Starting phenix.real_space_refine on Fri Dec 27 09:31:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hn1_34906/12_2024/8hn1_34906.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hn1_34906/12_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/cci-nas-00/data/ceres_data/8hn1_34906/12_2024/8hn1_34906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hn1_34906/12_2024/8hn1_34906.map" model { file = "/net/cci-nas-00/data/ceres_data/8hn1_34906/12_2024/8hn1_34906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hn1_34906/12_2024/8hn1_34906.cif" } 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. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 2.96, per 1000 atoms: 0.83 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 - 3.00 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: 0.88 Conformation dependent library (CDL) restraints added in 480.3 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: 0.40 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: 0.95 Time building geometry restraints manager: 1.04 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: 0.00 - 1.06: 4686 1.06 - 2.12: 216 2.12 - 3.18: 36 3.18 - 4.24: 15 4.24 - 5.30: 7 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 3.040 nonbonded pdb=" O ARG D 68 " pdb=" OG SER D 85 " model vdw 2.027 3.040 nonbonded pdb=" NH2 ARG D 68 " pdb=" O SER D 86 " model vdw 2.232 3.120 nonbonded pdb=" OD2 ASP D 74 " pdb=" NZ LYS D 77 " model vdw 2.287 3.120 nonbonded pdb=" O THR C 5 " pdb=" OG SER C 6 " model vdw 2.299 3.040 ... (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 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=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: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.490 Find NCS groups from input model: 0.040 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:11.720 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.840 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.409 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: 0.7200 time to fit residues: 51.5636 Evaluate side-chains 55 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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: 10.0000 chunk 34 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.7710 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3646 Z= 0.264 Angle : 0.646 7.047 4960 Z= 0.336 Chirality : 0.045 0.200 570 Planarity : 0.005 0.040 616 Dihedral : 4.415 23.313 502 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.59 % Allowed : 9.07 % Favored : 88.34 % 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: -0.45 (0.40), residues: 449 helix: 1.52 (0.34), residues: 229 sheet: -1.96 (0.57), residues: 82 loop : -2.33 (0.45), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 165 HIS 0.002 0.000 HIS A 54 PHE 0.010 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 63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 107 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6751 (tp30) REVERT: D 108 GLU cc_start: 0.8173 (pt0) cc_final: 0.7810 (pt0) outliers start: 10 outliers final: 5 residues processed: 58 average time/residue: 0.7969 time to fit residues: 48.5645 Evaluate side-chains 56 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ILE 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 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: 0.7980 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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: 0.7712 moved from start: 0.1830 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= 0.237 Angle : 0.603 7.367 4960 Z= 0.311 Chirality : 0.044 0.206 570 Planarity : 0.004 0.038 616 Dihedral : 4.224 21.410 502 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.33 % Allowed : 10.36 % Favored : 87.31 % 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: -0.16 (0.41), residues: 449 helix: 1.70 (0.35), residues: 231 sheet: -1.68 (0.58), residues: 82 loop : -2.27 (0.47), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 165 HIS 0.001 0.000 HIS A 54 PHE 0.008 0.001 PHE A 289 TYR 0.011 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 60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASN cc_start: 0.7621 (m-40) cc_final: 0.7366 (t0) REVERT: D 108 GLU cc_start: 0.8236 (pt0) cc_final: 0.7911 (pt0) outliers start: 9 outliers final: 6 residues processed: 55 average time/residue: 0.8091 time to fit residues: 46.5722 Evaluate side-chains 56 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 TRP Chi-restraints excluded: chain A residue 283 LEU 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: 1.