Starting phenix.real_space_refine on Mon Sep 23 12:58:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul5_26592/09_2024/7ul5_26592.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul5_26592/09_2024/7ul5_26592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul5_26592/09_2024/7ul5_26592.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul5_26592/09_2024/7ul5_26592.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul5_26592/09_2024/7ul5_26592.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul5_26592/09_2024/7ul5_26592.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.088 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 24 5.16 5 C 1834 2.51 5 N 449 2.21 5 O 466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 2773 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2169 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 604 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 85} Chain breaks: 4 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 2.61, per 1000 atoms: 0.94 Number of scatterers: 2773 At special positions: 0 Unit cell: (67.3159, 57.9428, 109.069, 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 24 16.00 O 466 8.00 N 449 7.00 C 1834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 299.6 milliseconds 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 694 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 4 sheets defined 65.5% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 40 through 71 removed outlier: 3.985A pdb=" N ALA A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 105 removed outlier: 4.245A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 112 through 146 removed outlier: 3.649A pdb=" N VAL A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.940A pdb=" N ALA A 151 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 152 " --> pdb=" O LYS A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 152' Processing helix chain 'A' and resid 155 through 180 removed outlier: 3.515A pdb=" N ALA A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.532A pdb=" N ILE A 210 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.627A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 282 removed outlier: 3.531A pdb=" N ARG A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 288 through 315 removed outlier: 4.273A pdb=" N GLY A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Proline residue: A 309 - end of helix removed outlier: 3.732A pdb=" N TYR A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 185 Processing sheet with id=AA2, first strand: chain 'D' and resid 5 through 9 removed outlier: 3.687A pdb=" N SER D 23 " --> pdb=" O SER D 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 32 through 33 removed outlier: 3.630A pdb=" N ARG D 32 " --> pdb=" O ARG D 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 32 through 33 removed outlier: 3.630A pdb=" N ARG D 32 " --> pdb=" O ARG D 102 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 576 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: 0.66 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 842 1.34 - 1.46: 637 1.46 - 1.58: 1320 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 2835 Sorted by residual: bond pdb=" CB CYS A 306 " pdb=" SG CYS A 306 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" CG LEU D 33 " pdb=" CD1 LEU D 33 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 bond pdb=" CA LEU A 96 " pdb=" C LEU A 96 " ideal model delta sigma weight residual 1.525 1.537 -0.012 1.19e-02 7.06e+03 1.10e+00 bond pdb=" CB VAL D 80 " pdb=" CG2 VAL D 80 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 1.01e+00 bond pdb=" CA ASP D 111 " pdb=" CB ASP D 111 " ideal model delta sigma weight residual 1.535 1.555 -0.020 2.02e-02 2.45e+03 9.73e-01 ... (remaining 2830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 3740 1.59 - 3.18: 106 3.18 - 4.77: 20 4.77 - 6.36: 0 6.36 - 7.95: 1 Bond angle restraints: 3867 Sorted by residual: angle pdb=" N PHE A 127 " pdb=" CA PHE A 127 " pdb=" C PHE A 127 " ideal model delta sigma weight residual 112.68 116.13 -3.45 1.33e+00 5.65e-01 6.71e+00 angle pdb=" N ASN A 308 " pdb=" CA ASN A 308 " pdb=" C ASN A 308 " ideal model delta sigma weight residual 113.16 116.80 -3.64 1.42e+00 4.96e-01 6.57e+00 angle pdb=" CA LEU A 105 " pdb=" CB LEU A 105 " pdb=" CG LEU A 105 " ideal model delta sigma weight residual 116.30 124.25 -7.95 3.50e+00 8.16e-02 5.17e+00 angle pdb=" CA ASP D 111 " pdb=" CB ASP D 111 " pdb=" CG ASP D 111 " ideal model delta sigma weight residual 112.60 114.70 -2.10 1.00e+00 1.00e+00 4.39e+00 angle pdb=" N GLN A 126 " pdb=" CA GLN A 126 " pdb=" C GLN A 126 " ideal model delta sigma weight residual 111.36 113.62 -2.26 1.09e+00 8.42e-01 4.30e+00 ... (remaining 3862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 1455 14.03 - 28.05: 134 28.05 - 42.08: 33 42.08 - 56.10: 4 56.10 - 70.13: 1 Dihedral angle restraints: 1627 sinusoidal: 551 harmonic: 1076 Sorted by residual: dihedral pdb=" CG ARG A 249 " pdb=" CD ARG A 249 " pdb=" NE ARG A 249 " pdb=" CZ ARG A 249 " ideal model delta sinusoidal sigma weight residual 180.00 136.43 43.57 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB MET A 119 " pdb=" CG MET A 119 " pdb=" SD MET A 119 " pdb=" CE MET A 119 " ideal model delta sinusoidal sigma weight residual 60.00 111.66 -51.66 3 1.50e+01 4.44e-03 9.04e+00 dihedral pdb=" CA LEU A 105 " pdb=" C LEU A 105 " pdb=" N VAL A 106 " pdb=" CA VAL A 106 " ideal model delta harmonic sigma weight residual -180.00 -164.97 -15.03 0 5.00e+00 4.00e-02 9.03e+00 ... (remaining 1624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 280 0.032 - 0.063: 126 0.063 - 0.095: 41 0.095 - 0.126: 15 0.126 - 0.158: 3 Chirality restraints: 465 Sorted by residual: chirality pdb=" CA PHE A 127 " pdb=" N PHE A 127 " pdb=" C PHE A 127 " pdb=" CB PHE A 127 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ILE