Starting phenix.real_space_refine on Mon Sep 23 16:47:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1n_44085/09_2024/9b1n_44085.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1n_44085/09_2024/9b1n_44085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1n_44085/09_2024/9b1n_44085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1n_44085/09_2024/9b1n_44085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1n_44085/09_2024/9b1n_44085.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1n_44085/09_2024/9b1n_44085.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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 30 5.16 5 C 2578 2.51 5 N 665 2.21 5 O 681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3954 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3931 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 515, 3922 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Conformer: "B" Number of residues, atoms: 515, 3922 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} bond proxies already assigned to first conformer: 4010 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'NAG': 1, 'VGL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.67, per 1000 atoms: 1.43 Number of scatterers: 3954 At special positions: 0 Unit cell: (55.165, 88.913, 102.542, 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 30 16.00 O 681 8.00 N 665 7.00 C 2578 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 56 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 868.6 milliseconds 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 2 sheets defined 82.5% alpha, 1.6% 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 3 through 11 removed outlier: 3.849A pdb=" N LEU A 7 " --> pdb=" O PHE A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 37 removed outlier: 3.540A pdb=" N SER A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) 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 51 through 56 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.715A pdb=" N ASP A 97 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.997A pdb=" N TRP A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.756A pdb=" N GLY A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.585A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 220 removed outlier: 3.613A pdb=" N ALA A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 226 through 252 removed outlier: 4.193A pdb=" N APHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 264 through 273 removed outlier: 4.136A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 305 through 311 removed outlier: 4.063A pdb=" N ALA A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS A 309 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 311 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 320 through 325 Processing helix chain 'A' and resid 326 through 329 removed outlier: 3.769A pdb=" N GLU A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.989A pdb=" N PHE A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 364 removed outlier: 4.066A pdb=" N ARG A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.848A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.520A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 453 removed outlier: 3.560A pdb=" N ILE A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.528A pdb=" N ILE A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.867A pdb=" N VAL A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.715A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Proline residue: A 501 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 267 hydrogen bonds defined for protein. 