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 38 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3646 Z= 0.277 Angle : 0.619 7.449 4960 Z= 0.319 Chirality : 0.045 0.221 570 Planarity : 0.005 0.040 616 Dihedral : 4.239 21.505 502 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.15 % Allowed : 9.84 % Favored : 86.01 % 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: -0.16 (0.41), residues: 449 helix: 1.66 (0.34), residues: 231 sheet: -1.60 (0.58), residues: 83 loop : -2.23 (0.48), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 165 HIS 0.002 0.001 HIS A 54 PHE 0.009 0.001 PHE A 289 TYR 0.012 0.001 TYR A 316 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 69 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6495 (tt) REVERT: A 179 ASN cc_start: 0.7590 (m-40) cc_final: 0.7350 (t0) REVERT: A 213 ARG cc_start: 0.7782 (ttp-110) cc_final: 0.7395 (ttp-170) REVERT: D 36 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7325 (mtm) REVERT: D 108 GLU cc_start: 0.8271 (pt0) cc_final: 0.7936 (pt0) outliers start: 16 outliers final: 11 residues processed: 62 average time/residue: 0.7301 time to fit residues: 47.6460 Evaluate side-chains 65 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 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 55 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 TRP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain D residue 36 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3646 Z= 0.297 Angle : 0.622 7.487 4960 Z= 0.321 Chirality : 0.046 0.228 570 Planarity : 0.005 0.041 616 Dihedral : 4.249 21.568 502 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.66 % Allowed : 10.62 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.41), residues: 449 helix: 1.64 (0.35), residues: 231 sheet: -1.50 (0.58), residues: 83 loop : -2.17 (0.49), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 165 HIS 0.002 0.001 HIS C 29 PHE 0.010 0.002 PHE A 289 TYR 0.012 0.001 TYR A 316 ARG 0.002 0.000 ARG A 213 *********************** 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 69 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6597 (tt) REVERT: A 179 ASN cc_start: 0.7600 (m-40) cc_final: 0.7355 (t0) REVERT: D 108 GLU cc_start: 0.8310 (pt0) cc_final: 0.8086 (pt0) outliers start: 18 outliers final: 11 residues processed: 61 average time/residue: 0.8024 time to fit residues: 51.2793 Evaluate side-chains 63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 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 55 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 TRP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 321 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 3 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2234 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= 0.309 Angle : 0.627 7.474 4960 Z= 0.325 Chirality : 0.046 0.233 570 Planarity : 0.005 0.043 616 Dihedral : 4.248 21.742 502 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.66 % Allowed : 11.66 % 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: -0.10 (0.41), residues: 449 helix: 1.62 (0.35), residues: 231 sheet: -1.40 (0.62), residues: 74 loop : -2.14 (0.48), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 165 HIS 0.002 0.001 HIS A 54 PHE 0.010 0.002 PHE A 289 TYR 0.012 0.001 TYR A 316 ARG 0.002 0.000 ARG D 102 *********************** 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 to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6569 (tt) REVERT: A 179 ASN cc_start: 0.7578 (m-40) cc_final: 0.7158 (t0) REVERT: D 36 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7397 (mtm) outliers start: 18 outliers final: 13 residues processed: 60 average time/residue: 0.8171 time to fit residues: 51.3685 Evaluate side-chains 63 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 33 PRO Chi-restraints excluded: chain C residue 39 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 55 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 165 TRP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 294 ILE 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: 0.5980 chunk 36 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.7676 moved from start: 0.2403 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= 0.168 Angle : 0.555 7.020 4960 Z= 0.286 Chirality : 0.042 0.188 570 Planarity : 0.004 0.036 616 Dihedral : 3.952 21.926 502 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.59 % Allowed : 14.25 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.42), residues: 449 helix: 2.10 (0.35), residues: 232 sheet: -1.13 (0.63), residues: 73 loop : -1.96 (0.49), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 165 HIS 0.002 0.000 HIS A 54 PHE 0.008 0.001 PHE A 312 TYR 0.011 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 65 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ASN cc_start: 0.7542 (m-40) cc_final: 0.7231 (t0) REVERT: A 213 ARG cc_start: 0.7778 (ttp-110) cc_final: 0.7351 (ttp-170) outliers start: 10 outliers final: 6 residues processed: 61 average time/residue: 0.8066 time to fit residues: 51.6195 Evaluate side-chains 54 