Starting phenix.real_space_refine on Sun Mar 10 18:39:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn1_34906/03_2024/8hn1_34906.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn1_34906/03_2024/8hn1_34906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn1_34906/03_2024/8hn1_34906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn1_34906/03_2024/8hn1_34906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn1_34906/03_2024/8hn1_34906.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hn1_34906/03_2024/8hn1_34906.pdb" } resolution = 2.9 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= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 505 atoms to isotropic. 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 27 5.16 5 C 2314 2.51 5 N 593 2.21 5 O 626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3560 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 510 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 65, 505 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} Conformer: "B" Number of residues, atoms: 65, 505 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 60} bond proxies already assigned to first conformer: 509 Chain: "A" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2217 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 14, 'TRANS': 265} Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 833 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 2.61, per 1000 atoms: 0.73 Number of scatterers: 3560 At special positions: 0 Unit cell: (88.765, 84.435, 102.837, 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 27 16.00 O 626 8.00 N 593 7.00 C 2314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 24 " distance=2.03 Simple disulfide: pdb=" SG CYS C 17 " - pdb=" SG CYS C 42 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 57 " distance=2.03 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 63 " distance=2.03 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 801.4 milliseconds 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 842 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 5 sheets defined 54.4% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 25 through 53 Processing helix chain 'A' and resid 59 through 79 removed outlier: 3.551A pdb=" N TYR A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 94 through 130 removed outlier: 4.123A pdb=" N PHE A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 139 through 160 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 193 through 214 removed outlier: 3.611A pdb=" N ALA A 198 " --> pdb=" O TYR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 298 removed outlier: 3.686A pdb=" N ALA A 270 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Proline residue: A 287 - end of helix Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.590A pdb=" N PHE A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 330 Proline residue: A 323 - end of helix Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 331 through 343 removed outlier: 3.870A pdb=" N ILE A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 3 removed outlier: 3.612A pdb=" N GLU C 15 " --> pdb=" O CYS C 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AA3, first strand: chain 'C' and resid 23 through 32 removed outlier: 3.768A pdb=" N GLY C 41 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.759A pdb=" N THR D 79 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.591A pdb=" N ALA D 51 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU D 33 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ARG D 102 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP D 35 " --> pdb=" O GLU D 100 " (cutoff:3.500A) 212 hydrogen bonds defined for protein. 618 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: 0.89 Time building geometry restraints manager: 1.59 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: 1111 1.34 - 1.46: 897 1.46 - 1.58: 1606 1.58 - 1.70: 0 1.70 - 1.81: 32 Bond restraints: 3646 Sorted by residual: bond pdb=" CE2 PHE A 86 " pdb=" CZ PHE A 86 " ideal model delta sigma weight residual 1.382 1.353 0.029 3.00e-02 1.11e+03 9.13e-01 bond pdb=" CE1 PHE A 86 " pdb=" CZ PHE A 86 " ideal model delta sigma weight residual 1.382 1.355 0.027 3.00e-02 1.11e+03 8.33e-01 bond pdb=" CA ILE C 48 " pdb=" CB ILE C 48 " ideal model delta sigma weight residual 1.526 1.539 -0.013 1.55e-02 4.16e+03 7.22e-01 bond pdb=" C GLN A 167 " pdb=" N PRO A 168 " ideal model delta sigma weight residual 1.334 1.353 -0.020 2.34e-02 1.83e+03 7.00e-01 bond pdb=" CG PRO A 196 " pdb=" CD PRO A 196 " ideal model delta sigma weight residual 1.503 1.477 0.026 3.40e-02 8.65e+02 5.92e-01 ... (remaining 3641 not shown) Histogram of bond angle deviations from ideal: 100.82 - 107.47: 125 107.47 - 114.13: 2071 114.13 - 120.78: 1550 120.78 - 127.43: 1171 127.43 - 134.08: 43 Bond angle restraints: 4960 Sorted by residual: angle pdb=" N GLY D 37 " pdb=" CA GLY D 37 " pdb=" C GLY D 37 " ideal model delta sigma weight residual 110.18 114.00 -3.82 1.56e+00 4.11e-01 6.00e+00 angle pdb=" N ALA A 169 " pdb=" CA ALA A 169 " pdb=" C ALA A 169 " ideal model delta sigma weight residual 109.81 115.11 -5.30 2.21e+00 