Starting phenix.real_space_refine on Mon Sep 23 13:24:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/09_2024/7ymj_33930.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/09_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_33930/09_2024/7ymj_33930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/09_2024/7ymj_33930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/09_2024/7ymj_33930.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymj_33930/09_2024/7ymj_33930.cif" } 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. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 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: 2.64, per 1000 atoms: 0.86 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 383.2 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... Secondary structure from input PDB file: 14 helices and 3 sheets defined 59.6% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 25 through 54 removed outlier: 3.820A pdb=" N LEU A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) 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) removed outlier: 3.834A pdb=" N HIS A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 79 removed outlier: 3.713A pdb=" N ILE A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.578A pdb=" N SER A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 130 removed outlier: 3.651A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) 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) removed outlier: 3.639A pdb=" N TYR A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.688A pdb=" N ILE A 137 " --> pdb=" O ARG A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 159 removed outlier: 3.599A pdb=" N GLY A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.853A pdb=" N PHE A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 214 removed outlier: 3.590A pdb=" N LEU A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) 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 220 through 298 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 307 through 312 removed outlier: 4.060A pdb=" N VAL A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 312' Processing helix chain 'A' and resid 313 through 322 removed outlier: 3.986A pdb=" N SER A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 329 removed outlier: 3.763A pdb=" N CYS A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 343 removed outlier: 3.876A pdb=" N LYS A 335 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing sheet with id=AA1, 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=AA2, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.999A pdb=" N GLY D 12 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 119 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 93 " --> pdb=" O VAL D 119 " (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) removed outlier: 3.696A pdb=" N SER D 52 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.999A pdb=" N GLY D 12 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 119 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA D 93 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 99 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR D 101 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 110 " --> pdb=" O TYR D 101 " (cutoff:3.500A) 171 hydrogen bonds defined for protein. 489 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: 0.77 Time building geometry restraints manager: 0.96 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: 0.00 - 3.65: 4257 3.65 - 7.30: 42 7.30 - 10.95: 4 10.95 - 14.60: 1 14.60 - 18.25: 1 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: 2488 3.37 - 3.88: 4463 3.88 - 4.39: 4698 4.39 - 4.90: 8915 Nonbonded interactions: 21607 Sorted by model distance: nonbonded pdb=" OG SER D 9 " pdb=" OG SER D 23 " model vdw 2.349 3.040 nonbonded pdb=" O SER A 218 " pdb=" OG SER A 218 " model vdw 2.371 3.040 nonbonded pdb=" O GLY A 40 " pdb=" ND2 ASN A 44 " model vdw 2.391 3.120 nonbonded pdb=" N ASP D 111 " pdb=" OD1 ASP D 111 " model vdw 2.495 3.120 nonbonded pdb=" OD2 ASP A 72 " pdb=" NH1 ARG A 113 " model vdw 2.501 3.120 ... (remaining 21602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.660 Find NCS groups from input model: 0.020 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- 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= 0.322 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 : 0.338 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: 0.1348 time to fit residues: 6.8970 Evaluate side-chains 36 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 30.0000 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7921 moved from start: 0.0957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3159 Z= 0.199 Angle : 0.582 7.599 4305 Z= 0.298 Chirality : 0.041 0.125 501 Planarity : 0.005 0.046 527 Dihedral : 4.840 25.450 456 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.48 % Allowed : 9.94 % 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: -1.25 (0.42), residues: 390 helix: 0.64 (0.36), residues: 205 sheet: -0.14 (0.82), residues: 50 loop : -3.53 (0.42), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 106 HIS 0.001 0.001 HIS A 56 PHE 0.014 0.001 PHE A 312 TYR 0.014 0.001 TYR A 204 ARG 0.002 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 47 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.357 Fit side-chains REVERT: A 106 ASP cc_start: 0.8657 (t0) cc_final: 0.8187 (t0) REVERT: A 321 ILE cc_start: 0.7250 (tt) cc_final: 0.6850 (tt) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.1037 time to fit residues: 6.1707 Evaluate side-chains 40 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 294 ILE 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: 0.6980 chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 30.0000 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 0.0060 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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: 0.7887 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3159 Z= 0.168 Angle : 0.563 7.963 4305 Z= 0.283 Chirality : 0.040 0.124 501 Planarity : 0.004 0.038 527 Dihedral : 3.940 21.286 456 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.80 % Allowed : 13.35 % Favored : 83.85 % 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: 1.36 (0.38), residues: 206 sheet: 0.30 (0.84), residues: 50 loop : -3.25 (0.45), residues: 134 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 0.016 0.001 PHE A 312 TYR 0.013 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 *********************** 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 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.367 Fit side-chains REVERT: A 106 ASP cc_start: 0.8553 (t0) cc_final: 0.8089 (t0) REVERT: A 321 ILE cc_start: 0.7188 (tt) cc_final: 0.6780 (tt) outliers start: 9 outliers final: 8 residues processed: 37 average time/residue: 0.1122 time to fit residues: 5.8839 Evaluate side-chains 42 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 294 ILE Chi-restraints excluded: chain A residue 307 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: 0.8980 chunk 3 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3159 Z= 0.190 Angle : 0.552 6.161 4305 Z= 0.279 Chirality : 0.041 0.122 501 Planarity : 0.003 0.033 527 Dihedral : 3.785 21.772 456 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: -0.04 (0.45), residues: 390 helix: 1.84 (0.38), residues: 200 sheet: 0.47 (0.84), residues: 50 loop : -3.22 (0.45), residues: 140 