D 30 " pdb=" N ILE D 30 " pdb=" C ILE D 30 " pdb=" CB ILE D 30 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA PRO A 309 " pdb=" N PRO A 309 " pdb=" C PRO A 309 " pdb=" CB PRO A 309 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 462 not shown) Planarity restraints: 470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 46 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C LEU A 46 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU A 46 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 47 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 211 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.10e+00 pdb=" C TYR A 211 " 0.046 2.00e-02 2.50e+03 pdb=" O TYR A 211 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 212 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 219 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A 220 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.028 5.00e-02 4.00e+02 ... (remaining 467 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1094 2.90 - 3.40: 2578 3.40 - 3.90: 4120 3.90 - 4.40: 4429 4.40 - 4.90: 8105 Nonbonded interactions: 20326 Sorted by model distance: nonbonded pdb=" O ASN A 43 " pdb=" OG1 THR A 47 " model vdw 2.404 3.040 nonbonded pdb=" O GLY A 57 " pdb=" ND2 ASN A 61 " model vdw 2.439 3.120 nonbonded pdb=" O VAL A 298 " pdb=" OG1 THR A 301 " model vdw 2.458 3.040 nonbonded pdb=" OH TYR A 71 " pdb=" OD1 ASN A 325 " model vdw 2.463 3.040 nonbonded pdb=" O ASP D 111 " pdb=" OD1 ASP D 111 " model vdw 2.521 3.040 ... (remaining 20321 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.004 0.039 2835 Z= 0.251 Angle : 0.639 7.955 3867 Z= 0.363 Chirality : 0.042 0.158 465 Planarity : 0.006 0.050 470 Dihedral : 11.756 70.125 927 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -1.07 (0.41), residues: 355 helix: 0.01 (0.31), residues: 225 sheet: -0.48 (0.64), residues: 64 loop : -3.07 (0.57), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 38 HIS 0.003 0.002 HIS A 146 PHE 0.013 0.001 PHE A 217 TYR 0.014 0.002 TYR A 228 ARG 0.003 0.001 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.303 Fit side-chains REVERT: A 281 SER cc_start: 0.8448 (t) cc_final: 0.8085 (m) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1120 time to fit residues: 4.9200 Evaluate side-chains 30 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2835 Z= 0.238 Angle : 0.553 6.295 3867 Z= 0.307 Chirality : 0.040 0.125 465 Planarity : 0.005 0.041 470 Dihedral : 3.744 15.326 396 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.37 % Allowed : 6.72 % Favored : 92.91 % 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: 0.97 (0.44), residues: 355 helix: 1.57 (0.33), residues: 224 sheet: -0.08 (0.67), residues: 64 loop : -1.68 (0.73), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 106 HIS 0.003 0.002 HIS A 146 PHE 0.014 0.001 PHE A 213 TYR 0.014 0.001 TYR A 228 ARG 0.004 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.298 Fit side-chains REVERT: A 281 SER cc_start: 0.8279 (t) cc_final: 0.7873 (m) outliers start: 1 outliers final: 1 residues processed: 32 average time/residue: 0.0989 time to fit residues: 4.3842 Evaluate side-chains 33 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 0.0030 overall best weight: 0.3628 ------------------------------------------------------------------------------- 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: 0.8110 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2835 Z= 0.151 Angle : 0.468 5.440 3867 Z= 0.259 Chirality : 0.038 0.120 465 Planarity : 0.004 0.037 470 Dihedral : 3.519 14.045 396 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.12 % Allowed : 7.09 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.46), residues: 355 helix: 2.29 (0.34), residues: 226 sheet: 0.22 (0.67), residues: 64 loop : -0.90 (0.85), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 106 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 213 TYR 0.011 0.001 TYR A 211 ARG 0.001 0.000 ARG A 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.301 Fit side-chains REVERT: A 281 SER cc_start: 0.8223 (t) cc_final: 0.7773 (m) outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.1026 time to fit residues: 4.2312 Evaluate side-chains 31 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain D residue 105 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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: 0.8175 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2835 Z= 0.203 Angle : 0.495 4.966 3867 Z= 0.276 Chirality : 0.039 0.126 465 Planarity : 0.004 0.036 470 Dihedral : 3.513 14.675 396 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.12 % Allowed : 10.07 % Favored : 88.81 % 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: 2.19 (0.46), residues: 355 helix: 2.37 (0.34), residues: 226 sheet: 0.40 (0.67), residues: 64 loop : -0.75 (0.86), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.003 0.001 HIS A 146 PHE 0.013 0.001 PHE A 213 TYR 0.014 0.001 TYR A 228 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.316 Fit side-chains REVERT: A 281 SER cc_start: 0.8233 (t) cc_final: 0.7833 (m) outliers start: 3 outliers final: 2 residues processed: 31 average time/residue: 0.0980 time to fit residues: 4.2353 Evaluate side-chains 33 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 31 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.8183 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2835 Z= 0.206 Angle : 0.495 4.975 3867 Z= 0.276 Chirality : 0.039 0.125 465 Planarity : 0.004 0.035 470 Dihedral : 3.550 14.663 396 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.12 % Allowed : 10.82 % Favored : 88.06 % 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: 2.23 (0.46), residues: 355 helix: 2.32 (0.34), residues: 228 sheet: 0.46 (0.66), residues: 66 loop : -0.57 (0.91), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.003 