Starting phenix.real_space_refine on Sun Mar 10 15:41:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/03_2024/7ymj_33930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/03_2024/7ymj_33930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/03_2024/7ymj_33930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/03_2024/7ymj_33930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/03_2024/7ymj_33930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/03_2024/7ymj_33930_updated.pdb" } resolution = 3.35 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= -0.002 sd= 0.170 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2022 2.51 5 N 511 2.21 5 O 532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 215": "NH1" <-> "NH2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3085 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2215 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 265} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 842 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'JGX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.24, per 1000 atoms: 0.73 Number of scatterers: 3085 At special positions: 0 Unit cell: (63.64, 63.64, 127.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 532 8.00 N 511 7.00 C 2022 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 97 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 595.9 milliseconds 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 13 helices and 3 sheets defined 53.5% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 26 through 53 removed outlier: 3.924A pdb=" N LEU A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 98 through 129 removed outlier: 3.799A pdb=" N ALA A 103 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 137 No H-bonds generated for 'chain 'A' and resid 134 through 137' Processing helix chain 'A' and resid 140 through 159 removed outlier: 3.710A pdb=" N ILE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 182 through 192 Processing helix chain 'A' and resid 194 through 213 removed outlier: 4.010A pdb=" N ALA A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 297 removed outlier: 4.544A pdb=" N ARG A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Proline residue: A 287 - end of helix Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 314 through 328 removed outlier: 3.986A pdb=" N SER A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Proline residue: A 323 - end of helix removed outlier: 4.882A pdb=" N TYR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 332 through 342 Processing sheet with id= A, first strand: chain 'D' and resid 5 through 9 removed outlier: 3.856A pdb=" N SER D 72 " --> pdb=" O TYR D 81 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 93 through 95 removed outlier: 3.762A pdb=" N ALA D 93 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 119 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 110 through 113 removed outlier: 3.536A pdb=" N LEU D 110 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 101 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 99 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN D 98 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY D 37 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP D 35 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ARG D 102 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU D 33 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET D 36 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 53 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) 157 hydrogen bonds defined for protein. 456 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: 0.76 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 946 1.35 - 1.47: 830 1.47 - 1.59: 1356 1.59 - 1.71: 1 1.71 - 1.83: 26 Bond restraints: 3159 Sorted by residual: bond pdb=" C19 JGX A 401 " pdb=" O26 JGX A 401 " ideal model delta sigma weight residual 1.338 1.399 -0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" C9 JGX A 401 " pdb=" O10 JGX A 401 " ideal model delta sigma weight residual 1.347 1.406 -0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" N25 JGX A 401 " pdb=" S22 JGX A 401 " ideal model delta sigma weight residual 1.653 1.706 -0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C4 JGX A 401 " pdb=" O3 JGX A 401 " ideal model delta sigma weight residual 1.346 1.398 -0.052 2.00e-02 2.50e+03 6.67e+00 bond pdb=" C20 JGX A 401 " pdb=" S22 JGX A 401 " ideal model delta sigma weight residual 1.771 1.821 -0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 3154 not shown) Histogram of bond angle deviations from ideal: 100.13 - 106.93: 85 106.93 - 113.74: 1722 113.74 - 120.54: 1355 120.54 - 