Starting phenix.real_space_refine on Thu Nov 14 06:43:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5n_41929/11_2024/8u5n_41929.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5n_41929/11_2024/8u5n_41929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5n_41929/11_2024/8u5n_41929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5n_41929/11_2024/8u5n_41929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5n_41929/11_2024/8u5n_41929.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5n_41929/11_2024/8u5n_41929.cif" } resolution = 3.0 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= -0.000 sd= 0.017 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 3032 2.51 5 N 703 2.21 5 O 772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4535 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4522 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 21, 'TRANS': 555} Chain breaks: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.48, per 1000 atoms: 0.77 Number of scatterers: 4535 At special positions: 0 Unit cell: (72.0265, 63.1617, 95.2966, 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 772 8.00 N 703 7.00 C 3032 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 - 3.00 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: 1.26 Conformation dependent library (CDL) restraints added in 591.5 milliseconds 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 89.4% alpha, 0.0% 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 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.631A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 removed outlier: 3.687A pdb=" N LYS A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 164 through 196 removed outlier: 3.794A pdb=" N TYR A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.664A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.927A pdb=" N SER A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 336 removed outlier: 4.042A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.777A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 408 Processing helix chain 'A' and resid 409 through 436 removed outlier: 4.298A pdb=" N LEU A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 473 removed outlier: 3.581A pdb=" N GLY A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 503 Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 516 through 547 removed outlier: 3.563A pdb=" N MET A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 682 Processing helix chain 'A' and resid 687 through 712 removed outlier: 3.602A pdb=" N GLU A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1116 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: 1.31 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 858 1.33 - 1.45: 1109 1.45 - 1.57: 2632 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 4644 Sorted by residual: bond pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.433 1.357 0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C IAC A 901 " pdb=" C1 IAC A 901 " ideal model delta sigma weight residual 1.414 1.363 0.051 2.00e-02 2.50e+03 6.58e+00 bond pdb=" C PHE A 115 " pdb=" O PHE A 115 " ideal model delta sigma weight residual 1.236 1.210 0.026 1.15e-02 7.56e+03 5.28e+00 bond pdb=" C17 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.487 1.521 -0.034 2.00e-02 2.50e+03 2.96e+00 bond pdb=" CG LEU A 414 " pdb=" CD1 LEU A 414 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.31e+00 ... (remaining 4639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 6147 2.29 - 4.57: 143 4.57 - 6.86: 20 6.86 - 9.14: 1 9.14 - 11.43: 2 Bond angle restraints: 6313 Sorted by residual: angle pdb=" C PHE A 115 " pdb=" CA PHE A 115 " pdb=" CB PHE A 115 " ideal model delta sigma weight residual 110.88 103.53 7.35 1.57e+00 4.06e-01 2.19e+01 angle pdb=" CA PHE A 115 " pdb=" C PHE A 115 " pdb=" O PHE A 115 " ideal model delta sigma weight residual 120.82 116.58 4.24 1.05e+00 9.07e-01 1.63e+01 angle pdb=" C17 IAC A 901 " pdb=" C7 IAC A 901 " pdb=" C8 IAC A 901 " ideal model delta sigma weight residual 127.34 115.91 11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" O PHE A 115 " pdb=" C PHE A 115 " pdb=" N ILE A 116 " ideal model delta sigma weight residual 122.07 125.34 -3.27 1.03e+00 9.43e-01 1.01e+01 angle pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " pdb=" C17 IAC A 901 " ideal model delta sigma weight residual 126.92 136.15 -9.23 3.00e+00 1.11e-01 9.46e+00 ... (remaining 6308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 2434 15.42 - 30.84: 223 30.84 - 46.26: 32 46.26 - 61.68: 18 61.68 - 77.10: 4 Dihedral angle restraints: 2711 sinusoidal: 1036 harmonic: 1675 Sorted by residual: dihedral pdb=" CA GLY A 686 " pdb=" C GLY A 686 " pdb=" N ARG A 687 " pdb=" CA ARG A 687 " ideal model delta harmonic sigma weight residual -180.00 -153.02 -26.98 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA ASP A 508 " pdb=" C ASP A 508 " pdb=" N SER A 509 " pdb=" CA SER A 509 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LYS A 504 " pdb=" C LYS A 504 " pdb=" N HIS A 505 " pdb=" CA HIS A 505 " ideal model delta