Starting phenix.real_space_refine on Tue Feb 13 04:29:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnn_34917/02_2024/8hnn_34917_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnn_34917/02_2024/8hnn_34917.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnn_34917/02_2024/8hnn_34917_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnn_34917/02_2024/8hnn_34917_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnn_34917/02_2024/8hnn_34917_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnn_34917/02_2024/8hnn_34917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnn_34917/02_2024/8hnn_34917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnn_34917/02_2024/8hnn_34917_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hnn_34917/02_2024/8hnn_34917_updated.pdb" } resolution = 3.6 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= -0.001 sd= 0.080 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 S 17 5.16 5 Cl 2 4.86 5 C 1993 2.51 5 N 527 2.21 5 O 524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3063 Number of models: 1 Model: "" Number of chains: 3 Chain: "N" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 852 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2150 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'43I': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.27, per 1000 atoms: 0.74 Number of scatterers: 3063 At special positions: 0 Unit cell: (71.4, 52.7, 123.25, 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) Cl 2 17.00 S 17 16.00 O 524 8.00 N 527 7.00 C 1993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 124 " - pdb=" SG CYS R 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 680.0 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 722 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 3 sheets defined 52.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'N' and resid 89 through 91 No H-bonds generated for 'chain 'N' and resid 89 through 91' Processing helix chain 'R' and resid 55 through 81 removed outlier: 4.181A pdb=" N ARG R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 114 removed outlier: 3.851A pdb=" N ASP R 99 " --> pdb=" O LEU R 95 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU R 101 " --> pdb=" O VAL R 97 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU R 102 " --> pdb=" O ALA R 98 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) Proline residue: R 107 - end of helix Processing helix chain 'R' and resid 121 through 153 removed outlier: 4.064A pdb=" N PHE R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR R 136 " --> pdb=" O ASN R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 188 Proline residue: R 185 - end of helix Processing helix chain 'R' and resid 212 through 242 Proline residue: R 227 - end of helix Processing helix chain 'R' and resid 256 through 290 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 301 through 328 removed outlier: 4.207A pdb=" N CYS R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing sheet with id= A, first strand: chain 'N' and resid 4 through 9 Processing sheet with id= B, first strand: chain 'N' and resid 59 through 61 removed outlier: 6.842A pdb=" N TRP N 38 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER N 52 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET N 36 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLU N 100 " --> pdb=" O TYR N 34 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N MET N 36 " --> pdb=" O ASN N 98 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN N 98 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TRP N 38 " --> pdb=" O TYR N 96 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR N 96 " --> pdb=" O TRP N 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 93 through 95 180 hydrogen bonds defined for protein. 