Starting phenix.real_space_refine on Tue Feb 13 07:58:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/02_2024/8do2_27588_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/02_2024/8do2_27588.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/02_2024/8do2_27588_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/02_2024/8do2_27588_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/02_2024/8do2_27588_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/02_2024/8do2_27588.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/02_2024/8do2_27588.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/02_2024/8do2_27588_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do2_27588/02_2024/8do2_27588_trim_updated.pdb" } resolution = 2.95 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= 0.003 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2803 2.51 5 N 674 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4226 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "A" Number of atoms: 3502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3502 Unusual residues: {'SXU': 1} Classifications: {'peptide': 449, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 430, None: 1} Not linked: pdbres="VAL A 468 " pdbres="SXU A 501 " Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 2.85, per 1000 atoms: 0.67 Number of scatterers: 4226 At special positions: 0 Unit cell: (85.05, 76.65, 79.8, 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 28 16.00 O 721 8.00 N 674 7.00 C 2803 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.89 Conformation dependent library (CDL) restraints added in 830.5 milliseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 2 sheets defined 67.3% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 65 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 70 through 94 Processing helix chain 'A' and resid 10 through 13 No H-bonds generated for 'chain 'A' and resid 10 through 13' Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 108 through 133 Processing helix chain 'A' and resid 140 through 170 removed outlier: 5.903A pdb=" N ALA A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 196 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 242 through 259 Processing helix chain 'A' and resid 289 through 311 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 341 through 344 No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 358 through 382 Processing helix chain 'A' and resid 387 through 397 Processing helix chain 'A' and resid 409 through 437 Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 443 through 467 Processing sheet with id= A, first strand: chain 'A' and resid 262 through 265 Processing sheet with id= B, first strand: chain 'A' and resid 267 through 269 278 hydrogen bonds defined for protein. 831 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: 1.12 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 943 1.33 - 1.46: 1358 1.46 - 1.59: 1970 1.59 - 1.72: 0 1.72 - 1.85: 47 Bond restraints: 4318 Sorted by residual: bond pdb=" C30 SXU A 501 " pdb=" N19 SXU A 501 " ideal model delta sigma weight residual 1.553 1.464 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C30 SXU A 501 " pdb=" C31 SXU A 501 " ideal model delta sigma weight residual 1.645 1.560 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C18 SXU A 501 " pdb=" N19 SXU A 501 " ideal model delta sigma weight residual 1.539 1.462 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C17 SXU A 501 " pdb=" C18 SXU A 501 " ideal model delta sigma weight residual 1.594 1.536 0.058 2.00e-02 2.50e+03 8.55e+00 bond pdb=" N ARG A 231 " pdb=" CA ARG A 231 " ideal model delta sigma weight residual 1.459 1.426 0.033 1.23e-02 6.61e+03 7.11e+00 ... (remaining 4313 not shown) Histogram of bond angle deviations from ideal: 93.66 - 101.73: 17 101.73 - 109.80: 359 109.80 - 117.87: 2906 117.87 - 125.93: 2516 125.93 - 134.00: 52 Bond angle restraints: 5850 Sorted by residual: angle pdb=" C04 SXU A 501 " pdb=" C31 SXU A 501 " pdb=" C30 SXU A 501 " ideal model