768 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: 1.16 Time building geometry restraints manager: 1.09 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: 753 1.33 - 1.45: 1006 1.45 - 1.58: 2249 1.58 - 1.70: 0 1.70 - 1.83: 47 Bond restraints: 4055 Sorted by residual: bond pdb=" C ALA A 355 " pdb=" O ALA A 355 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.90e+00 bond pdb=" C PHE A 356 " pdb=" O PHE A 356 " ideal model delta sigma weight residual 1.237 1.209 0.028 1.17e-02 7.31e+03 5.64e+00 bond pdb=" CA GLY A 357 " pdb=" C GLY A 357 " ideal model delta sigma weight residual 1.514 1.483 0.032 1.41e-02 5.03e+03 5.06e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" CA ALA A 355 " pdb=" CB ALA A 355 " ideal model delta sigma weight residual 1.528 1.497 0.031 1.56e-02 4.11e+03 4.06e+00 ... (remaining 4050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 5172 1.41 - 2.81: 277 2.81 - 4.22: 66 4.22 - 5.63: 16 5.63 - 7.03: 1 Bond angle restraints: 5532 Sorted by residual: angle pdb=" CA TYR A 272 " pdb=" CB TYR A 272 " pdb=" CG TYR A 272 " ideal model delta sigma weight residual 113.90 120.93 -7.03 1.80e+00 3.09e-01 1.53e+01 angle pdb=" N ALA A 355 " pdb=" CA ALA A 355 " pdb=" C ALA A 355 " ideal model delta sigma weight residual 111.28 115.35 -4.07 1.09e+00 8.42e-01 1.40e+01 angle pdb=" C PHE A 358 " pdb=" N THR A 359 " pdb=" CA THR A 359 " ideal model delta sigma weight residual 120.44 115.91 4.53 1.36e+00 5.41e-01 1.11e+01 angle pdb=" C VAL A 264 " pdb=" CA VAL A 264 " pdb=" CB VAL A 264 " ideal model delta sigma weight residual 114.35 111.16 3.19 1.06e+00 8.90e-01 9.07e+00 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 118.78 -4.88 1.80e+00 3.09e-01 7.34e+00 ... (remaining 5527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.09: 2265 17.09 - 34.17: 106 34.17 - 51.26: 20 51.26 - 68.35: 4 68.35 - 85.43: 3 Dihedral angle restraints: 2398 sinusoidal: 922 harmonic: 1476 Sorted by residual: dihedral pdb=" CA PRO A 457 " pdb=" C PRO A 457 " pdb=" N THR A 458 " pdb=" CA THR A 458 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLU A 38 " pdb=" C GLU A 38 " pdb=" N ASN A 39 " pdb=" CA ASN A 39 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU A 54 " pdb=" C LEU A 54 " pdb=" N ASP A 55 " pdb=" CA ASP A 55 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 407 0.033 - 0.066: 168 0.066 - 0.099: 49 0.099 - 0.132: 20 0.132 - 0.165: 8 Chirality restraints: 652 Sorted by residual: chirality pdb=" CA TYR A 272 " pdb=" N TYR A 272 " pdb=" C TYR A 272 " pdb=" CB TYR A 272 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CB ILE A 153 " pdb=" CA ILE A 153 " pdb=" CG1 ILE A 153 " pdb=" CG2 ILE A 153 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA PHE A 361 " pdb=" N PHE A 361 " pdb=" C PHE A 361 " pdb=" CB PHE A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 649 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 272 " -0.022 2.00e-02 2.50e+03 1.47e-02 4.30e+00 pdb=" CG TYR A 272 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A 272 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 272 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 272 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 272 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 272 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 272 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 264 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 265 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 479 " -0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 480 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " -0.022 5.00e-02 4.00e+02 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1811 2.94 - 3.43: 4064 3.43 - 3.92: 6454 3.92 - 4.41: 7589 4.41 - 4.90: 12114 Nonbonded interactions: 32032 Sorted by model distance: nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.454 3.040 nonbonded pdb=" N ASP A 290 " pdb=" OD1 ASP A 290 " model vdw 2.522 3.120 nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.525 3.040 nonbonded pdb=" O ASP A 366 " pdb=" OD1 ASP A 366 " model vdw 2.530 3.040 nonbonded pdb=" O LEU A 417 " pdb=" OG1 THR A 420 " model vdw 2.534 3.040 ... (remaining 32027 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.360 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 0.048 4055 Z= 0.308 Angle : 0.788 7.034 5532 Z= 0.434 Chirality : 0.044 0.165 652 Planarity : 0.006 0.059 689 Dihedral : 11.087 85.433 1440 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -0.18 (0.35), residues: 515 helix: -0.24 (0.24), residues: 374 sheet: -0.97 (1.44), residues: 10 loop : 0.96 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 50 HIS 0.006 0.001 HIS A 424 PHE 0.021 0.003 PHE A 344 TYR 0.035 0.003 TYR A 272 ARG 0.004 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.394 