Starting phenix.real_space_refine on Tue Feb 13 10:03:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppj_13581/02_2024/7ppj_13581.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppj_13581/02_2024/7ppj_13581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppj_13581/02_2024/7ppj_13581.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppj_13581/02_2024/7ppj_13581.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppj_13581/02_2024/7ppj_13581.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ppj_13581/02_2024/7ppj_13581.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.081 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 3304 2.51 5 N 893 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 63": "OE1" <-> "OE2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 410": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5175 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5175 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 644, 5158 Unusual residues: {' ZN': 1} Classifications: {'peptide': 643, 'undetermined': 1} Link IDs: {'PTRANS': 27, 'TRANS': 615, None: 1} Not linked: pdbres="ASP A 684 " pdbres=" ZN A 901 " Chain breaks: 2 Conformer: "B" Number of residues, atoms: 644, 5158 Unusual residues: {' ZN': 1} Classifications: {'peptide': 643, 'undetermined': 1} Link IDs: {'PTRANS': 27, 'TRANS': 615, None: 1} Not linked: pdbres="ASP A 684 " pdbres=" ZN A 901 " Chain breaks: 2 bond proxies already assigned to first conformer: 5243 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1914 SG CYS A 268 27.819 26.355 48.835 1.00 67.67 S ATOM 2198 SG CYS A 303 26.980 29.739 48.695 1.00 50.58 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN A 901 " occ=0.83 Time building chain proxies: 5.64, per 1000 atoms: 1.09 Number of scatterers: 5175 At special positions: 0 Unit cell: (64.852, 91.002, 120.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 940 8.00 N 893 7.00 C 3304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 266 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 303 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 268 " 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1228 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 37.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 32 through 54 removed outlier: 3.765A pdb=" N ASN A 52 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.553A pdb=" N ARG A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 84 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.539A pdb=" N GLN A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 203 through 222 Proline residue: A 213 - end of helix Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.868A pdb=" N MET A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 424 through 430 removed outlier: 3.839A pdb=" N ASP A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 429 " --> pdb=" O TRP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 480 Processing helix chain 'A' and resid 525 through 538 removed outlier: 4.011A pdb=" N ILE A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 566 Processing helix chain 'A' and resid 582 through 599 removed outlier: 4.086A pdb=" N ARG A 590 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 604 No H-bonds generated for 'chain 'A' and resid 602 through 604' Processing helix chain 'A' and resid 612 through 621 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 651 through 654 Processing helix chain 'A' and resid 660 through 671 removed outlier: 3.743A pdb=" N LYS A 664 " --> pdb=" O ASP A 660 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 198 removed outlier: 6.946A pdb=" N VAL A 283 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR A 292 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU A 281 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N CYS A 294 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN A 279 " --> pdb=" O CYS A 294 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 296 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL A 277 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 316 Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA6, first strand: chain 'A' and resid 385 through 387 removed outlier: 6.325A pdb=" N VAL A 386 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE A 421 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS A 439 " --> pdb=" O ILE A 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 539 through 541 Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 575 removed outlier: 6.299A pdb=" N LEU A 607 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP A 649 " --> pdb=" O LEU A 607 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE A 609 " --> pdb=" O ASP A 649 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 628 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 608 " --> pdb=" O GLN A 628 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 568 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: 1.38 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1618 