Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 05:26:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdd_33144/04_2023/7xdd_33144.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdd_33144/04_2023/7xdd_33144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdd_33144/04_2023/7xdd_33144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdd_33144/04_2023/7xdd_33144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdd_33144/04_2023/7xdd_33144.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdd_33144/04_2023/7xdd_33144.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 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 38 5.16 5 C 5754 2.51 5 N 1541 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B GLU 543": "OE1" <-> "OE2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9021 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4062 Classifications: {'peptide': 512} Link IDs: {'PTRANS': 19, 'TRANS': 492} Chain breaks: 1 Chain: "B" Number of atoms: 4959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4959 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 22, 'TRANS': 588} Chain breaks: 1 Time building chain proxies: 5.00, per 1000 atoms: 0.55 Number of scatterers: 9021 At special positions: 0 Unit cell: (94.444, 132.222, 101.19, 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 38 16.00 O 1688 8.00 N 1541 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.5 seconds 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 5 sheets defined 65.5% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 removed outlier: 3.693A pdb=" N THR A 19 " --> pdb=" O VAL A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 36 removed outlier: 4.272A pdb=" N THR A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.923A pdb=" N LEU A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 133 Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 207 through 222 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.761A pdb=" N LEU A 244 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 270 Processing helix chain 'A' and resid 276 through 326 Proline residue: A 296 - end of helix Proline residue: A 312 - end of helix Processing helix chain 'A' and resid 332 through 339 Processing helix chain 'A' and resid 342 through 369 Processing helix chain 'A' and resid 378 through 403 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 418 through 430 removed outlier: 3.777A pdb=" N GLU A 422 " --> pdb=" O PRO A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 468 Processing helix chain 'A' and resid 471 through 495 Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 507 through 520 Processing helix chain 'B' and resid 2 through 8 Processing helix chain 'B' and resid 10 through 24 Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 87 through 98 Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 188 through 193 removed outlier: 4.531A pdb=" N MET B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 removed outlier: 3.644A pdb=" N VAL B 200 " --> pdb=" O ARG B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 Processing helix chain 'B' and resid 222 through 248 removed outlier: 3.551A pdb=" N THR B 248 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.160A pdb=" N SER B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 302 through 316 Proline residue: B 310 - end of helix removed outlier: 3.766A pdb=" N ILE B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 327 Processing helix chain 'B' and resid 328 through 330 No H-bonds generated for 'chain 'B' and resid 328 through 330' Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 351 through 381 Processing helix chain 'B' and resid 381 through 394 removed outlier: 3.847A pdb=" N LYS B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 388 " --> pdb=" O PHE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.617A pdb=" N LYS B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 Processing helix chain 'B' and resid 415 through 441 Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.140A pdb=" N GLU B 449 " --> pdb=" O ASP B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 476 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 477 through 481 Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'B' and resid 491 through 507 removed outlier: 3.606A pdb=" N ILE B 495 " --> pdb=" O PRO B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 510 No H-bonds generated for 'chain 'B' and resid 508 through 510' Processing helix chain 'B' and resid 512 through 525 removed outlier: 3.613A pdb=" N ASN B 525 " --> pdb=" O VAL B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 537 Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 547 through 556 Processing helix chain 'B' and resid 559 through 562 Processing helix chain 'B' and resid 563 through 580 removed outlier: 4.147A pdb=" N