Fit side-chains REVERT: A 89 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7257 (ttm110) REVERT: A 94 GLN cc_start: 0.8386 (pt0) cc_final: 0.8022 (pp30) REVERT: A 165 ASP cc_start: 0.7938 (m-30) cc_final: 0.7639 (m-30) REVERT: A 183 MET cc_start: 0.8551 (mmt) cc_final: 0.8278 (mmt) REVERT: A 281 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.7557 (ttm-80) REVERT: A 379 MET cc_start: 0.8414 (ttp) cc_final: 0.8208 (ttt) REVERT: A 497 TYR cc_start: 0.8436 (m-80) cc_final: 0.8153 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2024 time to fit residues: 16.3299 Evaluate side-chains 51 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 46 optimal weight: 0.7980 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 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4055 Z= 0.195 Angle : 0.604 7.233 5532 Z= 0.304 Chirality : 0.040 0.135 652 Planarity : 0.005 0.043 689 Dihedral : 4.221 17.151 572 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.24 % Allowed : 4.56 % Favored : 95.20 % 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: 1.37 (0.37), residues: 515 helix: 0.86 (0.26), residues: 372 sheet: None (None), residues: 0 loop : 1.47 (0.57), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 50 HIS 0.004 0.001 HIS A 139 PHE 0.017 0.002 PHE A 344 TYR 0.022 0.002 TYR A 272 ARG 0.006 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.328 Fit side-chains REVERT: A 165 ASP cc_start: 0.7919 (m-30) cc_final: 0.7665 (m-30) REVERT: A 281 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.7513 (ttm-80) REVERT: A 497 TYR cc_start: 0.8546 (m-80) cc_final: 0.8129 (m-80) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.1386 time to fit residues: 9.2807 Evaluate side-chains 45 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4055 Z= 0.195 Angle : 0.571 6.371 5532 Z= 0.282 Chirality : 0.039 0.126 652 Planarity : 0.005 0.046 689 Dihedral : 3.839 13.825 572 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.24 % Allowed : 6.24 % Favored : 93.53 % 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: 1.62 (0.37), residues: 515 helix: 1.07 (0.26), residues: 373 sheet: None (None), residues: 0 loop : 1.49 (0.57), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 50 HIS 0.002 0.001 HIS A 242 PHE 0.018 0.002 PHE A 344 TYR 0.021 0.002 TYR A 272 ARG 0.006 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.413 Fit side-chains REVERT: A 120 ASP cc_start: 0.8150 (t70) cc_final: 0.7777 (t0) REVERT: A 165 ASP cc_start: 0.7878 (m-30) cc_final: 0.7572 (m-30) REVERT: A 281 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.7545 (ttm-80) REVERT: A 294 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7306 (tp40) REVERT: A 497 TYR cc_start: 0.8594 (m-80) cc_final: 0.8074 (m-80) outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.1432 time to fit residues: 8.5224 Evaluate side-chains 45 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 22 optimal weight: 0.0370 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4055 Z= 0.182 Angle : 0.554 7.037 5532 Z= 0.270 Chirality : 0.039 0.134 652 Planarity : 0.005 0.044 689 Dihedral : 3.635 13.088 572 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.72 % Allowed : 6.47 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.37), residues: 515 helix: 1.50 (0.27), residues: 364 sheet: -2.12 (1.54), residues: 10 loop : 1.51 (0.58), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 50 HIS 0.002 0.001 HIS A 242 PHE 0.017 0.002 PHE A 344 TYR 0.019 0.002 TYR A 272 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.442 Fit side-chains REVERT: A 120 ASP cc_start: 0.8107 (t70) cc_final: 0.7689 (t0) REVERT: A 126 SER cc_start: 0.8967 (t) cc_final: 0.8764 (t) REVERT: A 165 ASP cc_start: 0.7811 (m-30) cc_final: 0.7530 (m-30) REVERT: A 281 ARG cc_start: 0.7923 (mtp-110) cc_final: 0.7535 (ttm-80) REVERT: A 294 GLN cc_start: 0.7581 (mm-40) cc_final: 0.7325 (tp40) REVERT: A 497 TYR cc_start: 0.8636 (m-80) cc_final: 0.8183 (m-80) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.1394 time to fit residues: 9.0967 Evaluate side-chains 47 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 447 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.0570 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4055 