1.34 - 1.45: 679 1.45 - 1.57: 2940 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 5287 Sorted by residual: bond pdb=" N THR A 222 " pdb=" CA THR A 222 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 1.01e+01 bond pdb=" N VAL A 386 " pdb=" CA VAL A 386 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.28e-02 6.10e+03 9.91e+00 bond pdb=" N ILE A 451 " pdb=" CA ILE A 451 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.91e+00 bond pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta sigma weight residual 1.446 1.474 -0.028 9.50e-03 1.11e+04 8.79e+00 bond pdb=" N ILE A 5 " pdb=" CA ILE A 5 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.22e-02 6.72e+03 8.40e+00 ... (remaining 5282 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.20: 96 105.20 - 112.40: 2708 112.40 - 119.61: 1766 119.61 - 126.82: 2514 126.82 - 134.03: 65 Bond angle restraints: 7149 Sorted by residual: angle pdb=" N VAL A 7 " pdb=" CA VAL A 7 " pdb=" C VAL A 7 " ideal model delta sigma weight residual 112.83 107.38 5.45 9.90e-01 1.02e+00 3.03e+01 angle pdb=" CA GLN A 446 " pdb=" C GLN A 446 " pdb=" O GLN A 446 " ideal model delta sigma weight residual 121.56 117.28 4.28 1.09e+00 8.42e-01 1.54e+01 angle pdb=" CA VAL A 386 " pdb=" C VAL A 386 " pdb=" O VAL A 386 " ideal model delta sigma weight residual 121.72 118.20 3.52 9.60e-01 1.09e+00 1.34e+01 angle pdb=" CA HIS A 577 " pdb=" C HIS A 577 " pdb=" O HIS A 577 " ideal model delta sigma weight residual 121.55 117.82 3.73 1.06e+00 8.90e-01 1.24e+01 angle pdb=" CA THR A 9 " pdb=" C THR A 9 " pdb=" O THR A 9 " ideal model delta sigma weight residual 121.87 117.80 4.07 1.16e+00 7.43e-01 1.23e+01 ... (remaining 7144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 2859 17.04 - 34.07: 305 34.07 - 51.11: 46 51.11 - 68.14: 8 68.14 - 85.18: 7 Dihedral angle restraints: 3225 sinusoidal: 1328 harmonic: 1897 Sorted by residual: dihedral pdb=" CA PHE A 381 " pdb=" C PHE A 381 " pdb=" N SER A 382 " pdb=" CA SER A 382 " ideal model delta harmonic sigma weight residual -180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" C ASN A 447 " pdb=" N ASN A 447 " pdb=" CA ASN A 447 " pdb=" CB ASN A 447 " ideal model delta harmonic sigma weight residual -122.60 -130.75 8.15 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CA GLN A 90 " pdb=" C GLN A 90 " pdb=" N LYS A 91 " pdb=" CA LYS A 91 " ideal model delta harmonic sigma weight residual 180.00 163.72 16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 571 0.045 - 0.090: 151 0.090 - 0.134: 57 0.134 - 0.179: 13 0.179 - 0.224: 9 Chirality restraints: 801 Sorted by residual: chirality pdb=" CA ASN A 447 " pdb=" N ASN A 447 " pdb=" C ASN A 447 " pdb=" CB ASN A 447 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA VAL A 576 " pdb=" N VAL A 576 " pdb=" C VAL A 576 " pdb=" CB VAL A 576 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE A 5 " pdb=" N ILE A 5 " pdb=" C ILE A 5 " pdb=" CB ILE A 5 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 798 not shown) Planarity restraints: 913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 613 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 614 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 614 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 614 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 108 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 109 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 109 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 109 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 602 " -0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 603 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 603 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 603 " -0.022 5.00e-02 4.00e+02 ... (remaining 910 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1037 2.78 - 3.31: 5079 3.31 - 3.84: 8303 3.84 - 4.37: 9891 4.37 - 4.90: 17121 Nonbonded interactions: 41431 Sorted by model distance: nonbonded pdb=" ND2 ASN A 52 " pdb=" O TRP A 313 " model vdw 2.245 2.520 nonbonded pdb=" NZ LYS A 481 " pdb=" O GLY A 539 " model vdw 2.275 2.520 nonbonded pdb=" O LYS A 616 " pdb=" OG SER A 620 " model vdw 2.297 2.440 nonbonded pdb=" O PRO A 310 " pdb=" NE2 GLN A 322 " model vdw 2.306 2.520 nonbonded pdb=" O SER A 353 " pdb=" OG SER A 353 " model vdw 2.307 2.440 ... (remaining 41426 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.780 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.970 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 0.040 5287 Z= 0.354 Angle : 0.719 7.221 7149 Z= 0.454 Chirality : 0.054 0.224 801 Planarity : 0.004 0.042 913 Dihedral : 14.044 85.176 1997 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.75 % Favored : 92.94 % Rotamer: Outliers : 1.20 % Allowed : 3.43 % Favored : 95.37 % 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: -3.05 (0.29), residues: 642 helix: -1.57 (0.29), residues: 230 sheet: -2.24 (0.50), residues: 89 loop : -2.27 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 313 HIS 0.003 0.001 HIS A 119 PHE 0.013 0.001 PHE A 381 TYR 0.010 0.001 TYR A 608 ARG 0.002 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.7701 (tpt) cc_final: 0.7483 (tpp) outliers start: 5 outliers final: 1 residues processed: 107 average time/residue: 0.2253 time to fit residues: 29.7382 Evaluate side-chains 71 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.0570 chunk 58 optimal weight: 6.