GLY B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 589 removed outlier: 3.968A pdb=" N ILE B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 589 " --> pdb=" O ASP B 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 584 through 589' Processing helix chain 'B' and resid 593 through 600 Processing helix chain 'B' and resid 603 through 610 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 43 removed outlier: 6.245A pdb=" N THR A 47 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR A 115 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL A 49 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N HIS A 117 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE A 51 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 116 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 64 Processing sheet with id=AA3, first strand: chain 'A' and resid 153 through 154 removed outlier: 4.506A pdb=" N GLY A 153 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 35 removed outlier: 4.447A pdb=" N HIS B 122 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 63 through 65 535 hydrogen bonds defined for protein. 1554 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: 2.71 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2582 1.33 - 1.45: 1541 1.45 - 1.57: 5044 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 9225 Sorted by residual: bond pdb=" N VAL A 85 " pdb=" CA VAL A 85 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.11e-02 8.12e+03 1.15e+01 bond pdb=" N ILE B 379 " pdb=" CA ILE B 379 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.06e-02 8.90e+03 9.72e+00 bond pdb=" N VAL B 412 " pdb=" CA VAL B 412 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.43e+00 bond pdb=" C ARG B 490 " pdb=" N PRO B 491 " ideal model delta sigma weight residual 1.332 1.370 -0.038 1.30e-02 5.92e+03 8.63e+00 bond pdb=" N LYS B 58 " pdb=" CA LYS B 58 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.12e-02 7.97e+03 8.56e+00 ... (remaining 9220 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.10: 172 106.10 - 113.08: 4911 113.08 - 120.06: 3458 120.06 - 127.05: 3821 127.05 - 134.03: 106 Bond angle restraints: 12468 Sorted by residual: angle pdb=" C SER B 123 " pdb=" CA SER B 123 " pdb=" CB SER B 123 " ideal model delta sigma weight residual 116.54 110.79 5.75 1.15e+00 7.56e-01 2.50e+01 angle pdb=" N GLU B 416 " pdb=" CA GLU B 416 " pdb=" C GLU B 416 " ideal model delta sigma weight residual 111.71 106.98 4.73 1.15e+00 7.56e-01 1.69e+01 angle pdb=" N PRO A 81 " pdb=" CA PRO A 81 " pdb=" C PRO A 81 " ideal model delta sigma weight residual 112.47 104.47 8.00 2.06e+00 2.36e-01 1.51e+01 angle pdb=" N GLN A 230 " pdb=" CA GLN A 230 " pdb=" C GLN A 230 " ideal model delta sigma weight residual 113.16 108.58 4.58 1.24e+00 6.50e-01 1.36e+01 angle pdb=" CA ARG B 490 " pdb=" C ARG B 490 " pdb=" N PRO B 491 " ideal model delta sigma weight residual 118.85 122.26 -3.41 9.50e-01 1.11e+00 1.29e+01 ... (remaining 12463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4993 17.91 - 35.83: 426 35.83 - 53.74: 82 53.74 - 71.65: 21 71.65 - 89.57: 9 Dihedral angle restraints: 5531 sinusoidal: 2255 harmonic: 3276 Sorted by residual: dihedral pdb=" CA ARG A 339 " pdb=" C ARG A 339 " pdb=" N TYR A 340 " pdb=" CA TYR A 340 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA SER B 184 " pdb=" C SER B 184 " pdb=" N ARG B 185 " pdb=" CA ARG B 185 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLU B 392 " pdb=" C GLU B 392 " pdb=" N ASP B 393 " pdb=" CA ASP B 393 " ideal model delta harmonic sigma weight residual -180.00 -161.93 -18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 942 0.044 - 0.088: 317 0.088 - 0.132: 80 0.132 - 0.176: 9 0.176 - 0.220: 8 Chirality restraints: 1356 Sorted by residual: chirality pdb=" CB ILE B 188 " pdb=" CA ILE B 188 " pdb=" CG1 ILE B 188 " pdb=" CG2 ILE B 188 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA SER B 413 " pdb=" N SER B 413 " pdb=" C SER B 413 " pdb=" CB SER B 413 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA GLU A 80 " pdb=" N GLU A 80 " pdb=" C GLU A 80 " pdb=" CB GLU A 80 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1353 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 483 " 0.046 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO A 484 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 484 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 484 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 187 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C ASP B 187 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP B 187 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE B 188 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 130 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C ILE B 130 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE B 130 