harmonic sigma weight residual -180.00 -155.88 -24.12 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 2708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 422 0.033 - 0.067: 221 0.067 - 0.100: 73 0.100 - 0.134: 29 0.134 - 0.167: 11 Chirality restraints: 756 Sorted by residual: chirality pdb=" CA VAL A 98 " pdb=" N VAL A 98 " pdb=" C VAL A 98 " pdb=" CB VAL A 98 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.98e-01 chirality pdb=" CA TYR A 451 " pdb=" N TYR A 451 " pdb=" C TYR A 451 " pdb=" CB TYR A 451 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.97e-01 chirality pdb=" CB VAL A 389 " pdb=" CA VAL A 389 " pdb=" CG1 VAL A 389 " pdb=" CG2 VAL A 389 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 753 not shown) Planarity restraints: 764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 285 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ALA A 285 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA A 285 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 286 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 447 " 0.026 2.00e-02 2.50e+03 1.70e-02 5.03e+00 pdb=" CG PHE A 447 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 447 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 447 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 447 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 447 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 447 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 689 " 0.028 2.00e-02 2.50e+03 1.50e-02 4.48e+00 pdb=" CG TYR A 689 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 689 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 689 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 689 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 689 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 689 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 689 " 0.011 2.00e-02 2.50e+03 ... (remaining 761 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1183 2.80 - 3.33: 4820 3.33 - 3.85: 7890 3.85 - 4.38: 9503 4.38 - 4.90: 15518 Nonbonded interactions: 38914 Sorted by model distance: nonbonded pdb=" OG SER A 144 " pdb=" OD1 ASP A 146 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR A 359 " pdb=" OD2 ASP A 385 " model vdw 2.351 3.040 nonbonded pdb=" O VAL A 340 " pdb=" OG1 THR A 344 " model vdw 2.438 3.040 nonbonded pdb=" N ASP A 508 " pdb=" OD1 ASP A 508 " model vdw 2.468 3.120 nonbonded pdb=" O ILE A 357 " pdb=" OG SER A 361 " model vdw 2.550 3.040 ... (remaining 38909 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 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 : 0.006 0.076 4644 Z= 0.406 Angle : 0.855 11.427 6313 Z= 0.478 Chirality : 0.048 0.167 756 Planarity : 0.007 0.048 764 Dihedral : 12.971 77.103 1631 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.80 % Allowed : 4.59 % Favored : 94.61 % 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: -0.95 (0.32), residues: 573 helix: -0.38 (0.22), residues: 454 sheet: None (None), residues: 0 loop : -1.01 (0.55), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP A 193 HIS 0.004 0.002 HIS A 658 PHE 0.033 0.004 PHE A 447 TYR 0.028 0.005 TYR A 689 ARG 0.003 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 181 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 139 ILE cc_start: 0.8523 (mt) cc_final: 0.8161 (mt) REVERT: A 178 MET cc_start: 0.6546 (ptt) cc_final: 0.6333 (tmt) outliers start: 4 outliers final: 3 residues processed: 184 average time/residue: 0.7796 time to fit residues: 152.6568 Evaluate side-chains 100 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 695 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 14 optimal weight: 0.1980 chunk 29 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 380 GLN A 409 GLN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4644 Z= 0.243 Angle : 0.788 13.780 6313 Z= 0.389 Chirality : 0.045 0.178 756 Planarity : 0.005 0.038 764 Dihedral : 6.556 53.614 615 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.59 % Allowed : 18.36 % Favored : 76.05 % 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: 0.70 (0.34), residues: 573 helix: 0.80 (0.23), residues: 465 sheet: None (None), residues: 0 loop : -0.61 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 363 HIS 0.001 0.001 HIS A 505 PHE 0.018 0.002 PHE A 681 TYR 0.037 0.003 TYR A 104 ARG 0.009 0.001 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.7374 (ptt) cc_final: 0.7080 (tpt) REVERT: A 499 LEU cc_start: 0.8278 (mt) cc_final: 0.8062 (mt) outliers start: 28 outliers final: 8 residues processed: 135 average time/residue: 0.5837 time to fit residues: 84.8715 Evaluate side-chains 100 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 481 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 26 optimal weight: 0.0060 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4644 Z= 0.219 Angle : 0.709 8.623 6313 Z= 0.348 Chirality : 0.043 0.146 756 Planarity : 0.004 0.036 764 Dihedral : 5.307 51.324 609 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 6.39 % Allowed : 21.36 % Favored : 72.26 % 