERT: O 92 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7390 (tm-30) REVERT: O 110 MET cc_start: 0.7853 (mtp) cc_final: 0.7497 (mtm) REVERT: P 127 LYS cc_start: 0.8652 (tttp) cc_final: 0.8126 (tttp) outliers start: 19 outliers final: 17 residues processed: 93 average time/residue: 1.2435 time to fit residues: 121.7115 Evaluate side-chains 97 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 130 GLN Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 106 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 0.0770 chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS P 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6354 Z= 0.204 Angle : 1.896 34.844 8715 Z= 0.659 Chirality : 0.184 1.834 953 Planarity : 0.004 0.038 1014 Dihedral : 35.105 179.118 1315 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.54 % Allowed : 13.18 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.32), residues: 712 helix: 2.35 (0.26), residues: 388 sheet: 0.45 (0.50), residues: 121 loop : -1.80 (0.38), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 465 HIS 0.004 0.001 HIS A 120 PHE 0.026 0.001 PHE A 17 TYR 0.020 0.002 TYR A 180 ARG 0.003 0.000 ARG P 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.643 Fit side-chains REVERT: A 238 LYS cc_start: 0.7249 (tptt) cc_final: 0.6797 (tppt) REVERT: A 403 ARG cc_start: 0.7772 (ttp80) cc_final: 0.6894 (tpp-160) REVERT: O 110 MET cc_start: 0.7825 (mtp) cc_final: 0.7596 (mtm) REVERT: P 127 LYS cc_start: 0.8646 (tttp) cc_final: 0.8116 (tttp) outliers start: 22 outliers final: 17 residues processed: 91 average time/residue: 1.2038 time to fit residues: 115.3727 Evaluate side-chains 94 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 130 GLN Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 106 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 16 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 57 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 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 234 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6354 Z= 0.179 Angle : 1.886 34.505 8715 Z= 0.653 Chirality : 0.185 1.834 953 Planarity : 0.004 0.037 1014 Dihedral : 35.098 179.272 1315 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.05 % Allowed : 13.83 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.61 (0.32), residues: 712 helix: 2.55 (0.26), residues: 388 sheet: 0.60 (0.51), residues: 121 loop : -1.73 (0.38), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 465 HIS 0.003 0.001 HIS A 120 PHE 0.023 0.001 PHE A 17 TYR 0.021 0.001 TYR A 180 ARG 0.003 0.000 ARG P 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.688 Fit side-chains REVERT: A 238 LYS cc_start: 0.7100 (tptt) cc_final: 0.6692 (tppt) REVERT: A 403 ARG cc_start: 0.7749 (ttp80) cc_final: 0.6897 (tpp-160) REVERT: O 110 MET cc_start: 0.7833 (mtp) cc_final: 0.7603 (mtm) REVERT: P 127 LYS cc_start: 0.8624 (tttp) cc_final: 0.8104 (tttp) outliers start: 19 outliers final: 12 residues processed: 90 average time/residue: 1.1816 time to fit residues: 112.0557 Evaluate side-chains 86 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 30 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6354 Z= 0.164 Angle : 1.877 34.209 8715 Z= 0.649 Chirality : 0.185 1.834 953 Planarity : 0.003 0.037 1014 Dihedral : 35.082 179.538 1315 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.57 % Allowed : 14.79 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.79 (0.33), residues: 712 helix: 2.68 (0.26), residues: 388 sheet: 0.73 (0.52), residues: 120 loop : -1.62 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 465 HIS 0.003 0.001 HIS A 120 PHE 0.021 0.001 PHE A 17 TYR 0.021 0.001 TYR A 180 ARG 0.003 0.000 ARG P 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.012 Fit side-chains REVERT: A 238 LYS cc_start: 0.7052 (tptt) cc_final: 0.6634 (tppt) REVERT: A 403 ARG cc_start: 0.7739 (ttp80) cc_final: 0.6913 (tpp-160) REVERT: O 110 MET cc_start: 0.7849 (mtp) cc_final: 0.7586 (mtm) REVERT: P 127 LYS cc_start: 0.8656 (tttp) cc_final: 0.8138 (tttp) outliers start: 16 outliers final: 15 residues processed: 86 average time/residue: 1.1631 time to fit residues: 105.5252 Evaluate side-chains 89 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 106 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN ** P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6354 Z= 0.193 Angle : 1.890 34.345 8715 Z= 0.655 Chirality : 0.185 1.838 953 Planarity : 0.004 0.037 1014 Dihedral : 35.096 179.385 1315 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.89 % Allowed : 15.27 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.77 (0.32), residues: 712 helix: 