Starting phenix.real_space_refine on Fri Dec 27 17:16:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7urd_26709/12_2024/7urd_26709.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urd_26709/12_2024/7urd_26709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7urd_26709/12_2024/7urd_26709.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urd_26709/12_2024/7urd_26709.map" model { file = "/net/cci-nas-00/data/ceres_data/7urd_26709/12_2024/7urd_26709.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urd_26709/12_2024/7urd_26709.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.087 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 35 5.16 5 C 3642 2.51 5 N 897 2.21 5 O 959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5534 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3449 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 158 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "H" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 926 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 172 Unusual residues: {' ZN': 1, 'AJP': 1, 'CLR': 2, 'O50': 1, 'OLA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 9 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2833 SG CYS A 370 56.521 29.274 19.732 1.00108.35 S ATOM 2880 SG CYS A 376 55.636 28.723 23.034 1.00118.02 S ATOM 2908 SG CYS A 380 59.361 29.098 21.112 1.00127.74 S Time building chain proxies: 4.27, per 1000 atoms: 0.77 Number of scatterers: 5534 At special positions: 0 Unit cell: (98.77, 69.72, 93.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 35 16.00 O 959 8.00 N 897 7.00 C 3642 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 217 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.69 Conformation dependent library (CDL) restraints added in 821.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 506 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 370 " pdb="ZN ZN A 506 " - pdb=" ND1 HIS A 382 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 376 " pdb="ZN ZN A 506 " - pdb=" SG CYS A 380 " Number of angles added : 3 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1254 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 51.5% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 5 through 28 removed outlier: 4.921A pdb=" N LEU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N LEU A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Proline residue: A 20 - end of helix Processing helix chain 'A' and resid 29 through 43 Processing helix chain 'A' and resid 48 through 68 Processing helix chain 'A' and resid 72 through 89 removed outlier: 3.952A pdb=" N LEU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 111 Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.686A pdb=" N HIS A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 143 removed outlier: 3.570A pdb=" N ILE A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.842A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 209 removed outlier: 3.870A pdb=" N LEU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 264 removed outlier: 3.654A pdb=" N VAL A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 292 through 301 removed outlier: 4.359A pdb=" N ASN A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 320 through 336 Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.610A pdb=" N ALA A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 410 Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 439 through 455 removed outlier: 3.713A pdb=" N PHE A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 103 removed outlier: 3.891A pdb=" N PHE L 103 " --> pdb=" O PRO L 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 4.201A pdb=" N TYR H 51 " --> pdb=" O PHE H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.740A pdb=" N SER H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 206 Processing sheet with id=AA3, first strand: chain 'L' and resid 24 through 27 removed outlier: 5.677A pdb=" N THR L 89 " --> pdb=" O THR L 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 30 through 33 removed outlier: 6.863A pdb=" N LEU L 31 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP L 55 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.573A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY H 68 " --> pdb=" O TRP H 55 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LYS H 57 " --> pdb=" O TRP H 66 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N TRP H 66 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.573A pdb=" N GLU H 29 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR H 127 " --> pdb=" O ARG H 117 " (cutoff:3.500A) 300 hydrogen bonds defined for protein. 