522 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: 0.78 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 972 1.34 - 1.46: 711 1.46 - 1.58: 1424 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 3131 Sorted by residual: bond pdb=" C23 43I R 401 " pdb=" N6 43I R 401 " ideal model delta sigma weight residual 1.454 1.318 0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" C20 43I R 401 " pdb=" N7 43I R 401 " ideal model delta sigma weight residual 1.453 1.324 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" C19 43I R 401 " pdb=" N1 43I R 401 " ideal model delta sigma weight residual 1.457 1.346 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C16 43I R 401 " pdb="CL1 43I R 401 " ideal model delta sigma weight residual 1.786 1.727 0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" C22 43I R 401 " pdb="CL2 43I R 401 " ideal model delta sigma weight residual 1.785 1.730 0.055 2.00e-02 2.50e+03 7.58e+00 ... (remaining 3126 not shown) Histogram of bond angle deviations from ideal: 100.56 - 107.25: 79 107.25 - 113.93: 1795 113.93 - 120.62: 1322 120.62 - 127.31: 1045 127.31 - 133.99: 31 Bond angle restraints: 4272 Sorted by residual: angle pdb=" C19 43I R 401 " pdb=" N1 43I R 401 " pdb=" C5 43I R 401 " ideal model delta sigma weight residual 109.47 124.82 -15.35 3.00e+00 1.11e-01 2.62e+01 angle pdb=" C8 43I R 401 " pdb=" C7 43I R 401 " pdb=" N2 43I R 401 " ideal model delta sigma weight residual 109.07 123.35 -14.28 3.00e+00 1.11e-01 2.27e+01 angle pdb=" C19 43I R 401 " pdb=" N1 43I R 401 " pdb=" C4 43I R 401 " ideal model delta sigma weight residual 109.48 121.82 -12.34 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C LEU R 225 " pdb=" N LEU R 226 " pdb=" CA LEU R 226 " ideal model delta sigma weight residual 121.80 115.59 6.21 2.44e+00 1.68e-01 6.47e+00 angle pdb=" C HIS R 94 " pdb=" N LEU R 95 " pdb=" CA LEU R 95 " ideal model delta sigma weight residual 121.58 117.00 4.58 1.95e+00 2.63e-01 5.52e+00 ... (remaining 4267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.22: 1754 22.22 - 44.43: 97 44.43 - 66.65: 13 66.65 - 88.86: 2 88.86 - 111.08: 3 Dihedral angle restraints: 1869 sinusoidal: 741 harmonic: 1128 Sorted by residual: dihedral pdb=" CB CYS R 124 " pdb=" SG CYS R 124 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual 93.00 -178.02 -88.98 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CA SER R 251 " pdb=" C SER R 251 " pdb=" N ARG R 252 " pdb=" CA ARG R 252 " ideal model delta harmonic sigma weight residual 180.00 160.58 19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" N1 43I R 401 " pdb=" C3 43I R 401 " pdb=" C4 43I R 401 " pdb=" N2 43I R 401 " ideal model delta sinusoidal sigma weight residual -52.93 58.15 -111.08 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 1866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 507 0.158 - 0.315: 0 0.315 - 0.473: 0 0.473 - 0.631: 0 0.631 - 0.788: 1 Chirality restraints: 508 Sorted by residual: chirality pdb=" C7 43I R 401 " pdb=" C11 43I R 401 " pdb=" C8 43I R 401 " pdb=" N2 43I R 401 " both_signs ideal model delta sigma weight residual False -2.55 -1.76 -0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" CG LEU R 321 " pdb=" CB LEU R 321 " pdb=" CD1 LEU R 321 " pdb=" CD2 LEU R 321 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA LEU R 106 " pdb=" N LEU R 106 " pdb=" C LEU R 106 " pdb=" CB LEU R 106 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 505 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA R 222 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ALA R 222 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA R 222 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY R 223 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU R 196 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" C GLU R 196 " 0.022 2.00e-02 2.50e+03 pdb=" O GLU R 196 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG R 197 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 135 " 0.010 2.00e-02 2.50e+03 7.74e-03 1.05e+00 pdb=" CG PHE R 135 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE R 135 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 135 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 135 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 135 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 135 " 0.004 2.00e-02 2.50e+03 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 318 2.74 - 3.28: 2961 3.28 - 3.82: 4862 3.82 - 4.36: 5273 4.36 - 4.90: 9456 Nonbonded interactions: 22870 Sorted by model distance: nonbonded pdb=" O ALA R 273 " pdb=" OG1 THR R 277 " model vdw 2.206 2.440 nonbonded pdb=" NZ LYS R 125 " pdb=" O LEU R 190 " model vdw 