2.53 (0.26), residues: 394 sheet: 0.78 (0.53), residues: 120 loop : -1.50 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 128 HIS 0.004 0.001 HIS A 120 PHE 0.024 0.001 PHE A 17 TYR 0.019 0.002 TYR A 180 ARG 0.004 0.000 ARG P 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.707 Fit side-chains REVERT: A 238 LYS cc_start: 0.7080 (tptt) cc_final: 0.6673 (tppt) REVERT: A 403 ARG cc_start: 0.7764 (ttp80) cc_final: 0.6912 (tpp-160) REVERT: O 110 MET cc_start: 0.7869 (mtp) cc_final: 0.7596 (mtm) REVERT: P 127 LYS cc_start: 0.8655 (tttp) cc_final: 0.8140 (tttp) outliers start: 18 outliers final: 17 residues processed: 85 average time/residue: 1.1731 time to fit residues: 105.1082 Evaluate side-chains 90 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 26 THR Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 106 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 19 optimal weight: 0.0870 chunk 57 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 65 optimal weight: 0.0770 chunk 56 optimal weight: 5.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6354 Z= 0.156 Angle : 1.873 34.080 8715 Z= 0.647 Chirality : 0.186 1.835 953 Planarity : 0.003 0.037 1014 Dihedral : 35.065 179.625 1315 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.41 % Allowed : 15.59 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.90 (0.33), residues: 712 helix: 2.76 (0.26), residues: 388 sheet: 0.84 (0.53), residues: 120 loop : -1.62 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 66 HIS 0.002 0.001 HIS A 120 PHE 0.020 0.001 PHE A 17 TYR 0.021 0.001 TYR A 180 ARG 0.004 0.000 ARG P 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.652 Fit side-chains REVERT: A 41 GLU cc_start: 0.6764 (mp0) cc_final: 0.6156 (mp0) REVERT: A 238 LYS cc_start: 0.7002 (tptt) cc_final: 0.6610 (tppt) REVERT: A 403 ARG cc_start: 0.7731 (ttp80) cc_final: 0.6897 (tpp-160) REVERT: O 110 MET cc_start: 0.7863 (mtp) cc_final: 0.7622 (mtm) REVERT: P 127 LYS cc_start: 0.8654 (tttp) cc_final: 0.8138 (tttp) outliers start: 15 outliers final: 13 residues processed: 83 average time/residue: 1.1754 time to fit residues: 102.8623 Evaluate side-chains 84 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 32 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 5 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6354 Z= 0.209 Angle : 1.894 34.406 8715 Z= 0.657 Chirality : 0.185 1.840 953 Planarity : 0.004 0.036 1014 Dihedral : 35.101 179.308 1315 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.41 % Allowed : 15.43 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.79 (0.32), residues: 712 helix: 2.53 (0.26), residues: 394 sheet: 0.84 (0.53), residues: 120 loop : -1.48 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 128 HIS 0.004 0.001 HIS A 120 PHE 0.026 0.001 PHE A 17 TYR 0.020 0.002 TYR A 300 ARG 0.004 0.000 ARG P 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1424 Ramachandran restraints generated. 712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.622 Fit side-chains REVERT: A 238 LYS cc_start: 0.7150 (tptt) cc_final: 0.6719 (tppt) REVERT: A 403 ARG cc_start: 0.7762 (ttp80) cc_final: 0.6906 (tpp-160) REVERT: O 110 MET cc_start: 0.7896 (mtp) cc_final: 0.7630 (mtm) REVERT: P 127 LYS cc_start: 0.8660 (tttp) cc_final: 0.8144 (tttp) outliers start: 15 outliers final: 15 residues processed: 82 average time/residue: 1.1742 time to fit residues: 101.4419 Evaluate side-chains 89 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 265 MET Chi-restraints excluded: chain O residue 70 ILE Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 29 SER Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 106 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 0.0270 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.116545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.090452 restraints weight = 8074.238| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.75 r_work: 0.2884 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6354 Z= 0.172 Angle : 1.883 34.280 8715 Z= 0.651 Chirality : 0.185 1.835 953 Planarity : 0.003 0.037 1014 Dihedral : 35.075 179.442 1315 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.57 % Allowed : 15.59 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: 1.90 (0.33), residues: 712 helix: 2.63 (0.26), residues: 394 sheet: 0.86 (0.53), residues: 120 loop : -1.45 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 128 HIS 0.003 0.001 HIS A 120 PHE 0.022 0.001 PHE A 17 TYR 0.020 0.001 TYR A 180 ARG 0.004 0.000 ARG P 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2628.02 seconds wall clock time: 47 minutes 18.13 seconds (2838.13 seconds total)