Z= 0.192 Angle : 0.561 7.286 5532 Z= 0.272 Chirality : 0.039 0.133 652 Planarity : 0.004 0.044 689 Dihedral : 3.547 13.061 572 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.48 % Allowed : 8.39 % Favored : 91.13 % 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: 2.11 (0.37), residues: 515 helix: 1.58 (0.27), residues: 364 sheet: -2.13 (1.49), residues: 10 loop : 1.52 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 93 HIS 0.002 0.001 HIS A 242 PHE 0.016 0.002 PHE A 344 TYR 0.018 0.002 TYR A 272 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8090 (t70) cc_final: 0.7687 (t0) REVERT: A 126 SER cc_start: 0.8948 (t) cc_final: 0.8744 (t) REVERT: A 165 ASP cc_start: 0.7800 (m-30) cc_final: 0.7516 (m-30) REVERT: A 281 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7550 (ttm-80) REVERT: A 294 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7359 (tp40) outliers start: 2 outliers final: 1 residues processed: 48 average time/residue: 0.1377 time to fit residues: 8.8053 Evaluate side-chains 46 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.0980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4055 Z= 0.165 Angle : 0.555 8.847 5532 Z= 0.265 Chirality : 0.038 0.136 652 Planarity : 0.004 0.042 689 Dihedral : 3.455 12.626 572 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.24 % Allowed : 9.59 % Favored : 90.17 % 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: 2.22 (0.37), residues: 515 helix: 1.64 (0.27), residues: 367 sheet: -2.10 (1.58), residues: 10 loop : 1.64 (0.57), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.015 0.001 PHE A 344 TYR 0.017 0.002 TYR A 272 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8055 (t70) cc_final: 0.7704 (t0) REVERT: A 126 SER cc_start: 0.8941 (t) cc_final: 0.8737 (t) REVERT: A 165 ASP cc_start: 0.7779 (m-30) cc_final: 0.7504 (m-30) REVERT: A 219 MET cc_start: 0.5874 (mmp) cc_final: 0.4923 (mtp) REVERT: A 281 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7556 (ttm-80) REVERT: A 294 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7350 (tp40) REVERT: A 497 TYR cc_start: 0.8594 (m-80) cc_final: 0.8340 (m-80) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.1412 time to fit residues: 8.9726 Evaluate side-chains 45 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.0030 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 31 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4055 Z= 0.168 Angle : 0.552 7.639 5532 Z= 0.262 Chirality : 0.038 0.134 652 Planarity : 0.004 0.040 689 Dihedral : 3.395 11.943 572 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.24 % Allowed : 9.59 % Favored : 90.17 % 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: 2.32 (0.38), residues: 515 helix: 1.68 (0.27), residues: 368 sheet: -2.26 (1.52), residues: 10 loop : 1.79 (0.58), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.002 0.001 HIS A 242 PHE 0.014 0.001 PHE A 344 TYR 0.017 0.001 TYR A 272 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8062 (t70) cc_final: 0.7713 (t0) REVERT: A 126 SER cc_start: 0.8935 (t) cc_final: 0.8729 (t) REVERT: A 165 ASP cc_start: 0.7762 (m-30) cc_final: 0.7489 (m-30) REVERT: A 219 MET cc_start: 0.5935 (mmp) cc_final: 0.4979 (mtp) REVERT: A 281 ARG cc_start: 0.7949 (mtp-110) cc_final: 0.7568 (ttm-80) REVERT: A 294 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7278 (tp40) REVERT: A 497 TYR cc_start: 0.8612 (m-80) cc_final: 0.8385 (m-80) outliers start: 1 outliers final: 1 residues processed: 45 average time/residue: 0.1082 time to fit residues: 6.4902 Evaluate side-chains 45 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4055 Z= 0.233 Angle : 0.585 8.025 5532 Z= 0.281 Chirality : 0.039 0.129 652 Planarity : 0.004 0.042 689 Dihedral : 3.491 11.945 572 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.24 % Allowed : 9.83 % Favored : 89.93 % 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: 2.13 (0.38), residues: 515 helix: 1.51 (0.27), residues: 369 sheet: -2.42 (1.51), residues: 10 loop : 1.82 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 50 HIS 0.002 0.001 HIS A 242 PHE 0.016 0.002 PHE A 344 TYR 0.017 0.002 TYR A 272 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8064 (t70) cc_final: 0.7706 (t0) REVERT: A 126 SER cc_start: 0.8951 (t) cc_final: 0.8746 (t) REVERT: A 165 ASP cc_start: 0.7825 (m-30) cc_final: 0.7546 (m-30) REVERT: A 219 MET cc_start: 0.5971 (mmp) cc_final: 0.4998 (mtp) REVERT: A 281 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7625 (ttm-80) REVERT: A 294 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7390 (tp40) REVERT: A 497 TYR cc_start: 0.8664 (m-80) cc_final: 0.8405 (m-80) outliers start: 1 outliers final: 1 residues processed: 50 average time/residue: 0.1537 time to fit residues: 9.9378 Evaluate side-chains 50 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 0.0870 chunk 50 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4055 Z= 0.163 Angle : 0.548 8.362 5532 Z= 0.261 Chirality : 0.038 0.132 652 Planarity : 0.004 0.040 689 Dihedral : 3.386 12.110 572 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.24 % Allowed : 10.07 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.38), residues: 515 helix: 1.66 (0.27), residues: 368 sheet: -2.60 (1.39), residues: 10 loop : 1.84 (0.58), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.014 0.001 PHE A 344 TYR 0.016 0.001 TYR A 272 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8045 (t70) cc_final: 0.7700 (t0) REVERT: A 126 SER cc_start: 0.8944 (t) cc_final: 0.8727 (t) REVERT: A 165 ASP cc_start: 0.7768 (m-30) cc_final: 0.7492 (m-30) REVERT: A 219 MET cc_start: 0.5878 (mmp) cc_final: 0.4922 (mtp) REVERT: A 281 ARG cc_start: 0.7974 (mtp-110) cc_final: 0.7594 (ttm-80) REVERT: A 294 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7285 (tp40) REVERT: A 497 TYR cc_start: 0.8620 (m-80) cc_final: 0.8388 (m-80) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1474 time to fit residues: 8.3882 Evaluate side-chains 44 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.0770 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4055 Z= 0.192 Angle : 0.570 8.801 5532 Z= 0.273 Chirality : 0.039 0.131 652 Planarity : 0.004 0.041 689 Dihedral : 3.390 11.761 572 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.24 % Allowed : 10.07 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.38), residues: 515 helix: 1.62 (0.27), residues: 369 sheet: -2.57 (1.45), residues: 10 loop : 1.80 (0.58), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 50 HIS 0.002 0.001 HIS A 242 PHE 0.015 0.001 PHE A 344 TYR 0.017 0.002 TYR A 272 ARG 0.004 0.000 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1030 Ramachandran restraints generated. 515 Oldfield, 0 Emsley, 515 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8073 (t70) cc_final: 0.7728 (t0) REVERT: A 126 SER cc_start: 0.8940 (t) cc_final: 0.8718 (t) REVERT: A 165 ASP cc_start: 0.7771 (m-30) cc_final: 0.7497 (m-30) REVERT: A 219 MET cc_start: 0.5876 (mmp) cc_final: 0.4917 (mtp) REVERT: A 281 ARG cc_start: 0.8012 (mtp-110) cc_final: 0.7625 (ttm-80) REVERT: A 294 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7294 (tp40) REVERT: A 497 TYR cc_start: 0.8638 (m-80) cc_final: 0.8393 (m-80) outliers start: 1 outliers final: 1 residues processed: 48 average time/residue: 0.1366 time to fit residues: 8.7352 Evaluate side-chains 49 residues out of total 415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.178886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147497 restraints weight = 15287.803| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 5.34 r_work: 0.3135 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3304 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3304 r_free = 0.3304 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3304 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4055 Z= 0.182 Angle : 0.565 8.762 5532 Z= 0.271 Chirality : 0.038 0.131 652 Planarity : 0.004 0.041 689 Dihedral : 3.371 11.737 572 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.24 % Allowed : 10.07 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.38), residues: 515 helix: 1.65 (0.27), residues: 368 sheet: -2.60 (1.46), residues: 10 loop : 1.81 (0.57), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 242 PHE 0.014 0.001 PHE A 344 TYR 0.016 0.001 TYR A 272 ARG 0.004 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1354.63 seconds wall clock time: 27 minutes 38.17 seconds (1658.17 seconds total)