Starting phenix.real_space_refine on Wed Sep 25 04:37:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e40_27875/09_2024/8e40_27875.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e40_27875/09_2024/8e40_27875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e40_27875/09_2024/8e40_27875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e40_27875/09_2024/8e40_27875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e40_27875/09_2024/8e40_27875.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e40_27875/09_2024/8e40_27875.cif" } resolution = 3.57 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3868 atoms to isotropic. 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 2 6.06 5 P 47 5.49 5 S 30 5.16 5 C 3835 2.51 5 N 1122 2.21 5 O 1261 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6297 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3085 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 347} Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1000 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1220 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain: "R" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 456 Classifications: {'RNA': 22} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 14} Link IDs: {'rna3p': 21} Chain: "r" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 534 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 13, 'rna3p_pyr': 8} Link IDs: {'rna2p': 3, 'rna3p': 21} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 757 SG CYS A 97 34.707 53.781 84.146 1.00 27.23 S ATOM 781 SG CYS A 100 30.843 53.501 86.010 1.00 32.88 S ATOM 2300 SG CYS A 287 59.635 23.728 72.488 1.00 60.84 S Time building chain proxies: 4.81, per 1000 atoms: 0.76 Number of scatterers: 6297 At special positions: 0 Unit cell: (92.92, 98.44, 134.32, 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 2 29.99 S 30 16.00 P 47 15.00 O 1261 8.00 N 1122 7.00 C 3835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 759.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 65 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 100 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 287 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 257 " 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 38.5% alpha, 16.7% beta 17 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 65 through 79 Processing helix chain 'A' and resid 97 through 111 removed outlier: 4.056A pdb=" N THR A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 142 removed outlier: 3.851A pdb=" N ALA A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 removed outlier: 3.825A pdb=" N VAL A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.962A pdb=" N THR A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 259 through 266 removed outlier: 3.890A pdb=" N LEU A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 270 Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.758A pdb=" N MET A 294 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 331 removed outlier: 4.049A pdb=" N GLY A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 362 through 379 Processing helix chain 'B' and resid 14 through 31 Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 166 through 171 Processing helix chain 'C' and resid 6 through 13 Processing helix chain 'C' and resid 15 through 22 removed outlier: 3.866A pdb=" N ARG C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS C 20 " --> pdb=" O GLU C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 70 through 75 removed outlier: 4.295A pdb=" N GLN C 74 " --> pdb=" O PRO C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.916A pdb=" N GLU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 149 removed outlier: 3.677A pdb=" N ARG C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87 removed outlier: 6.767A pdb=" N TYR A 86 " --> pdb=" O THR A 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 240 removed outlier: 5.035A pdb=" N VAL A 224 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N GLN A 237 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 11.077A pdb=" N TYR A 222 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG A 277 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR A 276 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N CYS A 307 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL A 278 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N PHE A 309 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS A 280 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA A 335 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 308 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 41 removed outlier: 6.492A pdb=" N THR B 68 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE B 66 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS B 56 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU B 64 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 65 " --> pdb=" O GLU B 88 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY B 84 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE B 87 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE B 9 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 11.161A pdb=" N TRP B 89 " --> pdb=" O