127.35: 1106 127.35 - 134.15: 37 Bond angle restraints: 4305 Sorted by residual: angle pdb=" O23 JGX A 401 " pdb=" S22 JGX A 401 " pdb=" O24 JGX A 401 " ideal model delta sigma weight residual 118.38 100.13 18.25 3.00e+00 1.11e-01 3.70e+01 angle pdb=" N LEU A 80 " pdb=" CA LEU A 80 " pdb=" C LEU A 80 " ideal model delta sigma weight residual 109.81 117.45 -7.64 2.21e+00 2.05e-01 1.20e+01 angle pdb=" N LEU A 286 " pdb=" CA LEU A 286 " pdb=" C LEU A 286 " ideal model delta sigma weight residual 109.81 117.44 -7.63 2.21e+00 2.05e-01 1.19e+01 angle pdb=" N ASN A 322 " pdb=" CA ASN A 322 " pdb=" C ASN A 322 " ideal model delta sigma weight residual 113.16 117.88 -4.72 1.42e+00 4.96e-01 1.11e+01 angle pdb=" N TYR A 326 " pdb=" CA TYR A 326 " pdb=" C TYR A 326 " ideal model delta sigma weight residual 109.81 116.37 -6.56 2.21e+00 2.05e-01 8.82e+00 ... (remaining 4300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.85: 1598 15.85 - 31.70: 177 31.70 - 47.54: 58 47.54 - 63.39: 7 63.39 - 79.24: 1 Dihedral angle restraints: 1841 sinusoidal: 702 harmonic: 1139 Sorted by residual: dihedral pdb=" CA ASP D 74 " pdb=" CB ASP D 74 " pdb=" CG ASP D 74 " pdb=" OD1 ASP D 74 " ideal model delta sinusoidal sigma weight residual -30.00 -84.82 54.82 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA GLU A 180 " pdb=" CB GLU A 180 " pdb=" CG GLU A 180 " pdb=" CD GLU A 180 " ideal model delta sinusoidal sigma weight residual 60.00 107.24 -47.24 3 1.50e+01 4.44e-03 8.46e+00 dihedral pdb=" N LEU A 283 " pdb=" CA LEU A 283 " pdb=" CB LEU A 283 " pdb=" CG LEU A 283 " ideal model delta sinusoidal sigma weight residual -60.00 -106.50 46.50 3 1.50e+01 4.44e-03 8.35e+00 ... (remaining 1838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 307 0.039 - 0.079: 137 0.079 - 0.118: 33 0.118 - 0.158: 20 0.158 - 0.197: 4 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB VAL A 214 " pdb=" CA VAL A 214 " pdb=" CG1 VAL A 214 " pdb=" CG2 VAL A 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CA GLU A 173 " pdb=" N GLU A 173 " pdb=" C GLU A 173 " pdb=" CB GLU A 173 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 498 not shown) Planarity restraints: 527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 80 " -0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO A 81 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 167 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO A 168 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 326 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 327 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.030 5.00e-02 4.00e+02 ... (remaining 524 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1043 2.86 - 3.37: 2497 3.37 - 3.88: 4472 3.88 - 4.39: 4722 4.39 - 4.90: 8921 Nonbonded interactions: 21655 Sorted by model distance: nonbonded pdb=" OG SER D 9 " pdb=" OG SER D 23 " model vdw 2.349 2.440 nonbonded pdb=" O SER A 218 " pdb=" OG SER A 218 " model vdw 2.371 2.440 nonbonded pdb=" O GLY A 40 " pdb=" ND2 ASN A 44 " model vdw 2.391 2.520 nonbonded pdb=" N ASP D 111 " pdb=" OD1 ASP D 111 " model vdw 2.495 2.520 nonbonded pdb=" OD2 ASP A 72 " pdb=" NH1 ARG A 113 " model vdw 2.501 2.520 ... (remaining 21650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 3.610 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.330 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3159 Z= 0.325 Angle : 0.953 18.250 4305 Z= 0.486 Chirality : 0.052 0.197 501 Planarity : 0.007 0.068 527 Dihedral : 14.746 79.241 1107 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % 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: -3.45 (0.34), residues: 390 helix: -1.37 (0.30), residues: 195 sheet: -0.56 (0.77), residues: 50 loop : -4.25 (0.34), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.001 0.001 HIS A 56 PHE 0.023 0.002 PHE A 312 TYR 0.015 0.002 TYR A 204 ARG 0.003 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.341 Fit side-chains REVERT: A 106 ASP cc_start: 0.8781 (t0) cc_final: 0.8302 (t0) REVERT: A 321 ILE cc_start: 0.7323 (tt) cc_final: 0.6977 (tt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1374 time to fit residues: 7.0440 Evaluate side-chains 36 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3159 Z= 0.184 Angle : 0.572 7.663 4305 Z= 0.292 Chirality : 0.041 0.124 501 Planarity : 0.005 0.046 527 Dihedral : 4.986 26.897 456 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.17 % Allowed : 10.25 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.42), residues: 390 helix: 0.71 (0.37), residues: 199 sheet: -0.24 (0.81), residues: 50 loop : -3.86 (0.38), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 106 HIS 0.001 0.000 HIS A 56 PHE 0.013 0.001 PHE A 312 TYR 0.014 