849 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: 1.54 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.19: 4 1.19 - 1.39: 2353 1.39 - 1.59: 3288 1.59 - 1.78: 10 1.78 - 1.98: 50 Bond restraints: 5705 Sorted by residual: bond pdb=" C07 AJP A 504 " pdb=" C08 AJP A 504 " ideal model delta sigma weight residual 1.550 1.980 -0.430 2.00e-02 2.50e+03 4.62e+02 bond pdb=" C01 AJP A 504 " pdb=" C02 AJP A 504 " ideal model delta sigma weight residual 1.521 1.947 -0.426 2.00e-02 2.50e+03 4.55e+02 bond pdb=" C08 AJP A 504 " pdb=" O09 AJP A 504 " ideal model delta sigma weight residual 1.410 0.998 0.412 2.00e-02 2.50e+03 4.24e+02 bond pdb=" C02 AJP A 504 " pdb=" C03 AJP A 504 " ideal model delta sigma weight residual 1.525 1.133 0.392 2.00e-02 2.50e+03 3.85e+02 bond pdb=" C05 AJP A 504 " pdb=" O09 AJP A 504 " ideal model delta sigma weight residual 1.407 1.784 -0.377 2.00e-02 2.50e+03 3.55e+02 ... (remaining 5700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 7706 4.20 - 8.40: 54 8.40 - 12.60: 7 12.60 - 16.80: 4 16.80 - 20.99: 1 Bond angle restraints: 7772 Sorted by residual: angle pdb=" C06 AJP A 504 " pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " ideal model delta sigma weight residual 120.30 141.29 -20.99 3.00e+00 1.11e-01 4.90e+01 angle pdb=" C11 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C81 AJP A 504 " ideal model delta sigma weight residual 114.35 98.09 16.26 3.00e+00 1.11e-01 2.94e+01 angle pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C13 AJP A 504 " ideal model delta sigma weight residual 114.18 129.16 -14.98 3.00e+00 1.11e-01 2.49e+01 angle pdb=" C07 AJP A 504 " pdb=" C08 AJP A 504 " pdb=" C10 AJP A 504 " ideal model delta sigma weight residual 107.39 93.44 13.95 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C PRO A 377 " pdb=" N PRO A 378 " pdb=" CA PRO A 378 " ideal model delta sigma weight residual 119.47 124.77 -5.30 1.16e+00 7.43e-01 2.09e+01 ... (remaining 7767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 3322 34.55 - 69.10: 79 69.10 - 103.65: 34 103.65 - 138.20: 37 138.20 - 172.75: 14 Dihedral angle restraints: 3486 sinusoidal: 1524 harmonic: 1962 Sorted by residual: dihedral pdb=" CA TYR H 74 " pdb=" C TYR H 74 " pdb=" N VAL H 75 " pdb=" CA VAL H 75 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" C06 AJP A 504 " pdb=" C07 AJP A 504 " pdb=" C12 AJP A 504 " pdb=" C13 AJP A 504 " ideal model delta sinusoidal sigma weight residual 109.15 -63.60 172.75 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C12 AJP A 504 " pdb=" C10 AJP A 504 " pdb=" C11 AJP A 504 " pdb=" O82 AJP A 504 " ideal model delta sinusoidal sigma weight residual 287.38 117.68 169.70 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 3483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.107: 849 1.107 - 2.213: 0 2.213 - 3.320: 0 3.320 - 4.426: 1 4.426 - 5.533: 24 Chirality restraints: 874 Sorted by residual: chirality pdb=" C15 AJP A 504 " pdb=" C14 AJP A 504 " pdb=" C16 AJP A 504 " pdb=" C20 AJP A 504 " both_signs ideal model delta sigma weight residual False -2.42 3.11 -5.53 2.00e-01 2.50e+01 7.65e+02 chirality pdb=" C16 AJP A 504 " pdb=" C11 AJP A 504 " pdb=" C15 AJP A 504 " pdb=" C17 AJP A 504 " both_signs ideal model delta sigma weight residual False -2.70 2.76 -5.46 2.00e-01 2.50e+01 7.45e+02 chirality pdb=" C20 AJP A 504 " pdb=" C15 AJP A 504 " pdb=" C19 AJP A 504 " pdb=" C21 AJP A 504 " both_signs ideal model delta sigma weight residual False 2.96 -2.42 5.38 2.00e-01 2.50e+01 7.23e+02 ... (remaining 871 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 215 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 216 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 