2.272 2.520 nonbonded pdb=" OG SER N 9 " pdb=" OG SER N 23 " model vdw 2.287 2.440 nonbonded pdb=" O GLN R 158 " pdb=" NH1 ARG R 162 " model vdw 2.317 2.520 nonbonded pdb=" O GLU R 253 " pdb=" ND2 ASN R 257 " model vdw 2.351 2.520 ... (remaining 22865 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.550 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.006 0.136 3131 Z= 0.409 Angle : 0.785 15.347 4272 Z= 0.361 Chirality : 0.054 0.788 508 Planarity : 0.003 0.021 521 Dihedral : 13.969 111.077 1141 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 0.62 (0.44), residues: 386 helix: 1.05 (0.35), residues: 217 sheet: 2.72 (0.80), residues: 44 loop : -1.64 (0.54), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.010 0.001 TYR R 233 ARG 0.002 0.000 ARG R 263 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 101 TYR cc_start: 0.8965 (p90) cc_final: 0.8449 (p90) REVERT: N 113 TRP cc_start: 0.8339 (m100) cc_final: 0.7985 (m-90) REVERT: R 254 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7233 (ttpt) REVERT: R 274 LEU cc_start: 0.8379 (tt) cc_final: 0.8176 (tp) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1227 time to fit residues: 9.3800 Evaluate side-chains 56 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 116 GLN R 318 HIS R 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3131 Z= 0.207 Angle : 0.669 10.387 4272 Z= 0.306 Chirality : 0.039 0.120 508 Planarity : 0.003 0.019 521 Dihedral : 9.683 93.335 514 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.21 % Allowed : 10.26 % Favored : 86.54 % 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: 0.74 (0.44), residues: 386 helix: 1.13 (0.36), residues: 216 sheet: 2.75 (0.76), residues: 44 loop : -1.51 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.021 0.002 PHE R 189 TYR 0.010 0.001 TYR R 233 ARG 0.001 0.000 ARG R 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 36 MET cc_start: 0.7695 (mtt) cc_final: 0.7394 (mmm) REVERT: N 101 TYR cc_start: 0.8880 (p90) cc_final: 0.8535 (p90) REVERT: N 113 TRP cc_start: 0.8333 (m100) cc_final: 0.7943 (m-90) REVERT: R 189 PHE cc_start: 0.8389 (m-10) cc_final: 0.8147 (m-10) outliers start: 10 outliers final: 6 residues processed: 62 average time/residue: 0.1095 time to fit residues: 8.9491 Evaluate side-chains 59 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 75 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3131 Z= 0.329 Angle : 0.737 9.085 4272 Z= 0.351 Chirality : 0.043 0.176 508 Planarity : 0.003 0.018 521 Dihedral : 9.053 80.973 514 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 4.17 % Allowed : 16.03 % Favored : 79.81 % 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: 0.34 (0.43), residues: 386 helix: 0.78 (0.36), residues: 216 sheet: 2.54 (0.78), residues: 44 loop : -1.61 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 106 HIS 0.004 0.001 HIS R 280 PHE 0.025 0.002 PHE R 328 TYR 0.015 0.001 TYR R 235 ARG 0.002 0.000 ARG R 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 36 MET cc_start: 0.7885 (mtt) cc_final: 0.7648 (mmm) REVERT: N 101 TYR cc_start: 0.8825 (p90) cc_final: 0.8591 (p90) REVERT: N 113 TRP cc_start: 0.8362 (m100) cc_final: 0.7938 (m-90) REVERT: R 189 PHE cc_start: 0.8590 (m-10) cc_final: 0.8269 (m-10) outliers start: 13 outliers final: 10 residues processed: 59 average time/residue: 0.1199 time to fit residues: 9.0119 Evaluate side-chains 59 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 126 VAL Chi-restraints excluded: chain R residue 202 HIS Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 251 SER Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7420 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 0.025 3131 Z= 0.186 Angle : 0.562 7.483 4272 Z= 0.277 Chirality : 0.037 0.122 508 Planarity : 0.003 0.019 521 Dihedral : 6.286 64.415 514 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.53 % Allowed : 18.91 % Favored : 77.56 % 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: 0.66 (0.43), residues: 386 helix: 1.09 (0.36), residues: 216 sheet: 2.66 (0.76), residues: 44 loop : -1.57 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.015 0.001 PHE R 135 TYR 0.008 0.001 TYR R 233 ARG 0.001 0.000 ARG N 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 36 MET