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.335 Fit side-chains REVERT: A 106 ASP cc_start: 0.8650 (t0) cc_final: 0.8154 (t0) REVERT: A 145 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6338 (mpp) REVERT: A 321 ILE cc_start: 0.7289 (tt) cc_final: 0.6887 (tt) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.0987 time to fit residues: 5.6009 Evaluate side-chains 41 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain D residue 84 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 24 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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: 0.7841 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3159 Z= 0.138 Angle : 0.528 8.290 4305 Z= 0.262 Chirality : 0.039 0.120 501 Planarity : 0.004 0.035 527 Dihedral : 3.756 19.528 456 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.80 % Allowed : 13.66 % Favored : 83.54 % 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: -0.47 (0.44), residues: 390 helix: 1.59 (0.38), residues: 199 sheet: 0.34 (0.85), residues: 50 loop : -3.60 (0.41), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.015 0.001 PHE A 312 TYR 0.011 0.001 TYR A 204 ARG 0.001 0.000 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.334 Fit side-chains REVERT: A 106 ASP cc_start: 0.8395 (t0) cc_final: 0.7972 (t0) outliers start: 9 outliers final: 6 residues processed: 39 average time/residue: 0.0983 time to fit residues: 5.3486 Evaluate side-chains 37 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 31 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain D residue 84 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.0070 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3159 Z= 0.217 Angle : 0.566 6.378 4305 Z= 0.286 Chirality : 0.041 0.120 501 Planarity : 0.003 0.031 527 Dihedral : 3.850 22.662 456 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.73 % Allowed : 14.29 % Favored : 81.99 % 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: -0.25 (0.45), residues: 390 helix: 1.72 (0.38), residues: 199 sheet: 0.45 (0.85), residues: 50 loop : -3.41 (0.43), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 106 HIS 0.001 0.000 HIS A 56 PHE 0.014 0.001 PHE A 312 TYR 0.016 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.332 Fit side-chains REVERT: A 106 ASP cc_start: 0.8708 (t0) cc_final: 0.8219 (t0) outliers start: 12 outliers final: 9 residues processed: 39 average time/residue: 0.0995 time to fit residues: 5.3973 Evaluate side-chains 41 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 0.0040 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 0.0470 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.4290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3159 Z= 0.132 Angle : 0.501 5.915 4305 Z= 0.251 Chirality : 0.039 0.117 501 Planarity : 0.003 0.029 527 Dihedral : 3.528 20.894 456 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.80 % Allowed : 15.84 % Favored : 81.37 % 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: 0.17 (0.46), residues: 390 helix: 2.10 (0.38), residues: 199 sheet: 0.50 (0.84), residues: 52 loop : -3.26 (0.45), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.016 0.001 PHE A 312 TYR 0.010 0.001 TYR A 204 ARG 0.001 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 30 time to evaluate : 0.289 Fit side-chains REVERT: A 106 ASP cc_start: 0.8354 (t0) cc_final: 0.7912 (t0) outliers start: 9 outliers final: 7 residues processed: 35 average time/residue: 0.1004 time to fit residues: 4.8581 Evaluate side-chains 37 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain D residue 84 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7924 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3159 Z= 0.186 Angle : 0.540 6.194 4305 Z= 0.271 Chirality : 0.041 0.153 501 Planarity : 0.003 0.028 527 Dihedral : 3.608 22.252 456 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.42 % Allowed : 15.22 % Favored : 81.37 % 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: 0.26 (0.45), residues: 390 helix: 2.08 (0.38), residues: 200 sheet: 0.58 (0.83), residues: 52 loop : -3.12 (0.46), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 106 HIS 0.001 0.000 HIS A 56 PHE 0.015 0.001 PHE A 312 TYR 0.015 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 31 time to evaluate : 0.323 Fit side-chains REVERT: A 106 ASP cc_start: 0.8611 (t0) cc_final: 0.8120 (t0) outliers start: 11 outliers final: 9 residues processed: 36 average time/residue: 0.1043 time to fit residues: 5.2448 Evaluate side-chains 40 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7885 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3159 Z= 0.156 Angle : 0.521 5.922 4305 Z= 0.263 Chirality : 0.040 0.138 501 