216 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 216 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 219 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 220 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 14 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C LEU A 14 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 14 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 15 " -0.009 2.00e-02 2.50e+03 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 267 2.72 - 3.27: 5456 3.27 - 3.81: 9026 3.81 - 4.36: 11401 4.36 - 4.90: 19866 Nonbonded interactions: 46016 Sorted by model distance: nonbonded pdb=" OG SER A 242 " pdb=" OD1 ASP A 413 " model vdw 2.177 3.040 nonbonded pdb=" NH1 ARG A 360 " pdb=" O VAL A 371 " model vdw 2.196 3.120 nonbonded pdb=" OG SER H 26 " pdb=" OG SER H 40 " model vdw 2.251 3.040 nonbonded pdb=" OG SER L 27 " pdb=" OG1 THR L 42 " model vdw 2.266 3.040 nonbonded pdb=" OG SER A 79 " pdb=" OH TYR A 160 " model vdw 2.280 3.040 ... (remaining 46011 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.880 Find NCS groups from input model: 0.050 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:13.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.017 0.430 5705 Z= 1.120 Angle : 0.954 20.994 7772 Z= 0.412 Chirality : 0.833 5.533 874 Planarity : 0.004 0.043 924 Dihedral : 26.242 172.752 2217 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.28), residues: 666 helix: -0.91 (0.25), residues: 324 sheet: -1.58 (0.42), residues: 129 loop : -2.50 (0.37), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.006 0.001 HIS A 94 PHE 0.018 0.001 PHE A 403 TYR 0.013 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.7350 (mmt180) cc_final: 0.6938 (mtm180) REVERT: A 361 LYS cc_start: 0.7957 (tttt) cc_final: 0.7605 (ttpt) REVERT: A 432 HIS cc_start: 0.8143 (t-90) cc_final: 0.7735 (t70) REVERT: L 23 HIS cc_start: 0.8141 (m-70) cc_final: 0.7933 (m-70) REVERT: H 101 GLN cc_start: 0.8481 (tt0) cc_final: 0.8253 (tt0) REVERT: H 119 TYR cc_start: 0.6625 (t80) cc_final: 0.6393 (t80) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 1.1950 time to fit residues: 126.2259 Evaluate side-chains 73 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 GLN A 24 GLN A 66 HIS A 91 HIS A 94 HIS A 174 HIS A 247 HIS L 111 HIS H 52 ASN H 78 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5705 Z= 0.181 Angle : 1.095 32.247 7772 Z= 0.414 Chirality : 0.118 2.107 874 Planarity : 0.004 0.040 924 Dihedral : 20.285 179.650 1059 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.73 % Allowed : 9.71 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.32), residues: 666 helix: 0.62 (0.27), residues: 329 sheet: -1.03 (0.43), residues: 129 loop : -1.58 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.005 0.001 HIS A 53 PHE 0.015 0.001 PHE A 403 TYR 0.018 0.001 TYR A 83 ARG 0.005 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.6663 (mmt) cc_final: 0.6376 (mtm) REVERT: A 124 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6937 (mtm-85) REVERT: A 142 ASP cc_start: 0.8110 (m-30) cc_final: 0.7792 (m-30) REVERT: A 154 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: A 235 ARG cc_start: 0.7336 (mmt180) cc_final: 0.6948 (mtm180) REVERT: A 361 LYS cc_start: 0.7925 (tttt) cc_final: 0.7673 (ttpt) REVERT: A 375 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7758 (mtt-85) REVERT: A 432 HIS cc_start: 0.8080 (t-90) cc_final: 0.7787 (t70) REVERT: L 23 HIS cc_start: 0.8080 (m-70) cc_final: 0.7837 (m-70) REVERT: H 101 GLN cc_start: 0.8510 (tt0) cc_final: 0.8247 (tt0) REVERT: H 119 TYR cc_start: 0.6549 (t80) cc_final: 0.6276 (t80) outliers start: 10 outliers final: 2 residues processed: 94 average time/residue: 1.2196 time to fit residues: 119.8557 Evaluate side-chains 87 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 375 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5705 Z= 0.187 Angle : 1.074 31.444 7772 Z= 0.404 Chirality : 0.118 2.111 874 Planarity : 0.004 0.040 924 Dihedral : 20.145 179.491 1059 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.08 % Allowed : 13.69 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.33), residues: 666 helix: 1.34 (0.28), residues: 329 sheet: -0.76 (0.43), residues: 129 loop : -1.16 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 66 HIS 0.004 0.001 HIS A 53 PHE 0.014 0.001 PHE A 403 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7600 (ptt) REVERT: A 109 MET cc_start: 0.6645 (mmt) cc_final: 0.6301 (mtm) REVERT: A 124 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.7008 (mtm-85) REVERT: A 154 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: A 235 ARG cc_start: 0.7320 (mmt180) cc_final: 0.6964 (mtm180) REVERT: A 375 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7761 (mtt-85) REVERT: H 101 GLN cc_start: 0.8499 (tt0) cc_final: 0.8276 (tt0) REVERT: H 119 TYR cc_start: 0.6530 (t80) cc_final: 0.6312 (t80) outliers start: 12 outliers final: 2 residues processed: 90 average time/residue: 1.2296 time to fit residues: 115.7813 Evaluate side-chains 88 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 375 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 0.0770 chunk 53 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5705 Z= 0.170 Angle : 1.068 31.626 7772 Z= 0.400 Chirality : 0.118 2.115 874 Planarity : 0.004 0.039 924 Dihedral : 20.083 179.996 1059 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.43 % Allowed : 15.42 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.34), residues: 666 helix: 1.68 (0.29), residues: 331 sheet: -0.53 (0.44), residues: 128 loop : -0.87 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.005 0.001 HIS A 432 PHE 0.013 0.001 PHE A 403 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7521 (ptt) REVERT: A 109 MET cc_start: 0.6646 (mmt) cc_final: 0.6324 (mtm) REVERT: A 112 MET cc_start: 0.7804 (mtp) cc_final: 0.7423 (mtt) REVERT: A 124 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6878 (mtt-85) REVERT: A 154 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7491 (mt-10) REVERT: A 235 ARG cc_start: 0.7272 (mmt180) cc_final: 0.6977 (mtm180) REVERT: A 338 PHE cc_start: 0.7292 (t80) cc_final: 0.6534 (m-80) REVERT: A 375 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7796 (mtt-85) REVERT: A 427 MET cc_start: 0.7264 (ttt) cc_final: 0.7039 (ttt) REVERT: L 89 THR cc_start: 0.8973 (p) cc_final: 0.8395 (m) REVERT: H 101 GLN cc_start: 0.8515 (tt0) cc_final: 0.8273 (tt0) REVERT: H 119 TYR cc_start: 0.6542 (t80) cc_final: 0.6301 (t80) outliers start: 14 outliers final: 2 residues processed: 92 average time/residue: 1.2049 time to fit residues: 116.3242 Evaluate side-chains 84 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 388 LEU 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: 7.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5705 Z= 0.187 Angle : 1.070 31.326 7772 Z= 0.401 Chirality : 0.118 2.109 874 Planarity : 0.004 0.039 924 Dihedral : 20.059 179.492 1059 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.39 % Allowed : 16.98 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.34), residues: 666 helix: 1.80 (0.29), residues: 331 sheet: -0.36 (0.45), residues: 127 loop : -0.86 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 66 HIS 0.004 0.001 HIS A 432 PHE 0.014 0.001 PHE A 403 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.6588 (mmt) cc_final: 0.6274 (mtm) REVERT: A 124 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6938 (mtm-85) REVERT: A 154 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: A 235 ARG cc_start: 0.7300 (mmt180) cc_final: 0.6981 (mtm180) REVERT: L 89 THR cc_start: 0.8944 (p) cc_final: 0.8380 (m) REVERT: H 29 GLU cc_start: 0.6768 (mt-10) cc_final: 0.5991 (mm-30) REVERT: H 101 GLN cc_start: 0.8508 (tt0) cc_final: 0.8240 (tt0) REVERT: H 119 TYR cc_start: 0.6583 (t80) cc_final: 0.6348 (t80) outliers start: 8 outliers final: 4 residues processed: 81 average time/residue: 1.2776 time to fit residues: 108.4167 Evaluate side-chains 83 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 388 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 36 optimal weight: 0.0270 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5705 Z= 0.158 Angle : 1.064 31.329 7772 Z= 0.397 Chirality : 0.118 2.109 874 Planarity : 0.004 0.039 924 Dihedral : 20.009 179.689 1059 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.73 % Allowed : 17.68 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.34), residues: 666 helix: 1.95 (0.29), residues: 331 sheet: -0.37 (0.45), residues: 128 loop : -0.83 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.003 0.001 HIS A 53 PHE 0.012 0.001 PHE A 403 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.6600 (mmt) cc_final: 0.6273 (mtm) REVERT: A 112 MET cc_start: 0.7738 (mtp) cc_final: 0.7358 (mtt) REVERT: A 124 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6918 (mtm-85) REVERT: A 154 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: A 235 ARG cc_start: 0.7283 (mmt180) cc_final: 0.6981 (mtm180) REVERT: L 89 THR cc_start: 0.8911 (p) cc_final: 0.8433 (m) REVERT: H 30 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8531 (tm) REVERT: H 101 GLN cc_start: 0.8505 (tt0) cc_final: 0.8290 (tt0) REVERT: H 119 TYR cc_start: 0.6615 (t80) cc_final: 0.6338 (t80) outliers start: 10 outliers final: 2 residues processed: 86 average time/residue: 1.2623 time to fit residues: 113.6931 Evaluate side-chains 84 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 30 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.0970 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5705 Z= 0.133 Angle : 1.058 31.353 7772 Z= 0.392 Chirality : 0.118 2.105 874 Planarity : 0.004 0.040 924 Dihedral : 19.954 179.803 1059 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.39 % Allowed : 18.37 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.34), residues: 666 helix: 2.10 (0.29), residues: 331 sheet: -0.16 (0.46), residues: 128 loop : -0.71 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 128 HIS 0.008 0.001 HIS A 432 PHE 0.010 0.001 PHE A 403 TYR 0.016 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: A 109 MET cc_start: 0.6561 (mmt) cc_final: 0.6201 (mtm) REVERT: A 112 MET cc_start: 0.7680 (mtp) cc_final: 0.7340 (mtt) REVERT: A 124 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6857 (mtm-85) REVERT: A 154 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: A 235 ARG cc_start: 0.7267 (mmt180) cc_final: 0.6971 (mtm180) REVERT: A 298 THR cc_start: 0.8684 (t) cc_final: 0.8183 (p) REVERT: L 23 HIS cc_start: 0.7873 (m-70) cc_final: 0.7607 (m-70) REVERT: L 89 THR cc_start: 0.8929 (p) cc_final: 0.8526 (m) REVERT: H 74 TYR cc_start: 0.7751 (OUTLIER) cc_final: 0.7186 (p90) REVERT: H 119 TYR cc_start: 0.6600 (t80) cc_final: 0.6296 (t80) outliers start: 8 outliers final: 0 residues processed: 87 average time/residue: 1.2683 time to fit residues: 115.4036 Evaluate side-chains 81 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 0.0570 chunk 57 optimal weight: 0.4980 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5705 Z= 0.153 Angle : 1.063 31.429 7772 Z= 0.396 Chirality : 0.118 2.103 874 Planarity : 0.004 0.039 924 Dihedral : 19.949 179.735 1059 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.21 % Allowed : 18.20 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.34), residues: 666 helix: 2.11 (0.29), residues: 331 sheet: -0.17 (0.45), residues: 136 loop : -0.56 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 128 HIS 0.007 0.001 HIS A 432 PHE 0.011 0.001 PHE A 403 TYR 0.017 0.001 TYR A 83 ARG 0.002 0.000 ARG A 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 72 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7371 (ptt) REVERT: A 109 MET cc_start: 0.6555 (mmt) cc_final: 0.6183 (mtm) REVERT: A 112 MET cc_start: 0.7710 (mtp) cc_final: 0.7359 (mtt) REVERT: A 124 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6883 (mtm-85) REVERT: A 154 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: A 235 ARG cc_start: 0.7202 (mmt180) cc_final: 0.6985 (mtm180) REVERT: A 298 THR cc_start: 0.8686 (t) cc_final: 0.8184 (p) REVERT: L 23 HIS cc_start: 0.7845 (m-70) cc_final: 0.7454 (m-70) REVERT: L 89 THR cc_start: 0.8914 (p) cc_final: 0.8551 (m) REVERT: H 30 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8358 (tm) REVERT: H 74 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.7172 (p90) REVERT: H 119 TYR cc_start: 0.6611 (t80) cc_final: 0.6254 (t80) outliers start: 7 outliers final: 1 residues processed: 81 average time/residue: 1.2999 time