cc_start: 0.7800 (mtt) cc_final: 0.7600 (mmm) REVERT: N 113 TRP cc_start: 0.8339 (m100) cc_final: 0.7902 (m-90) REVERT: R 189 PHE cc_start: 0.8359 (m-10) cc_final: 0.8064 (m-10) REVERT: R 247 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8441 (mp) outliers start: 11 outliers final: 8 residues processed: 63 average time/residue: 0.1108 time to fit residues: 9.0758 Evaluate side-chains 64 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain R residue 320 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 HIS R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3131 Z= 0.246 Angle : 0.596 7.656 4272 Z= 0.298 Chirality : 0.039 0.132 508 Planarity : 0.003 0.019 521 Dihedral : 6.512 70.062 514 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.77 % Allowed : 19.23 % Favored : 75.00 % 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: 0.52 (0.43), residues: 386 helix: 0.94 (0.36), residues: 217 sheet: 2.62 (0.77), residues: 44 loop : -1.59 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.019 0.002 PHE R 135 TYR 0.012 0.001 TYR R 235 ARG 0.001 0.000 ARG R 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8350 (m100) cc_final: 0.7918 (m-90) REVERT: R 189 PHE cc_start: 0.8458 (m-10) cc_final: 0.8138 (m-10) REVERT: R 226 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6922 (mp) REVERT: R 241 ARG cc_start: 0.7741 (tpt-90) cc_final: 0.7133 (tpp80) REVERT: R 247 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8468 (mp) outliers start: 18 outliers final: 12 residues processed: 65 average time/residue: 0.1226 time to fit residues: 10.1302 Evaluate side-chains 67 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 251 SER Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7503 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3131 Z= 0.229 Angle : 0.582 6.661 4272 Z= 0.290 Chirality : 0.038 0.126 508 Planarity : 0.003 0.019 521 Dihedral : 6.415 66.389 514 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.45 % Allowed : 19.55 % Favored : 75.00 % 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: 0.59 (0.43), residues: 386 helix: 0.94 (0.36), residues: 218 sheet: 2.83 (0.76), residues: 44 loop : -1.54 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.001 PHE R 135 TYR 0.010 0.001 TYR R 235 ARG 0.001 0.000 ARG R 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 53 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8347 (m100) cc_final: 0.7921 (m-90) REVERT: R 189 PHE cc_start: 0.8442 (m-10) cc_final: 0.8132 (m-10) REVERT: R 226 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6895 (mp) REVERT: R 241 ARG cc_start: 0.7760 (tpt-90) cc_final: 0.7186 (tpp80) REVERT: R 247 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8460 (mp) outliers start: 17 outliers final: 13 residues processed: 62 average time/residue: 0.1208 time to fit residues: 9.5512 Evaluate side-chains 67 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.0970 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3131 Z= 0.148 Angle : 0.532 6.132 4272 Z= 0.264 Chirality : 0.036 0.111 508 Planarity : 0.003 0.020 521 Dihedral : 6.046 58.715 514 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.81 % Allowed : 20.19 % Favored : 75.00 % 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: 0.85 (0.44), residues: 386 helix: 1.25 (0.36), residues: 216 sheet: 3.00 (0.75), residues: 44 loop : -1.62 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.014 0.001 PHE R 135 TYR 0.010 0.001 TYR N 101 ARG 0.001 0.000 ARG N 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 56 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8357 (m100) cc_final: 0.7935 (m-90) REVERT: R 189 PHE cc_start: 0.8280 (m-10) cc_final: 0.7998 (m-10) REVERT: R 241 ARG cc_start: 0.7708 (tpt-90) cc_final: 0.7134 (tpp80) outliers start: 15 outliers final: 12 residues processed: 63 average time/residue: 0.1374 time to fit residues: 10.9429 Evaluate side-chains 67 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7507 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3131 Z= 0.238 Angle : 0.619 12.271 4272 Z= 0.298 Chirality : 0.039 0.127 508 Planarity : 0.003 0.019 521 Dihedral : 6.367 65.110 514 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.13 % Allowed : 20.83 % Favored : 74.04 % 