VAL B 7 " (cutoff:3.500A) removed outlier: 14.398A pdb=" N VAL B 7 " --> pdb=" O TRP B 89 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 55 " --> pdb=" O PHE C 68 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 1.97 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1818 1.34 - 1.46: 1791 1.46 - 1.58: 2826 1.58 - 1.70: 92 1.70 - 1.82: 43 Bond restraints: 6570 Sorted by residual: bond pdb=" N LEU C 119 " pdb=" CA LEU C 119 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.18e+00 bond pdb=" N ASP C 34 " pdb=" CA ASP C 34 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.35e-02 5.49e+03 6.11e+00 bond pdb=" C VAL C 5 " pdb=" N PRO C 6 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.08e+00 bond pdb=" N ASP C 120 " pdb=" CA ASP C 120 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.82e+00 bond pdb=" N ARG C 118 " pdb=" CA ARG C 118 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.33e-02 5.65e+03 4.32e+00 ... (remaining 6565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 8712 2.02 - 4.05: 321 4.05 - 6.07: 56 6.07 - 8.09: 15 8.09 - 10.12: 7 Bond angle restraints: 9111 Sorted by residual: angle pdb=" CA LYS A 113 " pdb=" CB LYS A 113 " pdb=" CG LYS A 113 " ideal model delta sigma weight residual 114.10 124.22 -10.12 2.00e+00 2.50e-01 2.56e+01 angle pdb=" CA GLU C 38 " pdb=" CB GLU C 38 " pdb=" CG GLU C 38 " ideal model delta sigma weight residual 114.10 123.28 -9.18 2.00e+00 2.50e-01 2.11e+01 angle pdb=" CA GLU A 302 " pdb=" CB GLU A 302 " pdb=" CG GLU A 302 " ideal model delta sigma weight residual 114.10 123.07 -8.97 2.00e+00 2.50e-01 2.01e+01 angle pdb=" N LEU A 260 " pdb=" CA LEU A 260 " pdb=" C LEU A 260 " ideal model delta sigma weight residual 111.36 106.48 4.88 1.09e+00 8.42e-01 2.01e+01 angle pdb=" O3' U r 2 " pdb=" C3' U r 2 " pdb=" C2' U r 2 " ideal model delta sigma weight residual 113.70 120.40 -6.70 1.50e+00 4.44e-01 2.00e+01 ... (remaining 9106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 3447 26.56 - 53.11: 357 53.11 - 79.67: 65 79.67 - 106.23: 4 106.23 - 132.79: 2 Dihedral angle restraints: 3875 sinusoidal: 2013 harmonic: 1862 Sorted by residual: dihedral pdb=" CA LYS B 161 " pdb=" C LYS B 161 " pdb=" N PRO B 162 " pdb=" CA PRO B 162 " ideal model delta harmonic sigma weight residual 180.00 153.24 26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA THR B 68 " pdb=" C THR B 68 " pdb=" N TYR B 69 " pdb=" CA TYR B 69 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA THR A 32 " pdb=" C THR A 32 " pdb=" N VAL A 33 " pdb=" CA VAL A 33 " ideal model delta harmonic sigma weight residual 180.00 159.48 20.52 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 828 0.067 - 0.135: 132 0.135 - 0.202: 16 0.202 - 0.269: 1 0.269 - 0.336: 1 Chirality restraints: 978 Sorted by residual: chirality pdb=" C3' U r 2 " pdb=" C4' U r 2 " pdb=" O3' U r 2 " pdb=" C2' U r 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB THR A 231 " pdb=" CA THR A 231 " pdb=" OG1 THR A 231 " pdb=" CG2 THR A 231 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR C 62 " pdb=" N THR C 62 " pdb=" C THR C 62 " pdb=" CB THR C 62 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 8.19e-01 ... (remaining 975 not shown) Planarity restraints: 1008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 13 " -0.080 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO A 14 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 14 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 14 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 198 " 0.060 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO A 199 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 233 " 0.053 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 234 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.044 5.00e-02 4.00e+02 ... (remaining 1005 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 837 2.76 - 3.29: 5650 3.29 - 3.83: 11067 3.83 - 4.36: 12501 4.36 - 4.90: 20514 Nonbonded interactions: 50569 Sorted by model distance: nonbonded pdb=" CB ALA A 258 " pdb=" SG CYS A 290 " model vdw 2.225 3.820 nonbonded pdb=" O ASP A 31 " pdb=" CG1 VAL A 58 " model vdw 2.235 3.460 nonbonded pdb=" N TYR A 59 " pdb=" CD PRO A 60 " model vdw 2.278 3.520 nonbonded pdb=" O PHE A 268 " pdb=" N6 A r 17 " model vdw 2.304 3.120 nonbonded pdb=" N GLN A 259 " pdb=" OE1 GLN A 259 " model vdw 2.316 3.120 ... (remaining 50564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.130 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 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 : 0.005 0.058 6570 Z= 0.323 Angle : 0.932 10.118 9111 Z= 0.510 Chirality : 0.050 0.336 978 Planarity : 0.008 0.118 1008 Dihedral : 19.336 132.785 2669 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.91 % Favored : 93.93 % Rotamer: Outliers : 2.12 % Allowed : 27.43 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.30), residues: 626 helix: -1.56 (0.30), residues: 205 sheet: -1.40 (0.55), residues: 109 loop : -2.27 (0.30), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 211 HIS 0.007 0.001 HIS A 75 PHE 0.034 0.002 PHE C 12 TYR 0.018 0.002 TYR A 219 ARG 0.010 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7123 (t0) outliers start: 12 outliers final: 