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: 1.52 (0.35), residues: 573 helix: 1.29 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.09 (0.69), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 363 HIS 0.004 0.001 HIS A 412 PHE 0.026 0.002 PHE A 384 TYR 0.029 0.002 TYR A 104 ARG 0.002 0.000 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 178 MET cc_start: 0.7345 (ptt) cc_final: 0.7108 (tpt) REVERT: A 186 ILE cc_start: 0.8057 (mt) cc_final: 0.7754 (mt) REVERT: A 451 TYR cc_start: 0.7480 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: A 691 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7700 (mp0) outliers start: 32 outliers final: 8 residues processed: 132 average time/residue: 0.5422 time to fit residues: 77.4344 Evaluate side-chains 104 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 691 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.2980 chunk 45 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.7376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4644 Z= 0.225 Angle : 0.720 8.752 6313 Z= 0.356 Chirality : 0.043 0.168 756 Planarity : 0.004 0.033 764 Dihedral : 5.165 47.486 609 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.59 % Allowed : 23.35 % Favored : 72.06 % 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: 1.66 (0.36), residues: 573 helix: 1.41 (0.24), residues: 467 sheet: None (None), residues: 0 loop : -0.00 (0.69), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 363 HIS 0.006 0.002 HIS A 412 PHE 0.026 0.002 PHE A 695 TYR 0.025 0.002 TYR A 104 ARG 0.004 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 186 ILE cc_start: 0.8342 (mt) cc_final: 0.8097 (mt) REVERT: A 351 THR cc_start: 0.8590 (m) cc_final: 0.8306 (m) REVERT: A 429 MET cc_start: 0.7648 (tmm) cc_final: 0.7090 (tmm) REVERT: A 451 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.7357 (m-80) outliers start: 23 outliers final: 11 residues processed: 134 average time/residue: 0.4959 time to fit residues: 72.2969 Evaluate side-chains 113 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 669 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 443 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.8175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4644 Z= 0.243 Angle : 0.769 12.857 6313 Z= 0.377 Chirality : 0.044 0.174 756 Planarity : 0.004 0.030 764 Dihedral : 4.988 44.863 609 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.19 % Allowed : 28.34 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.36), residues: 573 helix: 1.47 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -0.28 (0.70), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 363 HIS 0.007 0.002 HIS A 412 PHE 0.014 0.002 PHE A 384 TYR 0.022 0.002 TYR A 104 ARG 0.001 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 177 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 221 PHE cc_start: 0.7292 (t80) cc_final: 0.6990 (t80) REVERT: A 429 MET cc_start: 0.7771 (tmm) cc_final: 0.7176 (tmm) REVERT: A 451 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7513 (m-80) outliers start: 21 outliers final: 9 residues processed: 120 average time/residue: 0.4937 time to fit residues: 64.8242 Evaluate side-chains 109 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 481 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.0040 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 230 ASN ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.8576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4644 Z= 0.223 Angle : 0.771 9.635 6313 Z= 0.382 Chirality : 0.046 0.199 756 Planarity : 0.004 0.030 764 Dihedral : 4.921 42.791 609 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.99 % Allowed : 28.54 % Favored : 67.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.36), residues: 573 helix: 1.37 (0.24), residues: 473 sheet: None (None), residues: 0 loop : -0.39 (0.72), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 363 HIS 0.003 0.001 HIS A 412 PHE 0.018 0.001 PHE A 695 TYR 0.028 0.002 TYR A 170 ARG 0.002 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 268 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8075 (tp) REVERT: A 349 ILE cc_start: 0.9203 (mp) cc_final: 0.8942 (mp) REVERT: A 429 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7202 (tmm) REVERT: A 692 LEU cc_start: 0.9200 (tm) cc_final: 0.8362 (pp) outliers start: 20 outliers final: 11 residues processed: 114 average time/residue: 0.4719 time to fit residues: 58.9894 Evaluate side-chains 106 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 429 MET Chi-restraints excluded: chain A residue 481 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN A 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.9043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4644 Z= 0.254 Angle : 0.800 9.560 6313 Z= 0.398 Chirality : 0.047 0.222 756 Planarity : 0.004 0.029 764 Dihedral : 4.887 40.939 609 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.59 % Allowed : 30.94 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.36), residues: 573 helix: 1.46 (0.24), residues: 467 sheet: None (None), residues: 0 loop : -0.27 (0.69), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 193 HIS 0.003 0.001 HIS A 412 PHE 0.039 0.002 PHE A 221 TYR 0.028 0.002 TYR A 170 ARG 0.002 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.514 Fit side-chains REVERT: A 268 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8043 (tp) REVERT: A 320 TYR cc_start: 0.7986 (t80) cc_final: 0.7388 (t80) REVERT: A 349 ILE cc_start: 0.9145 (mp) cc_final: 0.8906 (mp) REVERT: A 451 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7655 (m-80) outliers start: 23 outliers final: 10 residues processed: 123 average time/residue: 0.4317 time to fit residues: 58.4708 Evaluate side-chains 101 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 481 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN A 433 ASN ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.9502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4644 Z= 0.254 Angle : 0.833 9.099 6313 Z= 0.419 Chirality : 0.049 0.223 756 Planarity : 0.004 0.031 764 Dihedral : 4.868 39.287 609 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.59 % Allowed : 33.33 % Favored : 63.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.36), residues: 573 helix: 1.23 (0.24), residues: 473 sheet: None (None), residues: 0 loop : -0.35 (0.68), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 363 HIS 0.002 0.001 HIS A 412 PHE 0.040 0.002 PHE A 221 TYR 0.039 0.002 TYR A 170 ARG 0.001 0.000 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8076 (tp) REVERT: A 320 TYR cc_start: 0.8092 (t80) cc_final: 0.7492 (t80) REVERT: A 349 ILE cc_start: 0.9163 (mp) cc_final: 0.8873 (mp) outliers start: 18 outliers final: 5 residues processed: 111 average time/residue: 0.4799 time to fit residues: 58.4527 Evaluate side-chains 100 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 481 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 51 optimal weight: 0.0170 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.9850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4644 Z= 0.265 Angle : 0.876 10.987 6313 Z= 0.430 Chirality : 0.050 0.257 756 Planarity : 0.005 0.029 764 Dihedral : 4.991 37.104 609 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.79 % Allowed : 36.53 % Favored : 60.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.35), residues: 573 helix: 1.11 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -0.39 (0.66), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 363 HIS 0.004 0.001 HIS A 412 PHE 0.041 0.002 PHE A 221 TYR 0.048 0.003 TYR A 170 ARG 0.001 0.000 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 TYR cc_start: 0.8112 (t80) cc_final: 0.7503 (t80) REVERT: A 692 LEU cc_start: 0.9233 (tm) cc_final: 0.8844 (pp) outliers start: 14 outliers final: 6 residues processed: 111 average time/residue: 0.5191 time to fit residues: 62.8766 Evaluate side-chains 103 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 481 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 4 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 1.0131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4644 Z= 0.254 Angle : 0.917 13.651 6313 Z= 0.444 Chirality : 0.053 0.309 756 Planarity : 0.004 0.030 764 Dihedral : 4.928 33.684 609 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.60 % Allowed : 37.33 % Favored : 61.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.35), residues: 573 helix: 1.11 (0.24), residues: 471 sheet: None (None), residues: 0 loop : -0.56 (0.63), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 100 HIS 0.002 0.001 HIS A 412 PHE 0.043 0.002 PHE A 221 TYR 0.045 0.003 TYR A 458 ARG 0.002 0.000 ARG A 657 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 TYR cc_start: 0.8105 (t80) cc_final: 0.7665 (t80) outliers start: 8 outliers final: 7 residues processed: 114 average time/residue: 0.5053 time to fit residues: 62.8139 Evaluate side-chains 100 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 481 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 0.0570 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.0070 chunk 39 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** 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 = 0.4046 r_free = 0.4046 target = 0.111671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.099283 restraints weight = 12886.344| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 4.07 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 1.0365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 4644 Z= 0.252 Angle : 0.954 13.924 6313 Z= 0.456 Chirality : 0.053 0.304 756 Planarity : 0.005 0.039 764 Dihedral : 4.795 30.685 609 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.20 % Allowed : 37.52 % Favored : 60.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.35), residues: 573 helix: 1.00 (0.24), residues: 465 sheet: None (None), residues: 0 loop : -0.63 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 100 HIS 0.001 0.001 HIS A 505 PHE 0.042 0.002 PHE A 221 TYR 0.047 0.003 TYR A 458 ARG 0.002 0.000 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1877.36 seconds wall clock time: 34 minutes 34.79 seconds (2074.79 seconds total)