0.001 HIS A 146 PHE 0.011 0.001 PHE A 213 TYR 0.014 0.001 TYR A 211 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.300 Fit side-chains REVERT: A 281 SER cc_start: 0.8057 (t) cc_final: 0.7689 (m) outliers start: 3 outliers final: 3 residues processed: 33 average time/residue: 0.1023 time to fit residues: 4.6088 Evaluate side-chains 34 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2835 Z= 0.202 Angle : 0.488 5.002 3867 Z= 0.272 Chirality : 0.039 0.122 465 Planarity : 0.004 0.036 470 Dihedral : 3.529 14.444 396 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.49 % Allowed : 10.82 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.46), residues: 355 helix: 2.39 (0.34), residues: 228 sheet: 0.59 (0.66), residues: 66 loop : -0.57 (0.91), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.003 0.001 HIS A 146 PHE 0.011 0.001 PHE A 213 TYR 0.014 0.001 TYR A 211 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.310 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 32 average time/residue: 0.1053 time to fit residues: 4.6134 Evaluate side-chains 33 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.0270 chunk 29 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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: 0.8146 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2835 Z= 0.168 Angle : 0.461 4.985 3867 Z= 0.257 Chirality : 0.038 0.117 465 Planarity : 0.004 0.034 470 Dihedral : 3.466 14.077 396 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 11.57 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.47), residues: 355 helix: 2.53 (0.34), residues: 228 sheet: 0.74 (0.67), residues: 66 loop : -0.41 (0.93), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 106 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 213 TYR 0.012 0.001 TYR A 211 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.295 Fit side-chains REVERT: A 281 SER cc_start: 0.8125 (t) cc_final: 0.7738 (m) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.0996 time to fit residues: 4.5046 Evaluate side-chains 34 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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: 0.8144 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 0.030 2835 Z= 0.173 Angle : 0.467 4.971 3867 Z= 0.260 Chirality : 0.038 0.117 465 Planarity : 0.004 0.034 470 Dihedral : 3.471 14.174 396 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 12.69 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.47), residues: 355 helix: 2.54 (0.34), residues: 228 sheet: 0.91 (0.68), residues: 66 loop : -0.33 (0.94), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 106 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 213 TYR 0.013 0.001 TYR A 211 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.298 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.0978 time to fit residues: 4.1504 Evaluate side-chains 32 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 0.0470 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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: 0.8175 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2835 Z= 0.204 Angle : 0.488 4.975 3867 Z= 0.271 Chirality : 0.039 0.120 465 Planarity : 0.004 0.034 470 Dihedral : 3.530 14.356 396 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 12.69 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.58 (0.47), residues: 355 helix: 2.46 (0.34), residues: 228 sheet: 0.95 (0.67), residues: 66 loop : -0.36 (0.93), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.002 0.001 HIS A 146 PHE 0.011 0.001 PHE A 272 TYR 0.014 0.001 TYR A 228 ARG 0.003 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.293 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 30 average time/residue: 0.1009 time to fit residues: 4.1643 Evaluate side-chains 31 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 11 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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: 0.8120 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2835 Z= 0.158 Angle : 0.453 4.988 3867 Z= 0.252 Chirality : 0.038 0.113 465 Planarity : 0.004 0.033 470 Dihedral : 3.444 13.997 396 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.87 % Allowed : 12.31 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.79 (0.47), residues: 355 helix: 2.63 (0.34), residues: 228 sheet: 1.01 (0.68), residues: 66 loop : -0.26 (0.94), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 106 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 213 TYR 0.012 0.001 TYR A 211 ARG 0.002 0.000 ARG A 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 710 Ramachandran restraints generated. 355 Oldfield, 0 Emsley, 355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.271 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 32 average time/residue: 0.0970 time to fit residues: 4.2572 Evaluate side-chains 32 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 0.0010 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.139534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.112233 restraints weight = 3232.983| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.82 r_work: 0.3052 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2835 Z= 0.181 Angle : 0.469 4.984 3867 Z= 0.260 Chirality : 0.038 0.117 465 Planarity : 0.004 0.033 470 Dihedral : 3.461 14.383 396 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 12.69 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.47), residues: 355 helix: 2.57 (0.34), residues: 228 sheet: 1.04 (0.68), residues: 66 loop : -0.28 (0.94), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 106 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 272 TYR 0.013 0.001 TYR A 211 ARG 0.003 0.000 ARG A 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1040.26 seconds wall clock time: 18 minutes 56.76 seconds (1136.76 seconds total)