4 residues processed: 114 average time/residue: 0.2350 time to fit residues: 33.5266 Evaluate side-chains 59 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 266 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 195 HIS ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6570 Z= 0.240 Angle : 0.675 10.298 9111 Z= 0.338 Chirality : 0.040 0.221 978 Planarity : 0.006 0.069 1008 Dihedral : 13.983 133.852 1363 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.78 % Allowed : 27.79 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.32), residues: 626 helix: -0.48 (0.34), residues: 218 sheet: -1.77 (0.46), residues: 131 loop : -1.90 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 70 HIS 0.004 0.001 HIS A 250 PHE 0.022 0.002 PHE A 241 TYR 0.013 0.001 TYR A 91 ARG 0.007 0.001 ARG B 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 59 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7191 (t0) outliers start: 27 outliers final: 13 residues processed: 83 average time/residue: 0.1843 time to fit residues: 20.3580 Evaluate side-chains 64 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 50 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 117 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.0470 chunk 16 optimal weight: 0.0000 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.2088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS A 257 HIS ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6570 Z= 0.247 Angle : 0.652 9.213 9111 Z= 0.324 Chirality : 0.040 0.220 978 Planarity : 0.005 0.040 1008 Dihedral : 14.273 133.432 1357 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.96 % Allowed : 25.49 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.33), residues: 626 helix: 0.04 (0.35), residues: 217 sheet: -1.80 (0.44), residues: 140 loop : -1.51 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 70 HIS 0.011 0.001 HIS A 81 PHE 0.022 0.002 PHE A 241 TYR 0.012 0.002 TYR A 339 ARG 0.009 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 55 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 167 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8153 (t) outliers start: 28 outliers final: 16 residues processed: 79 average time/residue: 0.1894 time to fit residues: 20.0547 Evaluate side-chains 64 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 47 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 53 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 81 HIS A 195 HIS ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN C 45 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6570 Z= 0.209 Angle : 0.623 9.509 9111 Z= 0.310 Chirality : 0.039 0.223 978 Planarity : 0.004 0.058 1008 Dihedral : 14.297 131.845 1353 Min Nonbonded Distance : 1.303 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.13 % Allowed : 25.66 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.34), residues: 626 helix: 0.31 (0.35), residues: 213 sheet: -1.78 (0.44), residues: 141 loop : -1.41 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 77 HIS 0.050 0.002 HIS A 257 PHE 0.019 0.002 PHE A 241 TYR 0.010 0.001 TYR A 86 ARG 0.005 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 54 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 81 average time/residue: 0.1898 time to fit residues: 20.6024 Evaluate side-chains 69 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 46 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 287 CYS Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6570 Z= 0.323 Angle : 0.690 10.183 9111 Z= 0.343 Chirality : 0.040 0.219 978 Planarity : 0.004 0.037 1008 Dihedral : 14.850 130.737 1353 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.02 % Allowed : 25.66 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.34), residues: 626 helix: 0.34 (0.35), residues: 215 sheet: -1.96 (0.43), residues: 142 loop : -1.37 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 77 HIS 0.007 0.001 HIS A 257 PHE 0.017 0.002 PHE C 12 TYR 0.014 0.002 TYR A 91 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 50 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 MET cc_start: 0.3927 (tmm) cc_final: 0.3266 (tmm) outliers start: 34 outliers final: 25 residues processed: 79 average time/residue: 0.1803 time to fit residues: 19.0830 Evaluate side-chains 71 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 46 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6570 Z= 0.194 Angle : 0.626 9.088 9111 Z= 0.307 Chirality : 0.039 0.224 978 Planarity : 0.004 0.032 1008 Dihedral : 14.767 127.844 1353 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.60 % Allowed : 27.08 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.34), residues: 626 helix: 0.55 (0.35), residues: 217 sheet: -1.75 (0.44), residues: 142 loop : -1.27 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 77 HIS 0.004 0.001 HIS B 27 PHE 0.022 0.002 PHE C 12 TYR 0.008 0.001 TYR A 182 ARG 0.006 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 52 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 MET cc_start: 0.3875 (tmm) cc_final: 0.3224 (tmm) outliers start: 26 outliers final: 19 residues processed: 75 average time/residue: 0.1767 time to fit residues: 18.0083 Evaluate side-chains 64 