2.05e-01 5.74e+00 angle pdb=" N PRO C 33 " pdb=" CA PRO C 33 " pdb=" C PRO C 33 " ideal model delta sigma weight residual 112.47 117.22 -4.75 2.06e+00 2.36e-01 5.32e+00 angle pdb=" CA ALA A 169 " pdb=" C ALA A 169 " pdb=" N PRO A 170 " ideal model delta sigma weight residual 118.44 121.83 -3.39 1.59e+00 3.96e-01 4.54e+00 angle pdb=" N VAL A 207 " pdb=" CA VAL A 207 " pdb=" C VAL A 207 " ideal model delta sigma weight residual 110.62 108.52 2.10 1.02e+00 9.61e-01 4.22e+00 ... (remaining 4955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 1984 17.41 - 34.82: 147 34.82 - 52.23: 13 52.23 - 69.64: 4 69.64 - 87.05: 3 Dihedral angle restraints: 2151 sinusoidal: 833 harmonic: 1318 Sorted by residual: dihedral pdb=" CA GLN A 167 " pdb=" C GLN A 167 " pdb=" N PRO A 168 " pdb=" CA PRO A 168 " ideal model delta harmonic sigma weight residual -180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA ALA A 169 " pdb=" C ALA A 169 " pdb=" N PRO A 170 " pdb=" CA PRO A 170 " ideal model delta harmonic sigma weight residual 180.00 -162.31 -17.69 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP A 172 " pdb=" CB ASP A 172 " pdb=" CG ASP A 172 " pdb=" OD1 ASP A 172 " ideal model delta sinusoidal sigma weight residual -30.00 -89.98 59.98 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 2148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 418 0.042 - 0.083: 118 0.083 - 0.125: 32 0.125 - 0.166: 1 0.166 - 0.208: 1 Chirality restraints: 570 Sorted by residual: chirality pdb=" CA PRO C 33 " pdb=" N PRO C 33 " pdb=" C PRO C 33 " pdb=" CB PRO C 33 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PRO A 168 " pdb=" N PRO A 168 " pdb=" C PRO A 168 " pdb=" CB PRO A 168 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA VAL C 32 " pdb=" N VAL C 32 " pdb=" C VAL C 32 " pdb=" CB VAL C 32 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 567 not shown) Planarity restraints: 616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 32 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO C 33 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 33 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 33 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 298 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 299 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 86 " 0.014 2.00e-02 2.50e+03 1.20e-02 2.51e+00 pdb=" CG PHE A 86 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 86 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 86 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 86 " 0.003 2.00e-02 2.50e+03 ... (remaining 613 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 23 2.57 - 3.15: 2954 3.15 - 3.74: 5332 3.74 - 4.32: 7471 4.32 - 4.90: 12587 Nonbonded interactions: 28367 Sorted by model distance: nonbonded pdb=" OG1 THR D 103 " pdb=" OE1 GLU D 107 " model vdw 1.991 2.440 nonbonded pdb=" O ARG D 68 " pdb=" OG SER D 85 " model vdw 2.027 2.440 nonbonded pdb=" NH2 ARG D 68 " pdb=" O SER D 86 " model vdw 2.232 2.520 nonbonded pdb=" OD2 ASP D 74 " pdb=" NZ LYS D 77 " model vdw 2.287 2.520 nonbonded pdb=" O THR C 5 " pdb=" OG SER C 6 " model vdw 2.299 2.440 ... (remaining 28362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 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: 0.320 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 1.710 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.820 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 : 0.003 0.037 3646 Z= 0.204 Angle : 0.578 5.296 4960 Z= 0.325 Chirality : 0.040 0.208 570 Planarity : 0.004 0.044 616 Dihedral : 12.060 87.052 1291 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.40), residues: 449 helix: 1.35 (0.35), residues: 217 sheet: -2.36 (0.60), residues: 72 loop : -2.02 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 165 HIS 0.002 0.000 HIS C 29 PHE 0.027 0.001 PHE A 86 TYR 0.006 0.001 TYR A 204 ARG 0.003 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: D 108 GLU cc_start: 0.8247 (pt0) cc_final: 0.7832 (pt0) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.7208 time to fit residues: 51.5989 Evaluate side-chains 55 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3646 Z= 0.264 Angle : 0.635 7.137 4960 Z= 0.329 Chirality : 0.045 0.198 570 Planarity : 0.005 0.036 616 Dihedral : 4.436 23.291 502 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.63 % Allowed : 8.29 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.40), residues: 449 helix: 1.44 (0.34), residues: 229 sheet: -2.00 (0.57), residues: 83 loop : -2.34 (0.45), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 165 HIS 0.001 0.000 HIS A 54 PHE 0.011 0.002 PHE A 308 TYR 0.012 0.001 TYR A 316 ARG 0.004 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7573 (m-40) REVERT: D 107 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6705 (tp30) REVERT: D 108 GLU cc_start: 0.8240 (pt0) cc_final: 0.7885 (pt0) outliers start: 14 outliers final: 6 residues processed: 60 average time/residue: 0.7279 time to fit residues: 46.0022 Evaluate side-chains 57 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain D residue 107 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 12 optimal weight: 0.3980 chunk 