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 40 ASN A 94 HIS A 182 GLN A 221 ASN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN A 605 ASN A 670 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5287 Z= 0.222 Angle : 0.658 12.250 7149 Z= 0.329 Chirality : 0.046 0.187 801 Planarity : 0.004 0.052 913 Dihedral : 4.389 25.255 704 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.54 % Allowed : 13.04 % Favored : 85.42 % 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 (0.32), residues: 642 helix: -0.34 (0.34), residues: 237 sheet: -1.81 (0.51), residues: 85 loop : -1.55 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 661 HIS 0.006 0.001 HIS A 284 PHE 0.019 0.002 PHE A 575 TYR 0.016 0.002 TYR A 393 ARG 0.004 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 81 average time/residue: 0.1936 time to fit residues: 20.0937 Evaluate side-chains 68 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 393 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5287 Z= 0.227 Angle : 0.647 13.222 7149 Z= 0.319 Chirality : 0.047 0.267 801 Planarity : 0.004 0.050 913 Dihedral : 4.375 25.601 704 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.72 % Allowed : 13.72 % Favored : 84.56 % 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: -1.21 (0.33), residues: 642 helix: 0.11 (0.35), residues: 236 sheet: -1.51 (0.53), residues: 88 loop : -1.24 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 661 HIS 0.004 0.001 HIS A 284 PHE 0.014 0.002 PHE A 421 TYR 0.029 0.002 TYR A 183 ARG 0.009 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.609 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.1984 time to fit residues: 18.6401 Evaluate side-chains 62 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5287 Z= 0.296 Angle : 0.691 13.819 7149 Z= 0.335 Chirality : 0.049 0.385 801 Planarity : 0.004 0.048 913 Dihedral : 4.526 25.416 704 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.06 % Allowed : 14.58 % Favored : 83.36 % 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: -1.11 (0.33), residues: 642 helix: 0.15 (0.35), residues: 235 sheet: -1.18 (0.56), residues: 85 loop : -1.24 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 661 HIS 0.004 0.001 HIS A 119 PHE 0.017 0.002 PHE A 421 TYR 0.024 0.002 TYR A 183 ARG 0.005 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 526 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6708 (ptp) outliers start: 10 outliers final: 6 residues processed: 69 average time/residue: 0.1742 time to fit residues: 16.0338 Evaluate side-chains 67 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 678 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5287 Z= 0.197 Angle : 0.634 14.146 7149 Z= 0.305 Chirality : 0.046 0.250 801 Planarity : 0.004 0.049 913 Dihedral : 4.262 25.759 704 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.40 % Allowed : 14.92 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.33), residues: 642 helix: 0.41 (0.35), residues: 236 sheet: -1.02 (0.58), residues: 84 loop : -1.08 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 661 HIS 0.002 0.000 HIS A 265 PHE 0.009 0.001 PHE A 575 TYR 0.018 0.001 TYR A 183 ARG 0.005 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 446 GLN cc_start: 0.5420 (tp40) cc_final: 0.5065 (tp40) REVERT: A 447 ASN cc_start: 0.7284 (m110) cc_final: 0.6931 (m-40) REVERT: A 574 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8002 (tt) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.1673 time to fit residues: 16.7853 Evaluate side-chains 64 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 634 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5287 Z= 0.238 Angle : 0.644 13.400 7149 Z= 0.314 Chirality : 0.047 0.296 801 Planarity : 0.004 0.048 913 Dihedral : 4.195 15.828 702 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.57 % Allowed : 14.58 % Favored : 82.85 % 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: -0.75 (0.33), residues: 642 helix: 0.38 (0.35), residues: 236 sheet: -0.88 (0.59), residues: 81 loop : -1.02 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP A 328 HIS 0.004 0.001 HIS A 642 PHE 0.012 0.002 PHE A 421 TYR 0.008 0.001 TYR A 472 ARG 0.004 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.643 Fit side-chains REVERT: A 526 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.6606 (ptp) outliers start: 12 outliers final: 7 residues processed: 69 average time/residue: 0.1692 time to fit residues: 15.6077 Evaluate side-chains 65 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 634 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.0030 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5287 