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 45 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6570 Z= 0.300 Angle : 0.674 8.201 9111 Z= 0.335 Chirality : 0.040 0.218 978 Planarity : 0.004 0.031 1008 Dihedral : 15.127 126.512 1353 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.78 % Allowed : 27.26 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.35), residues: 626 helix: 0.77 (0.36), residues: 212 sheet: -1.89 (0.44), residues: 140 loop : -1.08 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 34 HIS 0.006 0.001 HIS A 81 PHE 0.018 0.002 PHE C 18 TYR 0.011 0.001 TYR A 91 ARG 0.004 0.000 ARG C 9 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 46 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 122 MET cc_start: 0.3879 (tmm) cc_final: 0.3272 (tmm) outliers start: 27 outliers final: 23 residues processed: 69 average time/residue: 0.1575 time to fit residues: 15.1928 Evaluate side-chains 70 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 47 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 276 TYR Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6570 Z= 0.181 Angle : 0.622 8.850 9111 Z= 0.305 Chirality : 0.039 0.219 978 Planarity : 0.004 0.031 1008 Dihedral : 14.908 123.027 1353 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.19 % Allowed : 28.85 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.35), residues: 626 helix: 0.90 (0.36), residues: 211 sheet: -1.70 (0.45), residues: 142 loop : -1.10 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 77 HIS 0.003 0.001 HIS A 250 PHE 0.015 0.002 PHE B 39 TYR 0.008 0.001 TYR A 339 ARG 0.004 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 52 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6862 (pm20) cc_final: 0.6551 (pm20) outliers start: 18 outliers final: 14 residues processed: 67 average time/residue: 0.1760 time to fit residues: 16.3101 Evaluate side-chains 62 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6570 Z= 0.252 Angle : 0.667 12.769 9111 Z= 0.328 Chirality : 0.040 0.213 978 Planarity : 0.004 0.030 1008 Dihedral : 15.055 122.334 1353 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.36 % Allowed : 29.73 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.35), residues: 626 helix: 0.83 (0.36), residues: 219 sheet: -1.75 (0.44), residues: 142 loop : -1.17 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 38 HIS 0.005 0.001 HIS A 75 PHE 0.015 0.002 PHE A 164 TYR 0.010 0.001 TYR B 30 ARG 0.003 0.000 ARG C 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 47 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 18 residues processed: 62 average time/residue: 0.1725 time to fit residues: 14.8461 Evaluate side-chains 65 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 47 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 379 GLN Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 7 optimal weight: 0.0570 chunk 14 optimal weight: 0.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6570 Z= 0.190 Angle : 0.639 11.849 9111 Z= 0.312 Chirality : 0.039 0.211 978 Planarity : 0.003 0.030 1008 Dihedral : 14.927 119.749 1353 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.54 % Allowed : 29.20 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.35), residues: 626 helix: 0.88 (0.36), residues: 218 sheet: -1.54 (0.46), residues: 140 loop : -1.13 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 77 HIS 0.004 0.001 HIS A 81 PHE 0.017 0.002 PHE B 39 TYR 0.009 0.001 TYR B 30 ARG 0.004 0.000 ARG C 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1252 Ramachandran restraints generated. 626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 53 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 GLN cc_start: 0.6974 (pm20) cc_final: 0.6665 (pm20) outliers start: 20 outliers final: 19 residues processed: 69 average time/residue: 0.1720 time to fit residues: 16.6702 Evaluate side-chains 70 residues out of total 567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 51 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 65 HIS Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 144 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 0.0010 chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 HIS ** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.078919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.060502 restraints weight = 34217.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.062352 restraints weight = 18324.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.063489 restraints weight = 12880.448| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6570 Z= 0.188 Angle : 0.633 9.704 9111 Z= 0.310 Chirality : 0.039 0.207 978 Planarity : 0.003 0.032 1008 Dihedral : 14.753 118.310 1353 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.54 % Allowed : 29.20 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.36), residues: 626 helix: 0.96 (0.36), residues: 218 sheet: -1.31 (0.49), residues: 131 loop : -1.05 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 77 HIS 0.005 0.001 HIS A 81 PHE 0.017 0.002 PHE B 39 TYR 0.009 0.001 TYR B 30 ARG 0.003 0.000 ARG A 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1607.36 seconds wall clock time: 29 minutes 29.30 seconds (1769.30 seconds total)