delta sigma weight residual 52.61 121.82 -69.21 3.00e+00 1.11e-01 5.32e+02 angle pdb=" C04 SXU A 501 " pdb=" N03 SXU A 501 " pdb=" C05 SXU A 501 " ideal model delta sigma weight residual 109.66 125.30 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" N GLY A 176 " pdb=" CA GLY A 176 " pdb=" C GLY A 176 " ideal model delta sigma weight residual 110.20 114.45 -4.25 1.32e+00 5.74e-01 1.04e+01 angle pdb=" N ARG A 223 " pdb=" CA ARG A 223 " pdb=" C ARG A 223 " ideal model delta sigma weight residual 110.23 114.84 -4.61 1.45e+00 4.76e-01 1.01e+01 angle pdb=" C31 SXU A 501 " pdb=" C04 SXU A 501 " pdb=" N03 SXU A 501 " ideal model delta sigma weight residual 109.53 118.61 -9.08 3.00e+00 1.11e-01 9.15e+00 ... (remaining 5845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.66: 2497 31.66 - 63.32: 36 63.32 - 94.98: 6 94.98 - 126.63: 0 126.63 - 158.29: 5 Dihedral angle restraints: 2544 sinusoidal: 998 harmonic: 1546 Sorted by residual: dihedral pdb=" C04 SXU A 501 " pdb=" C30 SXU A 501 " pdb=" C31 SXU A 501 " pdb=" N19 SXU A 501 " ideal model delta sinusoidal sigma weight residual -135.70 22.59 -158.29 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C06 SXU A 501 " pdb=" C07 SXU A 501 " pdb=" N08 SXU A 501 " pdb=" C16 SXU A 501 " ideal model delta sinusoidal sigma weight residual 103.65 -99.16 -157.19 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C07 SXU A 501 " pdb=" C05 SXU A 501 " pdb=" C06 SXU A 501 " pdb=" N03 SXU A 501 " ideal model delta sinusoidal sigma weight residual 224.09 73.07 151.02 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 2541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 402 0.029 - 0.057: 174 0.057 - 0.085: 80 0.085 - 0.114: 22 0.114 - 0.142: 10 Chirality restraints: 688 Sorted by residual: chirality pdb=" CB VAL A 14 " pdb=" CA VAL A 14 " pdb=" CG1 VAL A 14 " pdb=" CG2 VAL A 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CB ILE A 123 " pdb=" CA ILE A 123 " pdb=" CG1 ILE A 123 " pdb=" CG2 ILE A 123 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ASN A 288 " pdb=" N ASN A 288 " pdb=" C ASN A 288 " pdb=" CB ASN A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 685 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 239 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 240 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 82 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 83 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C22 SXU A 501 " 0.010 2.00e-02 2.50e+03 9.64e-03 1.86e+00 pdb=" C23 SXU A 501 " 0.000 2.00e-02 2.50e+03 pdb=" C24 SXU A 501 " 0.012 2.00e-02 2.50e+03 pdb=" C25 SXU A 501 " -0.006 2.00e-02 2.50e+03 pdb=" C26 SXU A 501 " -0.010 2.00e-02 2.50e+03 pdb=" C27 SXU A 501 " -0.000 2.00e-02 2.50e+03 pdb=" C28 SXU A 501 " 0.011 2.00e-02 2.50e+03 pdb=" S20 SXU A 501 " -0.016 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 955 2.78 - 3.31: 4268 3.31 - 3.84: 7319 3.84 - 4.37: 8139 4.37 - 4.90: 14585 Nonbonded interactions: 35266 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OG SER A 346 " model vdw 2.254 2.440 nonbonded pdb=" O ARG A 236 " pdb=" ND2 ASN A 241 " model vdw 2.261 2.520 nonbonded pdb=" O TYR A 131 " pdb=" OG1 THR A 134 " model vdw 2.362 2.440 nonbonded pdb=" O LEU A 181 " pdb=" OG1 THR A 185 " model vdw 2.372 2.440 nonbonded pdb=" OH TYR A 364 " pdb=" OD2 ASP A 436 " model vdw 2.394 2.440 ... (remaining 35261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.640 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.350 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 4318 Z= 0.305 Angle : 1.144 69.210 5850 Z= 0.454 Chirality : 0.040 0.142 688 Planarity : 0.004 0.049 711 Dihedral : 15.147 158.291 1552 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.22 % Allowed : 0.00 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.37), residues: 531 helix: 2.26 (0.26), residues: 398 sheet: -3.75 (0.84), residues: 20 loop : -0.55 (0.63), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 PHE 0.010 0.001 PHE B 52 TYR 0.008 0.001 TYR A 457 ARG 0.004 0.000 