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 TRP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 321 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 21 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 39 optimal weight: 40.0000 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.7711 moved from start: 0.2427 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= 0.221 Angle : 0.586 7.180 4960 Z= 0.300 Chirality : 0.044 0.205 570 Planarity : 0.004 0.036 616 Dihedral : 3.985 21.466 502 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.37 % Allowed : 15.03 % Favored : 81.61 % 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: 0.45 (0.41), residues: 449 helix: 2.06 (0.34), residues: 231 sheet: -1.03 (0.63), residues: 73 loop : -1.93 (0.48), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 165 HIS 0.002 0.000 HIS A 54 PHE 0.008 0.001 PHE A 289 TYR 0.010 0.001 TYR A 316 ARG 0.001 0.000 ARG D 102 *********************** 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 60 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6549 (tt) REVERT: A 179 ASN cc_start: 0.7589 (m-40) cc_final: 0.7183 (t0) REVERT: A 213 ARG cc_start: 0.7798 (ttp-110) cc_final: 0.7377 (ttp-170) outliers start: 13 outliers final: 8 residues processed: 55 average time/residue: 0.7415 time to fit residues: 42.9669 Evaluate side-chains 56 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 TRP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 321 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3646 Z= 0.292 Angle : 0.621 7.230 4960 Z= 0.320 Chirality : 0.046 0.224 570 Planarity : 0.004 0.039 616 Dihedral : 4.127 21.209 502 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.11 % Allowed : 16.06 % Favored : 80.83 % 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: 0.19 (0.41), residues: 449 helix: 1.82 (0.34), residues: 231 sheet: -1.11 (0.63), residues: 76 loop : -2.04 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 165 HIS 0.002 0.001 HIS A 54 PHE 0.010 0.002 PHE A 289 TYR 0.010 0.001 TYR A 326 ARG 0.002 0.000 ARG D 102 *********************** 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 59 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6565 (tt) REVERT: A 213 ARG cc_start: 0.7823 (ttp-110) cc_final: 0.7436 (ttp-170) outliers start: 12 outliers final: 11 residues processed: 56 average time/residue: 0.6976 time to fit residues: 41.2652 Evaluate side-chains 59 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 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 155 LEU Chi-restraints excluded: chain A residue 165 TRP Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 5 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.0170 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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: 0.7678 moved from start: 0.2579 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 : 0.567 6.930 4960 Z= 0.291 Chirality : 0.042 0.184 570 Planarity : 0.004 0.035 616 Dihedral : 3.918 21.103 502 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.33 % Allowed : 16.58 % Favored : 81.09 % 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 (0.42), residues: 449 helix: 2.26 (0.34), residues: 231 sheet: -0.84 (0.65), residues: 73 loop : -1.93 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 165 HIS 0.002 0.000 HIS A 54 PHE 0.008 0.001 PHE D 69 TYR 0.009 0.001 TYR A 316 ARG 0.002 0.000 ARG A 113 ********************** 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 58 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6505 (tt) REVERT: A 179 ASN cc_start: 0.7616 (m-40) cc_final: 0.7182 (t0) REVERT: A 213 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7435 (ttp-170) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.6907 time to fit residues: 41.7521 Evaluate side-chains 57 residues out of total 392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 165 TRP 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: 3.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.189731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110330 restraints weight = 8955.456| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.38 r_work: 0.2889 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3646 Z= 0.224 Angle : 0.587 7.028 4960 Z= 0.301 Chirality : 0.044 0.204 570 Planarity : 0.004 0.037 616 Dihedral : 3.961 21.247 502 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.33 % Allowed : 17.10 % Favored : 80.57 % 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: 2.16 (0.34), residues: 231 sheet: -0.76 (0.66), residues: 73 loop : -1.94 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 165 HIS 0.002 0.000 HIS A 54 PHE 0.012 0.001 PHE A 39 TYR 0.009 0.001 TYR A 316 ARG 0.002 0.000 ARG D 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1549.70 seconds wall clock time: 28 minutes 49.60 seconds (1729.60 seconds total)