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU B 131 " 0.011 2.00e-02 2.50e+03 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1007 2.74 - 3.28: 9273 3.28 - 3.82: 15467 3.82 - 4.36: 18622 4.36 - 4.90: 31330 Nonbonded interactions: 75699 Sorted by model distance: nonbonded pdb=" O SER B 19 " pdb=" NE2 GLN B 23 " model vdw 2.204 2.520 nonbonded pdb=" OD1 ASP B 408 " pdb=" OG1 THR B 594 " model vdw 2.234 2.440 nonbonded pdb=" O SER B 608 " pdb=" NH2 ARG B 613 " model vdw 2.236 2.520 nonbonded pdb=" OE1 GLU A 513 " pdb=" NZ LYS A 517 " model vdw 2.240 2.520 nonbonded pdb=" NZ LYS B 32 " pdb=" OE2 GLU B 34 " model vdw 2.248 2.520 ... (remaining 75694 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: 2.010 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: 6.300 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 26.530 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:12.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 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 0.080 9225 Z= 0.355 Angle : 0.717 8.262 12468 Z= 0.460 Chirality : 0.048 0.220 1356 Planarity : 0.004 0.068 1602 Dihedral : 14.359 89.568 3413 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 2.03 % 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: 0.32 (0.25), residues: 1115 helix: 1.00 (0.20), residues: 663 sheet: -0.81 (0.50), residues: 93 loop : -0.87 (0.33), residues: 359 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 2 residues processed: 169 average time/residue: 1.5119 time to fit residues: 269.5485 Evaluate side-chains 101 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.9831 time to fit residues: 3.6396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 chunk 101 optimal weight: 0.8980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 GLN A 403 ASN A 428 GLN ** B 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9225 Z= 0.165 Angle : 0.549 8.991 12468 Z= 0.285 Chirality : 0.040 0.153 1356 Planarity : 0.004 0.043 1602 Dihedral : 4.197 18.773 1221 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 2.03 % 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: 1.14 (0.26), residues: 1115 helix: 1.59 (0.21), residues: 684 sheet: -0.40 (0.49), residues: 93 loop : -0.55 (0.35), residues: 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 135 average time/residue: 1.4509 time to fit residues: 208.3222 Evaluate side-chains 108 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 4 average time/residue: 0.5917 time to fit residues: 4.0955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 539 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 9225 Z= 0.175 Angle : 0.510 7.030 12468 Z= 0.264 Chirality : 0.040 0.140 1356 Planarity : 0.004 0.042 1602 Dihedral : 4.054 18.602 1221 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 2.85 % 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: 1.41 (0.26), residues: 1115 helix: 1.78 (0.21), residues: 685 sheet: -0.28 (0.49), residues: 93 loop : -0.42 (0.34), residues: 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 125 average time/residue: 1.3631 time to fit residues: 181.6499 Evaluate side-chains 109 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 96 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 4 average time/residue: 0.4161 time to fit residues: 3.5459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 0.4980 chunk 53 optimal weight: 0.0170 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 9225 Z= 0.152 Angle : 0.495 6.185 12468 Z= 0.256 Chirality : 0.039 0.128 1356 Planarity : 0.004 0.040 1602 Dihedral : 3.906 18.750 1221 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 2.95 % 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: 1.63 (0.26), residues: 1115 helix: 1.94 (0.21), residues: 685 sheet: -0.24 (0.48), residues: 94 loop : -0.25 (0.35), residues: 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 110 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 126 average time/residue: 1.2344 time to fit residues: 166.5031 Evaluate side-chains 113 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 5 average time/residue: 0.1530 time to fit residues: 2.6385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.3980 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 9225 Z= 0.362 Angle : 0.598 8.835 12468 Z= 0.311 Chirality : 0.044 0.136 1356 Planarity : 0.004 0.041 1602 Dihedral : 4.268 19.416 1221 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 3.05 % 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: 1.36 (0.26), residues: 1115 helix: 1.68 (0.20), residues: 687 sheet: -0.28 (0.48), residues: 93 loop : -0.28 (0.35), residues: 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 21 residues processed: 124 average time/residue: 1.2391 time to fit residues: 164.5436 Evaluate side-chains 118 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 8 average