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.505 Fit side-chains REVERT: B 30 ARG cc_start: 0.7222 (ttt90) cc_final: 0.6850 (mmt180) REVERT: A 294 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 368 MET cc_start: 0.7431 (tpp) cc_final: 0.7038 (tpp) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 1.4957 time to fit residues: 90.9432 Evaluate side-chains 43 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN A 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4318 Z= 0.195 Angle : 0.777 32.286 5850 Z= 0.318 Chirality : 0.039 0.162 688 Planarity : 0.004 0.048 711 Dihedral : 14.918 179.020 593 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.55 % Allowed : 6.19 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.37), residues: 531 helix: 2.47 (0.26), residues: 397 sheet: -3.74 (0.84), residues: 20 loop : -0.47 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE A 423 TYR 0.004 0.001 TYR A 455 ARG 0.005 0.001 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.478 Fit side-chains REVERT: B 30 ARG cc_start: 0.7114 (ttt90) cc_final: 0.6754 (mmp-170) REVERT: A 189 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: A 231 ARG cc_start: 0.6980 (ttm-80) cc_final: 0.6064 (mmp-170) REVERT: A 294 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7347 (tm-30) REVERT: A 317 LEU cc_start: 0.8298 (mm) cc_final: 0.7769 (tp) REVERT: A 368 MET cc_start: 0.7427 (tpp) cc_final: 0.7021 (tpp) outliers start: 7 outliers final: 1 residues processed: 53 average time/residue: 1.3841 time to fit residues: 75.9303 Evaluate side-chains 49 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 320 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4318 Z= 0.259 Angle : 0.777 30.150 5850 Z= 0.322 Chirality : 0.039 0.157 688 Planarity : 0.004 0.049 711 Dihedral : 14.247 179.670 589 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.99 % Allowed : 8.41 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.37), residues: 531 helix: 2.42 (0.25), residues: 397 sheet: -3.79 (0.78), residues: 22 loop : -0.41 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.010 0.001 PHE A 261 TYR 0.005 0.001 TYR A 457 ARG 0.005 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.519 Fit side-chains REVERT: B 20 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6356 (ttp80) REVERT: B 30 ARG cc_start: 0.7028 (ttt90) cc_final: 0.6649 (mmp-170) REVERT: A 189 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: A 231 ARG cc_start: 0.6998 (ttm-80) cc_final: 0.6068 (mmp-170) REVERT: A 294 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 311 ARG cc_start: 0.6660 (mtm180) cc_final: 0.6262 (mtt180) REVERT: A 317 LEU cc_start: 0.8315 (mm) cc_final: 0.7771 (tp) REVERT: A 368 MET cc_start: 0.7530 (tpp) cc_final: 0.7054 (tpp) outliers start: 9 outliers final: 0 residues processed: 60 average time/residue: 1.3201 time to fit residues: 82.1386 Evaluate side-chains 52 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain A residue 189 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4318 Z= 0.196 Angle : 0.747 29.306 5850 Z= 0.306 Chirality : 0.038 0.154 688 Planarity : 0.004 0.046 711 Dihedral : 13.570 173.035 589 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.88 % Allowed : 11.50 % Favored : 87.61 % 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: 2.52 (0.37), residues: 531 helix: 2.52 (0.25), residues: 397 sheet: -3.67 (0.76), residues: 22 loop : -0.33 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE A 261 TYR 0.004 0.001 TYR A 457 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.673 Fit side-chains REVERT: B 30 ARG cc_start: 0.7113 (ttt90) cc_final: 0.6662 (mmp-170) REVERT: A 189 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: A 294 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 317 LEU cc_start: 0.8314 (mm) cc_final: 0.7760 (tp) outliers start: 4 outliers final: 0 residues processed: 54 average time/residue: 1.3224 time to fit residues: 74.2635 Evaluate side-chains 50 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4318 Z= 0.231 Angle : 0.754 29.022 