Planarity : 0.003 0.027 527 Dihedral : 3.513 21.802 456 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.73 % Allowed : 14.60 % Favored : 81.68 % 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: 0.39 (0.45), residues: 390 helix: 2.22 (0.38), residues: 199 sheet: 0.67 (0.83), residues: 52 loop : -3.10 (0.46), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.015 0.001 PHE A 312 TYR 0.013 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.326 Fit side-chains REVERT: A 106 ASP cc_start: 0.8488 (t0) cc_final: 0.7984 (t0) outliers start: 12 outliers final: 10 residues processed: 38 average time/residue: 0.0988 time to fit residues: 5.2285 Evaluate side-chains 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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: 0.7985 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3159 Z= 0.253 Angle : 0.580 6.571 4305 Z= 0.294 Chirality : 0.042 0.127 501 Planarity : 0.003 0.027 527 Dihedral : 3.749 23.182 456 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.42 % Allowed : 14.91 % Favored : 81.68 % 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: 0.28 (0.45), residues: 390 helix: 2.04 (0.38), residues: 199 sheet: 0.91 (0.80), residues: 56 loop : -3.23 (0.46), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 106 HIS 0.001 0.000 HIS A 56 PHE 0.014 0.001 PHE A 312 TYR 0.017 0.001 TYR A 204 ARG 0.001 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 37 time to evaluate : 0.295 Fit side-chains REVERT: A 106 ASP cc_start: 0.8792 (t0) cc_final: 0.8280 (t0) outliers start: 11 outliers final: 10 residues processed: 41 average time/residue: 0.0930 time to fit residues: 5.3386 Evaluate side-chains 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3159 Z= 0.213 Angle : 0.557 6.712 4305 Z= 0.283 Chirality : 0.041 0.123 501 Planarity : 0.003 0.027 527 Dihedral : 3.698 22.610 456 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.42 % Allowed : 15.53 % Favored : 81.06 % 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: 0.33 (0.45), residues: 390 helix: 2.08 (0.38), residues: 199 sheet: 0.90 (0.80), residues: 56 loop : -3.19 (0.47), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 106 HIS 0.001 0.000 HIS A 56 PHE 0.014 0.001 PHE A 312 TYR 0.016 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.299 Fit side-chains REVERT: A 106 ASP cc_start: 0.8739 (t0) cc_final: 0.8206 (t0) REVERT: A 224 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8133 (t0) outliers start: 11 outliers final: 10 residues processed: 39 average time/residue: 0.0910 time to fit residues: 4.9572 Evaluate side-chains 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 overall best weight: 0.4576 ------------------------------------------------------------------------------- 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: 0.7851 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3159 Z= 0.141 Angle : 0.505 6.281 4305 Z= 0.254 Chirality : 0.040 0.119 501 Planarity : 0.003 0.026 527 Dihedral : 3.449 21.499 456 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.80 % Allowed : 16.46 % Favored : 80.75 % 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 (0.46), residues: 390 helix: 2.36 (0.38), residues: 199 sheet: 0.98 (0.79), residues: 56 loop : -3.08 (0.46), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.001 0.000 HIS A 56 PHE 0.017 0.001 PHE A 312 TYR 0.012 0.001 TYR A 204 ARG 0.001 0.000 ARG D 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 780 Ramachandran restraints generated. 390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.338 Fit side-chains REVERT: A 106 ASP cc_start: 0.8423 (t0) cc_final: 0.7907 (t0) outliers start: 9 outliers final: 9 residues processed: 36 average time/residue: 0.1048 time to fit residues: 5.2796 Evaluate side-chains 40 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.187687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126760 restraints weight = 3266.944| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.52 r_work: 0.3284 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3159 Z= 0.163 Angle : 0.518 6.273 4305 Z= 0.261 Chirality : 0.040 0.117 501 Planarity : 0.003 0.025 527 Dihedral : 3.460 21.966 456 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.80 % Allowed : 16.15 % Favored : 81.06 % 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: 0.67 (0.46), residues: 390 helix: 2.36 (0.38), residues: 199 sheet: 1.01 (0.78), residues: 56 loop : -3.00 (0.47), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 106 HIS 0.001 0.000 HIS A 56 PHE 0.016 0.001 PHE A 312 TYR 0.013 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1107.74 seconds wall clock time: 20 minutes 28.94 seconds (1228.94 seconds total)