Z= 0.226 Angle : 0.645 13.919 7149 Z= 0.312 Chirality : 0.046 0.268 801 Planarity : 0.005 0.095 913 Dihedral : 4.163 15.258 702 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.23 % Allowed : 14.58 % Favored : 83.19 % 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: -0.64 (0.33), residues: 642 helix: 0.48 (0.35), residues: 236 sheet: -0.73 (0.59), residues: 81 loop : -0.98 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 328 HIS 0.004 0.001 HIS A 284 PHE 0.013 0.002 PHE A 136 TYR 0.008 0.001 TYR A 226 ARG 0.011 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.616 Fit side-chains REVERT: A 447 ASN cc_start: 0.7235 (m110) cc_final: 0.6970 (m-40) REVERT: A 526 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6563 (ptp) outliers start: 10 outliers final: 7 residues processed: 73 average time/residue: 0.1730 time to fit residues: 16.6608 Evaluate side-chains 66 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 585 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.0040 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5287 Z= 0.208 Angle : 0.649 13.874 7149 Z= 0.314 Chirality : 0.046 0.240 801 Planarity : 0.006 0.127 913 Dihedral : 4.204 17.689 702 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.72 % Allowed : 16.12 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.33), residues: 642 helix: 0.66 (0.35), residues: 236 sheet: -0.61 (0.59), residues: 83 loop : -0.84 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP A 328 HIS 0.003 0.001 HIS A 284 PHE 0.029 0.002 PHE A 654 TYR 0.008 0.001 TYR A 226 ARG 0.013 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.633 Fit side-chains REVERT: A 526 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6481 (ptp) outliers start: 7 outliers final: 6 residues processed: 69 average time/residue: 0.1543 time to fit residues: 14.5383 Evaluate side-chains 66 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 585 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.0270 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5287 Z= 0.259 Angle : 0.672 13.887 7149 Z= 0.327 Chirality : 0.049 0.372 801 Planarity : 0.005 0.107 913 Dihedral : 4.346 19.548 702 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.72 % Allowed : 16.30 % Favored : 81.99 % 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: -0.41 (0.33), residues: 642 helix: 0.56 (0.35), residues: 236 sheet: -0.34 (0.59), residues: 84 loop : -0.83 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP A 328 HIS 0.004 0.001 HIS A 284 PHE 0.021 0.002 PHE A 654 TYR 0.009 0.001 TYR A 472 ARG 0.018 0.001 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.605 Fit side-chains REVERT: A 526 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6573 (ptp) outliers start: 7 outliers final: 6 residues processed: 73 average time/residue: 0.1571 time to fit residues: 15.5306 Evaluate side-chains 66 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 585 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5287 Z= 0.223 Angle : 0.661 14.279 7149 Z= 0.320 Chirality : 0.046 0.227 801 Planarity : 0.005 0.074 913 Dihedral : 4.275 22.342 702 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.89 % Allowed : 16.81 % Favored : 81.30 % 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: -0.34 (0.33), residues: 642 helix: 0.54 (0.35), residues: 236 sheet: -0.20 (0.59), residues: 84 loop : -0.75 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP A 328 HIS 0.003 0.001 HIS A 284 PHE 0.019 0.002 PHE A 654 TYR 0.008 0.001 TYR A 472 ARG 0.013 0.000 ARG A 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.648 Fit side-chains REVERT: A 526 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6508 (ptp) outliers start: 8 outliers final: 7 residues processed: 71 average time/residue: 0.1556 time to fit residues: 15.0821 Evaluate side-chains 69 residues out of total 573 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 366 ASN Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 526 MET Chi-restraints excluded: chain A residue 585 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.156350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118372 restraints weight = 20929.923| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 8.08 r_work: 0.3115 rms_B_bonded: 6.78 restraints_weight: 2.0000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5287 Z= 0.251 Angle : 0.671 14.191 7149 Z= 0.325 Chirality : 0.047 0.218 801 Planarity : 0.005 0.071 913 Dihedral : 4.274 18.596 702 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.89 % Allowed : 17.50 % Favored : 80.62 % 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: -0.37 (0.33), residues: 642 helix: 0.52 (0.35), residues: 235 sheet: -0.38 (0.54), residues: 95 loop : -0.72 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP A 328 HIS 0.003 0.001 HIS A 284 PHE 0.022 0.002 PHE A 280 TYR 0.009 0.001 TYR A 472 ARG 0.013 0.000 ARG A 632 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1514.99 seconds wall clock time: 28 minutes 0.79 seconds (1680.79 seconds total)