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: 0.68 (0.43), residues: 386 helix: 1.03 (0.36), residues: 218 sheet: 2.99 (0.75), residues: 44 loop : -1.59 (0.52), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.018 0.002 PHE R 187 TYR 0.012 0.001 TYR R 235 ARG 0.001 0.000 ARG R 167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8357 (m100) cc_final: 0.7922 (m-90) REVERT: R 189 PHE cc_start: 0.8425 (m-10) cc_final: 0.8119 (m-10) outliers start: 16 outliers final: 14 residues processed: 62 average time/residue: 0.1128 time to fit residues: 9.0913 Evaluate side-chains 65 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 251 SER Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.7475 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3131 Z= 0.187 Angle : 0.585 12.557 4272 Z= 0.281 Chirality : 0.037 0.115 508 Planarity : 0.003 0.019 521 Dihedral : 6.169 60.647 514 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.13 % Allowed : 20.19 % Favored : 74.68 % 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: 0.70 (0.43), residues: 386 helix: 1.09 (0.36), residues: 217 sheet: 2.99 (0.75), residues: 44 loop : -1.64 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.016 0.001 PHE R 187 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG N 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8361 (m100) cc_final: 0.7927 (m-90) REVERT: R 189 PHE cc_start: 0.8387 (m-10) cc_final: 0.8057 (m-10) outliers start: 16 outliers final: 14 residues processed: 61 average time/residue: 0.1124 time to fit residues: 8.9489 Evaluate side-chains 65 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 251 SER Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7492 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3131 Z= 0.206 Angle : 0.599 12.300 4272 Z= 0.290 Chirality : 0.038 0.119 508 Planarity : 0.003 0.019 521 Dihedral : 6.181 60.921 514 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.81 % Allowed : 21.47 % Favored : 73.72 % 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: 0.63 (0.43), residues: 386 helix: 1.03 (0.36), residues: 217 sheet: 2.99 (0.75), residues: 44 loop : -1.68 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 106 HIS 0.005 0.001 HIS R 280 PHE 0.017 0.002 PHE R 135 TYR 0.010 0.001 TYR N 101 ARG 0.001 0.000 ARG N 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 113 TRP cc_start: 0.8359 (m100) cc_final: 0.7922 (m-90) REVERT: R 189 PHE cc_start: 0.8403 (m-10) cc_final: 0.8065 (m-10) outliers start: 15 outliers final: 15 residues processed: 61 average time/residue: 0.1159 time to fit residues: 9.1830 Evaluate side-chains 68 residues out of total 321 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 53 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 121 SER Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 239 LEU Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 251 SER Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 294 LEU Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain R residue 317 MET Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 322 ASN Chi-restraints excluded: chain R residue 328 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 194 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.201724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141716 restraints weight = 2937.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.143584 restraints weight = 2758.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146385 restraints weight = 1984.845| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3131 Z= 0.185 Angle : 0.582 12.204 4272 Z= 0.283 Chirality : 0.037 0.113 508 Planarity : 0.003 0.019 521 Dihedral : 6.020 58.549 514 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 5.45 % Allowed : 21.15 % Favored : 73.40 % 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: 0.71 (0.43), residues: 386 helix: 1.12 (0.36), residues: 217 sheet: 3.01 (0.75), residues: 44 loop : -1.70 (0.52), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 106 HIS 0.006 0.001 HIS R 194 PHE 0.016 0.001 PHE R 187 TYR 0.011 0.001 TYR N 101 ARG 0.001 0.000 ARG N 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 978.80 seconds wall clock time: 18 minutes 33.63 seconds (1113.63 seconds total)