5850 Z= 0.311 Chirality : 0.039 0.152 688 Planarity : 0.004 0.047 711 Dihedral : 13.382 172.602 589 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.77 % Allowed : 11.50 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.37), residues: 531 helix: 2.49 (0.25), residues: 397 sheet: -3.64 (0.76), residues: 22 loop : -0.41 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.009 0.001 PHE A 261 TYR 0.005 0.001 TYR A 137 ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.534 Fit side-chains REVERT: B 20 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6382 (ttp80) REVERT: B 30 ARG cc_start: 0.7102 (ttt90) cc_final: 0.6666 (mmp-170) REVERT: A 189 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: A 294 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 311 ARG cc_start: 0.6494 (mtm180) cc_final: 0.6223 (mtt180) REVERT: A 317 LEU cc_start: 0.8357 (mm) cc_final: 0.7789 (tp) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 1.2725 time to fit residues: 70.0748 Evaluate side-chains 52 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.0170 chunk 12 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.0980 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4318 Z= 0.158 Angle : 0.732 28.587 5850 Z= 0.298 Chirality : 0.038 0.147 688 Planarity : 0.004 0.046 711 Dihedral : 13.405 173.151 589 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.77 % Allowed : 12.17 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.37), residues: 531 helix: 2.60 (0.25), residues: 397 sheet: -3.58 (0.74), residues: 22 loop : -0.35 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.001 0.000 HIS A 360 PHE 0.008 0.001 PHE A 252 TYR 0.004 0.001 TYR A 131 ARG 0.007 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.518 Fit side-chains REVERT: B 20 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6278 (ttp80) REVERT: B 30 ARG cc_start: 0.7073 (ttt90) cc_final: 0.6660 (mmp-170) REVERT: A 10 LYS cc_start: 0.7433 (tptt) cc_final: 0.7147 (tptp) REVERT: A 65 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.7549 (mtp) REVERT: A 189 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: A 311 ARG cc_start: 0.6601 (mtm180) cc_final: 0.6349 (mtt180) REVERT: A 317 LEU cc_start: 0.8370 (mm) cc_final: 0.7829 (tp) outliers start: 8 outliers final: 3 residues processed: 53 average time/residue: 1.2854 time to fit residues: 70.7605 Evaluate side-chains 52 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 33 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4318 Z= 0.206 Angle : 0.743 28.552 5850 Z= 0.306 Chirality : 0.038 0.148 688 Planarity : 0.004 0.046 711 Dihedral : 13.438 172.871 589 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.33 % Allowed : 13.94 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.37), residues: 531 helix: 2.56 (0.25), residues: 397 sheet: -3.60 (0.75), residues: 22 loop : -0.37 (0.63), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.007 0.001 PHE A 261 TYR 0.005 0.001 TYR A 364 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.457 Fit side-chains REVERT: B 20 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6342 (ttp80) REVERT: B 30 ARG cc_start: 0.7073 (ttt90) cc_final: 0.6629 (mmp-170) REVERT: A 10 LYS cc_start: 0.7525 (tptt) cc_final: 0.7230 (tptp) REVERT: A 65 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7540 (mtp) REVERT: A 189 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7289 (tt0) REVERT: A 311 ARG cc_start: 0.6578 (mtm180) cc_final: 0.6213 (mtt180) REVERT: A 317 LEU cc_start: 0.8364 (mm) cc_final: 0.7810 (tp) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 1.2891 time to fit residues: 68.1983 Evaluate side-chains 53 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4318 Z= 0.248 Angle : 0.761 28.525 5850 Z= 0.316 Chirality : 0.039 0.150 688 Planarity : 0.004 0.045 711 Dihedral : 13.418 172.204 589 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.33 % Allowed : 14.38 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.37), residues: 531 helix: 2.46 (0.25), residues: 398 sheet: -3.59 (0.76), residues: 22 loop : -0.35 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.009 0.001 PHE A 261 TYR 0.008 0.001 TYR A 364 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.460 Fit side-chains REVERT: B 20 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6384 (ttp80) REVERT: B 30 ARG cc_start: 0.7055 (ttt90) cc_final: 0.6666 (mmp-170) REVERT: A 23 GLU cc_start: 0.7012 (pm20) cc_final: 0.6418 (mt-10) REVERT: A 65 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.7501 (mtp) REVERT: A 189 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: A 311 ARG cc_start: 0.6623 (mtm180) cc_final: 0.6283 (mtt180) REVERT: A 317 LEU cc_start: 0.8366 (mm) cc_final: 0.7806 (tp) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 1.2524 time to fit residues: 66.3976 Evaluate side-chains 52 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4318 Z= 0.262 Angle : 0.768 28.501 5850 Z= 0.319 Chirality : 0.040 0.149 688 Planarity : 0.004 0.046 711 Dihedral : 13.474 171.855 589 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.55 % Allowed : 14.82 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.37), residues: 531 helix: 2.40 (0.25), residues: 398 sheet: -3.61 (0.75), residues: 22 loop : -0.38 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.009 0.001 PHE A 261 TYR 0.008 0.001 TYR A 302 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.496 Fit side-chains REVERT: B 20 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6400 (ttp80) REVERT: B 30 ARG cc_start: 0.7026 (ttt90) cc_final: 0.6663 (mmp-170) REVERT: A 23 GLU cc_start: 0.7073 (pm20) cc_final: 0.6291 (tt0) REVERT: A 65 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.7507 (mtp) REVERT: A 189 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: A 311 ARG cc_start: 0.6532 (mtm180) cc_final: 0.6175 (mtt180) REVERT: A 317 LEU cc_start: 0.8370 (mm) cc_final: 0.7809 (tp) outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 1.2389 time to fit residues: 65.7029 Evaluate side-chains 50 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4318 Z= 0.225 Angle : 0.761 28.302 5850 Z= 0.314 Chirality : 0.039 0.148 688 Planarity : 0.004 0.046 711 Dihedral : 13.650 173.105 589 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.55 % Allowed : 15.04 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.37), residues: 531 helix: 2.46 (0.25), residues: 398 sheet: -3.61 (0.74), residues: 22 loop : -0.37 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 PHE 0.008 0.001 PHE A 423 TYR 0.010 0.001 TYR A 302 ARG 0.005 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.454 Fit side-chains REVERT: B 20 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.6364 (ttp80) REVERT: B 30 ARG cc_start: 0.7053 (ttt90) cc_final: 0.6669 (mmp-170) REVERT: A 23 GLU cc_start: 0.7046 (pm20) cc_final: 0.6200 (tt0) REVERT: A 65 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7469 (mtp) REVERT: A 189 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: A 311 ARG cc_start: 0.6461 (mtm180) cc_final: 0.6129 (mtt180) REVERT: A 317 LEU cc_start: 0.8372 (mm) cc_final: 0.7811 (tp) outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 1.3512 time to fit residues: 71.4006 Evaluate side-chains 51 residues out of total 460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113926 restraints weight = 4556.303| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.78 r_work: 0.3186 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4318 Z= 0.262 Angle : 0.772 28.281 5850 Z= 0.321 Chirality : 0.040 0.150 688 Planarity : 0.004 0.046 711 Dihedral : 13.772 173.143 589 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.33 % Allowed : 15.71 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.37), residues: 531 helix: 2.37 (0.25), residues: 398 sheet: -3.41 (0.79), residues: 22 loop : -0.43 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 PHE 0.009 0.001 PHE A 261 TYR 0.012 0.001 TYR A 302 ARG 0.005 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1935.96 seconds wall clock time: 35 minutes 4.72 seconds (2104.72 seconds total)