time/residue: 0.4264 time to fit residues: 5.5405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.0470 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 403 ASN A 428 GLN A 506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 9225 Z= 0.162 Angle : 0.525 7.798 12468 Z= 0.269 Chirality : 0.039 0.127 1356 Planarity : 0.004 0.041 1602 Dihedral : 4.024 18.270 1221 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 2.44 % 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: 1.69 (0.26), residues: 1115 helix: 1.95 (0.20), residues: 687 sheet: -0.18 (0.48), residues: 93 loop : -0.15 (0.35), residues: 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 18 residues processed: 113 average time/residue: 1.3228 time to fit residues: 160.1689 Evaluate side-chains 112 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 5 average time/residue: 0.1587 time to fit residues: 2.7325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9225 Z= 0.173 Angle : 0.526 10.015 12468 Z= 0.267 Chirality : 0.039 0.128 1356 Planarity : 0.004 0.040 1602 Dihedral : 3.921 18.158 1221 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.75 % 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: 1.82 (0.26), residues: 1115 helix: 2.04 (0.20), residues: 688 sheet: -0.17 (0.47), residues: 94 loop : -0.05 (0.36), residues: 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 115 average time/residue: 1.3156 time to fit residues: 161.7192 Evaluate side-chains 110 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.1511 time to fit residues: 2.3849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.092 9225 Z= 0.329 Angle : 0.614 11.055 12468 Z= 0.315 Chirality : 0.043 0.127 1356 Planarity : 0.004 0.039 1602 Dihedral : 4.215 18.257 1221 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 3.36 % 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: 1.57 (0.26), residues: 1115 helix: 1.83 (0.20), residues: 687 sheet: -0.21 (0.47), residues: 93 loop : -0.15 (0.36), residues: 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 100 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 21 residues processed: 117 average time/residue: 1.3925 time to fit residues: 174.0492 Evaluate side-chains 121 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 100 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 7 average time/residue: 0.1344 time to fit residues: 2.9142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN A 428 GLN ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9225 Z= 0.194 Angle : 0.579 11.521 12468 Z= 0.293 Chirality : 0.041 0.226 1356 Planarity : 0.004 0.041 1602 Dihedral : 4.053 18.176 1221 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 2.03 % 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: 1.74 (0.26), residues: 1115 helix: 1.98 (0.20), residues: 688 sheet: -0.19 (0.47), residues: 93 loop : -0.11 (0.36), residues: 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 113 average time/residue: 1.3318 time to fit residues: 160.6456 Evaluate side-chains 114 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 4 average time/residue: 0.1379 time to fit residues: 2.4276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 0.0000 chunk 94 optimal weight: 0.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9225 Z= 0.170 Angle : 0.558 12.072 12468 Z= 0.284 Chirality : 0.040 0.186 1356 Planarity : 0.004 0.041 1602 Dihedral : 3.925 18.009 1221 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 2.03 % 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: 1.87 (0.26), residues: 1115 helix: 2.07 (0.21), residues: 689 sheet: -0.22 (0.47), residues: 94 loop : -0.02 (0.36), residues: 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2230 Ramachandran restraints generated. 1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 1.2627 time to fit residues: 155.6307 Evaluate side-chains 108 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 1.084 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2653 time to fit residues: 1.8736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN B 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.094533 restraints weight = 13136.311| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.33 r_work: 0.3094 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9225 Z= 0.199 Angle : 0.571 11.809 12468 Z= 0.290 Chirality : 0.040 0.180 1356 Planarity : 0.004 0.040 1602 Dihedral : 3.947 18.096 1221 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 1.93 % 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: 1.85 (0.26), residues: 1115 helix: 2.06 (0.20), residues: 689 sheet: -0.21 (0.47), residues: 94 loop : -0.02 (0.36), residues: 332 =============================================================================== Job complete usr+sys time: 3462.09 seconds wall clock time: 62 minutes 14.00 seconds (3734.00 seconds total)