34 optimal weight: 0.0030 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 36 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.0270 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.2648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3646 Z= 0.150 Angle : 0.548 6.864 4960 Z= 0.279 Chirality : 0.041 0.169 570 Planarity : 0.004 0.030 616 Dihedral : 4.034 21.650 502 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.11 % Allowed : 9.07 % Favored : 87.82 % 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: 0.20 (0.41), residues: 449 helix: 2.14 (0.35), residues: 231 sheet: -1.81 (0.57), residues: 83 loop : -2.19 (0.46), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.002 0.000 HIS A 54 PHE 0.007 0.001 PHE D 69 TYR 0.010 0.001 TYR A 316 ARG 0.004 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 56 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7151 (m-40) REVERT: D 108 GLU cc_start: 0.8227 (pt0) cc_final: 0.7920 (pt0) outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 0.7550 time to fit residues: 49.9557 Evaluate side-chains 60 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 321 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3646 Z= 0.300 Angle : 0.624 7.500 4960 Z= 0.318 Chirality : 0.046 0.223 570 Planarity : 0.004 0.033 616 Dihedral : 4.200 20.832 502 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.63 % Allowed : 10.10 % Favored : 86.27 % 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: -0.14 (0.40), residues: 449 helix: 1.71 (0.34), residues: 231 sheet: -1.73 (0.59), residues: 83 loop : -2.19 (0.46), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 313 HIS 0.002 0.001 HIS C 56 PHE 0.009 0.002 PHE A 82 TYR 0.012 0.001 TYR A 326 ARG 0.002 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7390 (m-40) REVERT: D 108 GLU cc_start: 0.8213 (pt0) cc_final: 0.7887 (pt0) outliers start: 14 outliers final: 7 residues processed: 61 average time/residue: 0.7223 time to fit residues: 46.3997 Evaluate side-chains 58 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 321 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.7706 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3646 Z= 0.218 Angle : 0.578 7.344 4960 Z= 0.294 Chirality : 0.043 0.206 570 Planarity : 0.004 0.032 616 Dihedral : 4.083 20.391 502 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.89 % Allowed : 11.14 % Favored : 84.97 % 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: 0.09 (0.41), residues: 449 helix: 1.90 (0.35), residues: 231 sheet: -1.64 (0.59), residues: 83 loop : -2.06 (0.47), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 313 HIS 0.001 0.001 HIS A 54 PHE 0.008 0.001 PHE A 312 TYR 0.010 0.001 TYR A 316 ARG 0.001 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 50 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6634 (tt) REVERT: D 36 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7481 (mtm) REVERT: D 108 GLU cc_start: 0.8248 (pt0) cc_final: 0.8040 (pt0) outliers start: 15 outliers final: 7 residues processed: 57 average time/residue: 0.8045 time to fit residues: 48.1212 Evaluate side-chains 59 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain D residue 36 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 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: 0.7717 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3646 Z= 0.235 Angle : 0.585 7.404 4960 Z= 0.297 Chirality : 0.044 0.212 570 Planarity : 0.004 0.032 616 Dihedral : 4.048 19.603 502 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.89 % Allowed : 12.44 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.41), residues: 449 helix: 1.88 (0.34), residues: 231 sheet: -1.66 (0.59), residues: 83 loop : -2.02 (0.47), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 313 HIS 0.001 0.000 HIS C 56 PHE 0.008 0.001 PHE A 312 TYR 0.010 0.001 TYR A 316 ARG 0.001 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 51 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6610 (tt) REVERT: A 179 ASN cc_start: 0.7570 (OUTLIER) cc_final: 0.7335 (m-40) REVERT: D 36 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7478 (mtm) outliers start: 15 outliers final: 7 residues processed: 58 average time/residue: 0.7922 time to fit residues: 48.2738 Evaluate side-chains 60 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain D residue 36 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.7691 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3646 Z= 0.199 Angle : 0.563 7.146 4960 Z= 0.286 Chirality : 0.043 0.200 570 Planarity : 0.004 0.032 616 Dihedral : 3.956 19.762 502 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.15 % Allowed : 12.95 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.41), residues: 449 helix: 2.08 (0.34), residues: 232 sheet: -1.58 (0.59), residues: 83 loop : -1.96 (0.48), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 313 HIS 0.001 0.000 HIS A 54 PHE 0.008 0.001 PHE A 312 TYR 0.009 0.001 TYR A 316 ARG 0.001 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 50 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6600 (tt) REVERT: A 213 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7371 (ttp-170) REVERT: D 36 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7483 (mtm) outliers start: 16 outliers final: 9 residues processed: 59 average time/residue: 0.7700 time to fit residues: 48.0331 Evaluate side-chains 60 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain D residue 36 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7709 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3646 Z= 0.225 Angle : 0.577 7.260 4960 Z= 0.294 Chirality : 0.044 0.210 570 Planarity : 0.004 0.032 616 Dihedral : 3.963 19.665 502 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.40 % Allowed : 12.95 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.41), residues: 449 helix: 2.00 (0.34), residues: 231 sheet: -1.56 (0.58), residues: 83 loop : -1.92 (0.48), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 313 HIS 0.002 0.001 HIS A 54 PHE 0.008 0.001 PHE A 312 TYR 0.009 0.001 TYR A 316 ARG 0.001 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 49 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6593 (tt) REVERT: A 213 ARG cc_start: 0.7758 (ttp-110) cc_final: 0.7364 (ttp-170) outliers start: 17 outliers final: 12 residues processed: 59 average time/residue: 0.8028 time to fit residues: 49.6985 Evaluate side-chains 62 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain D residue 108 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.0170 chunk 44 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 overall best weight: 0.8420 ------------------------------------------------------------------------------- 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: 0.7699 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3646 Z= 0.213 Angle : 0.569 7.046 4960 Z= 0.290 Chirality : 0.043 0.205 570 Planarity : 0.004 0.033 616 Dihedral : 3.937 19.857 502 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.85 % Allowed : 14.77 % Favored : 82.38 % 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: 0.35 (0.41), residues: 449 helix: 2.09 (0.34), residues: 232 sheet: -1.56 (0.57), residues: 83 loop : -1.92 (0.48), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 313 HIS 0.002 0.000 HIS A 54 PHE 0.008 0.001 PHE A 312 TYR 0.009 0.001 TYR A 316 ARG 0.001 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6575 (tt) REVERT: A 179 ASN cc_start: 0.7413 (m-40) cc_final: 0.7039 (t0) REVERT: A 213 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7371 (ttp-170) REVERT: D 36 MET cc_start: 0.7834 (mtm) cc_final: 0.7541 (ptp) outliers start: 11 outliers final: 10 residues processed: 58 average time/residue: 0.7469 time to fit residues: 45.6337 Evaluate side-chains 60 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 49 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 321 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.0020 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- 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: 0.7663 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3646 Z= 0.169 Angle : 0.547 6.973 4960 Z= 0.278 Chirality : 0.042 0.192 570 Planarity : 0.004 0.032 616 Dihedral : 3.800 19.669 502 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.59 % Allowed : 15.54 % Favored : 81.87 % 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: 0.61 (0.41), residues: 449 helix: 2.36 (0.34), residues: 232 sheet: -1.49 (0.57), residues: 83 loop : -1.87 (0.49), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 313 HIS 0.002 0.000 HIS A 54 PHE 0.008 0.001 PHE A 312 TYR 0.008 0.001 TYR A 316 ARG 0.002 0.000 ARG C 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 898 Ramachandran restraints generated. 449 Oldfield, 0 Emsley, 449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6575 (tt) REVERT: A 179 ASN cc_start: 0.7289 (m-40) cc_final: 0.6941 (t0) REVERT: A 213 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7325 (ttp-170) REVERT: D 36 MET cc_start: 0.7781 (mtm) cc_final: 0.7438 (ptp) outliers start: 10 outliers final: 8 residues processed: 58 average time/residue: 0.7870 time to fit residues: 47.9865 Evaluate side-chains 59 residues out of total 392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 50 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 321 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 0.0570 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.191086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113476 restraints weight = 8906.104| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.26 r_work: 0.3062 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3646 Z= 0.182 Angle : 0.553 7.033 4960 Z= 0.281 Chirality : 0.042 0.196 570 Planarity : 0.004 0.032 616 Dihedral : 3.801 19.666 502 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.59 % Allowed : 15.54 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.41), residues: 449 helix: 2.35 (0.34), residues: 232 sheet: -1.46 (0.57), residues: 83 loop : -1.88 (0.49), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 313 HIS 0.002 0.000 HIS A 54 PHE 0.008 0.001 PHE A 312 TYR 0.008 0.001 TYR A 316 ARG 0.002 0.000 ARG C 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1603.00 seconds wall clock time: 29 minutes 45.71 seconds (1785.71 seconds total)