to fit residues: 109.9052 Evaluate side-chains 83 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5705 Z= 0.167 Angle : 1.068 31.464 7772 Z= 0.398 Chirality : 0.118 2.101 874 Planarity : 0.004 0.039 924 Dihedral : 19.952 179.773 1059 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.39 % Allowed : 18.54 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.34), residues: 666 helix: 2.12 (0.29), residues: 331 sheet: -0.17 (0.45), residues: 136 loop : -0.57 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 128 HIS 0.007 0.001 HIS A 432 PHE 0.013 0.001 PHE A 62 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: A 72 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7400 (ptt) REVERT: A 109 MET cc_start: 0.6585 (mmt) cc_final: 0.6194 (mtm) REVERT: A 112 MET cc_start: 0.7743 (mtp) cc_final: 0.7387 (mtt) REVERT: A 124 ARG cc_start: 0.7179 (OUTLIER) cc_final: 0.6891 (mtm-85) REVERT: A 154 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: A 235 ARG cc_start: 0.7201 (mmt180) cc_final: 0.6981 (mtm180) REVERT: L 23 HIS cc_start: 0.7835 (m-70) cc_final: 0.7462 (m-70) REVERT: L 89 THR cc_start: 0.8898 (p) cc_final: 0.8492 (m) REVERT: H 30 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8227 (tm) REVERT: H 74 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7122 (p90) REVERT: H 119 TYR cc_start: 0.6659 (t80) cc_final: 0.6315 (t80) outliers start: 8 outliers final: 2 residues processed: 77 average time/residue: 1.3182 time to fit residues: 106.0192 Evaluate side-chains 84 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 74 TYR 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: 2.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 14 optimal weight: 0.6980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5705 Z= 0.174 Angle : 1.073 31.476 7772 Z= 0.401 Chirality : 0.118 2.101 874 Planarity : 0.004 0.039 924 Dihedral : 19.955 179.805 1059 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.39 % Allowed : 19.06 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.34), residues: 666 helix: 2.11 (0.29), residues: 331 sheet: -0.18 (0.45), residues: 136 loop : -0.57 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 128 HIS 0.007 0.001 HIS A 432 PHE 0.012 0.001 PHE A 403 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 7 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: A 72 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7414 (ptt) REVERT: A 109 MET cc_start: 0.6581 (mmt) cc_final: 0.6200 (mtm) REVERT: A 112 MET cc_start: 0.7743 (mtp) cc_final: 0.7386 (mtt) REVERT: A 124 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6903 (mtm-85) REVERT: A 154 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: L 23 HIS cc_start: 0.7793 (m-70) cc_final: 0.7446 (m-70) REVERT: L 89 THR cc_start: 0.8890 (p) cc_final: 0.8511 (m) REVERT: H 74 TYR cc_start: 0.7806 (OUTLIER) cc_final: 0.7167 (p90) REVERT: H 119 TYR cc_start: 0.6673 (t80) cc_final: 0.6465 (t80) outliers start: 8 outliers final: 2 residues processed: 79 average time/residue: 1.3636 time to fit residues: 112.5505 Evaluate side-chains 82 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain H residue 74 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 0.8980 chunk 21 optimal weight: 0.0030 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.131073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.094385 restraints weight = 6165.010| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.33 r_work: 0.2889 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5705 Z= 0.181 Angle : 1.077 31.515 7772 Z= 0.403 Chirality : 0.118 2.102 874 Planarity : 0.004 0.039 924 Dihedral : 19.958 179.900 1059 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.39 % Allowed : 19.06 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.34), residues: 666 helix: 2.13 (0.29), residues: 331 sheet: -0.13 (0.44), residues: 137 loop : -0.56 (0.48), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 128 HIS 0.007 0.001 HIS A 432 PHE 0.015 0.001 PHE A 62 TYR 0.018 0.001 TYR A 83 ARG 0.002 0.000 ARG A 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2506.50 seconds wall clock time: 47 minutes 2.04 seconds (2822.04 seconds total)