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 0.016 0.001 PHE A 312 TYR 0.015 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 : 0.355 Fit side-chains REVERT: A 106 ASP cc_start: 0.8649 (t0) cc_final: 0.8162 (t0) outliers start: 12 outliers final: 8 residues processed: 39 average time/residue: 0.1037 time to fit residues: 5.6187 Evaluate side-chains 39 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7933 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 0.029 3159 Z= 0.195 Angle : 0.549 6.173 4305 Z= 0.279 Chirality : 0.041 0.122 501 Planarity : 0.003 0.031 527 Dihedral : 3.746 21.899 456 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.73 % Allowed : 15.22 % 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: 0.15 (0.45), residues: 390 helix: 1.98 (0.38), residues: 200 sheet: 0.37 (0.83), residues: 52 loop : -3.06 (0.46), residues: 138 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 0.015 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 *********************** 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 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.368 Fit side-chains REVERT: A 106 ASP cc_start: 0.8662 (t0) cc_final: 0.8173 (t0) outliers start: 12 outliers final: 9 residues processed: 37 average time/residue: 0.0950 time to fit residues: 4.9764 Evaluate side-chains 40 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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: 0.7937 moved from start: 0.1591 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= 0.199 Angle : 0.552 6.374 4305 Z= 0.280 Chirality : 0.041 0.123 501 Planarity : 0.003 0.030 527 Dihedral : 3.721 21.987 456 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.42 % Allowed : 16.15 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.45), residues: 390 helix: 2.04 (0.38), residues: 200 sheet: 0.38 (0.82), residues: 52 loop : -2.97 (0.47), residues: 138 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 0.016 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 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.341 Fit side-chains REVERT: A 106 ASP cc_start: 0.8672 (t0) cc_final: 0.8184 (t0) outliers start: 11 outliers final: 9 residues processed: 37 average time/residue: 0.1058 time to fit residues: 5.4627 Evaluate side-chains 40 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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: 0.7980 chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.0000 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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: 0.7839 moved from start: 0.1799 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= 0.136 Angle : 0.503 5.922 4305 Z= 0.254 Chirality : 0.039 0.118 501 Planarity : 0.003 0.029 527 Dihedral : 3.503 20.922 456 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.42 % Allowed : 16.15 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.46), residues: 390 helix: 2.35 (0.38), residues: 200 sheet: 0.50 (0.82), residues: 52 loop : -2.88 (0.47), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 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 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.355 Fit side-chains REVERT: A 106 ASP cc_start: 0.8412 (t0) cc_final: 0.7921 (t0) outliers start: 11 outliers final: 10 residues processed: 39 average time/residue: 0.0961 time to fit residues: 5.2536 Evaluate side-chains 44 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 34 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7955 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3159 Z= 0.220 Angle : 0.564 6.383 4305 Z= 0.285 Chirality : 0.042 0.135 501 Planarity : 0.003 0.028 527 Dihedral : 3.679 22.528 456 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.42 % Allowed : 16.15 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.46), residues: 390 helix: 2.23 (0.38), residues: 200 sheet: 0.46 (0.81), residues: 52 loop : -2.82 (0.48), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 106 HIS 0.001 0.001 HIS A 56 PHE 0.016 0.001 PHE A 312 TYR 0.016 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 *********************** 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 46 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.391 Fit side-chains REVERT: A 106 ASP cc_start: 0.8707 (t0) cc_final: 0.8211 (t0) outliers start: 11 outliers final: 9 residues processed: 40 average time/residue: 0.1431 time to fit residues: 8.1979 Evaluate side-chains 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7936 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3159 Z= 0.198 Angle : 0.550 6.490 4305 Z= 0.279 Chirality : 0.041 0.124 501 Planarity : 0.003 0.028 527 Dihedral : 3.661 22.140 456 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.42 % Allowed : 17.08 % Favored : 79.50 % 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: 0.55 (0.45), residues: 390 helix: 2.25 (0.38), residues: 200 sheet: 0.52 (0.81), residues: 52 loop : -2.77 (0.48), residues: 138 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 0.016 0.001 PHE A 312 TYR 0.015 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 44 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.306 Fit side-chains REVERT: A 106 ASP cc_start: 0.8669 (t0) cc_final: 0.8155 (t0) outliers start: 11 outliers final: 9 residues processed: 38 average time/residue: 0.0976 time to fit residues: 5.2397 Evaluate side-chains 41 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.0770 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.7884 moved from start: 0.1834 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= 0.156 Angle : 0.522 6.349 4305 Z= 0.264 Chirality : 0.040 0.122 501 Planarity : 0.003 0.028 527 Dihedral : 3.540 21.580 456 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.80 % Allowed : 17.39 % 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: 0.73 (0.46), residues: 390 helix: 2.42 (0.38), residues: 200 sheet: 0.58 (0.81), residues: 52 loop : -2.71 (0.48), residues: 138 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 0.013 0.001 TYR A 204 ARG 0.001 0.000 ARG A 113 ********************** 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 43 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.352 Fit side-chains REVERT: A 106 ASP cc_start: 0.8539 (t0) cc_final: 0.8038 (t0) outliers start: 9 outliers final: 8 residues processed: 36 average time/residue: 0.1038 time to fit residues: 5.2652 Evaluate side-chains 42 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.0670 chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.0050 overall best weight: 0.4732 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.189730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.133461 restraints weight = 3249.083| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.27 r_work: 0.3327 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1949 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= 0.138 Angle : 0.505 6.154 4305 Z= 0.255 Chirality : 0.040 0.119 501 Planarity : 0.003 0.029 527 Dihedral : 3.432 21.165 456 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.80 % Allowed : 17.39 % 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: 0.91 (0.46), residues: 390 helix: 2.58 (0.38), residues: 200 sheet: 0.64 (0.82), residues: 52 loop : -2.63 (0.48), residues: 138 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 0.018 0.001 PHE A 312 TYR 0.012 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: 1068.86 seconds wall clock time: 19 minutes 46.65 seconds (1186.65 seconds total)