Starting phenix.real_space_refine on Tue Sep 24 01:30:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/09_2024/8b7q_15899.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/09_2024/8b7q_15899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/09_2024/8b7q_15899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/09_2024/8b7q_15899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/09_2024/8b7q_15899.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b7q_15899/09_2024/8b7q_15899.cif" } resolution = 4.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3495 atoms to isotropic. 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 18 5.16 5 C 2236 2.51 5 N 594 2.21 5 O 663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3511 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1064 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 1 Chain: "B" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1637 Classifications: {'peptide': 206} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 190} Chain: "F" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.77, per 1000 atoms: 1.07 Number of scatterers: 3511 At special positions: 0 Unit cell: (79.584, 98.651, 88.703, 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 18 16.00 O 663 8.00 N 594 7.00 C 2236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 434 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 496 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 410 " distance=2.03 Simple disulfide: pdb=" SG CYS F 411 " - pdb=" SG CYS F 416 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG F 901 " - " ASN F 345 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 459.4 milliseconds 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 25.9% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 23 through 45 Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.870A pdb=" N GLN A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SER A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 50' Processing helix chain 'A' and resid 71 through 89 removed outlier: 3.647A pdb=" N SER A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 113 Processing helix chain 'A' and resid 130 through 138 Processing helix chain 'A' and resid 138 through 162 removed outlier: 4.117A pdb=" N ASP A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.963A pdb=" N VAL B 533 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing sheet with id=AA1, first strand: chain 'B' and resid 432 through 436 removed outlier: 3.536A pdb=" N TRP B 447 " --> pdb=" O TYR B 494 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.491A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 459 " --> pdb=" O ASN B 514 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 482 through 484 removed outlier: 4.491A pdb=" N LEU B 462 " --> pdb=" O LYS B 484 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 459 " --> pdb=" O ASN B 514 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 539 through 546 removed outlier: 5.035A pdb=" N ASN B 540 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU B 557 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 582 through 586 Processing sheet with id=AA6, first strand: chain 'F' and resid 331 through 334 Processing sheet with id=AA7, first strand: chain 'F' and resid 331 through 334 removed outlier: 3.552A pdb=" N ALA F 346 " --> pdb=" O PHE F 391 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 337 through 340 removed outlier: 7.582A pdb=" N HIS F 417 " --> pdb=" O ASN F 412 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ASN F 412 " --> pdb=" O HIS F 417 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG F 419 " --> pdb=" O CYS F 410 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N CYS F 410 " --> pdb=" O ARG F 419 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 474 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: 0.93 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1124 1.34 - 1.46: 812 1.46 - 1.58: 1630 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3588 Sorted by residual: bond pdb=" C1 NAG F 901 " pdb=" O5 NAG F 901 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C5 NAG F 901 " pdb=" O5 NAG F 901 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" C3 NAG F 901 " pdb=" O3 NAG F 901 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.76e-01 bond pdb=" C TRP B 447 " pdb=" N SER B 448 " ideal model delta sigma weight residual 1.332 1.347 -0.015 1.92e-02 2.71e+03 6.28e-01 bond pdb=" N SER A 114 " pdb=" CA SER A 114 " ideal model delta sigma weight residual 1.463 1.455 0.008 1.08e-02 8.57e+03 5.33e-01 ... (remaining 3583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 4692 1.40 - 2.81: 165 2.81 - 4.21: 26 4.21 - 5.62: 1 5.62 - 7.02: 1 Bond angle restraints: 4885 Sorted by residual: angle pdb=" C ILE A 63 " pdb=" N PRO A 64 " pdb=" CA PRO A 64 " ideal model delta sigma weight residual 119.84 122.92 -3.08 1.25e+00 6.40e-01 6.05e+00 angle pdb=" C PHE A 113 " pdb=" N SER A 114 " pdb=" CA SER A 114 " ideal model delta sigma weight residual 120.89 124.35 -3.46 1.50e+00 4.44e-01 5.32e+00 angle pdb=" N SER A 46 " pdb=" CA SER A 46 " pdb=" C SER A 46 " ideal model delta sigma weight residual 111.37 115.17 -3.80 1.65e+00 3.67e-01 5.30e+00 angle pdb=" C ILE A 45 " pdb=" N SER A 46 " pdb=" CA SER A 46 " ideal model delta sigma weight residual 120.82 124.00 -3.18 1.50e+00 4.44e-01 4.50e+00 angle pdb=" N LEU B 503 " pdb=" CA LEU B 503 " pdb=" C LEU B 503 " ideal model delta sigma weight residual 111.33 113.75 -2.42 1.21e+00 6.83e-01 4.01e+00 ... (remaining 4880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 2086 15.92 - 31.83: 94 31.83 - 47.75: 22 47.75 - 63.66: 4 63.66 - 79.58: 2 Dihedral angle restraints: 2208 sinusoidal: 903 harmonic: 1305 Sorted by residual: dihedral pdb=" CB CYS F 350 " pdb=" SG CYS F 350 " pdb=" SG CYS F 410 " pdb=" CB CYS F 410 " ideal model delta sinusoidal sigma weight residual 93.00 63.39 29.61 1 1.00e+01 1.00e-02 1.25e+01 dihedral pdb=" N LEU A 161 " pdb=" CA LEU A 161 " pdb=" CB LEU A 161 " pdb=" CG LEU A 161 " ideal model delta sinusoidal sigma weight residual -180.00 -121.82 -58.18 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N PHE F 334 " pdb=" CA PHE F 334 " pdb=" CB PHE F 334 " pdb=" CG PHE F 334 " ideal model delta sinusoidal sigma weight residual -60.00 -111.09 51.09 3 1.50e+01 4.44e-03 8.98e+00 ... (remaining 2205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 349 0.031 - 0.062: 154 0.062 - 0.092: 33 0.092 - 0.123: 31 0.123 - 0.154: 5 Chirality restraints: 572 Sorted by residual: chirality pdb=" CA ILE F 351 " pdb=" N ILE F 351 " pdb=" C ILE F 351 " pdb=" CB ILE F 351 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA PRO A 64 " pdb=" N PRO A 64 " pdb=" C PRO A 64 " pdb=" CB PRO A 64 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.73e-01 chirality pdb=" CA ILE F 374 " pdb=" N ILE F 374 " pdb=" C ILE F 374 " pdb=" CB ILE F 374 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 569 not shown) Planarity restraints: 616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 155 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C GLN A 155 " -0.028 2.00e-02 2.50e+03 pdb=" O GLN A 155 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP A 156 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 448 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 449 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 449 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 449 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 148 " 0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C SER A 148 " -0.022 2.00e-02 2.50e+03 pdb=" O SER A 148 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG A 149 " 0.007 2.00e-02 2.50e+03 ... (remaining 613 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 532 2.77 - 3.30: 3250 3.30 - 3.83: 5553 3.83 - 4.37: 6419 4.37 - 4.90: 11088 Nonbonded interactions: 26842 Sorted by model distance: nonbonded pdb=" OG SER A 141 " pdb=" OH TYR F 409 " model vdw 2.234 3.040 nonbonded pdb=" O PRO A 64 " pdb=" OH TYR A 82 " model vdw 2.242 3.040 nonbonded pdb=" OD2 ASP A 30 " pdb=" OH TYR B 470 " model vdw 2.256 3.040 nonbonded pdb=" NH2 ARG B 571 " pdb=" OE1 GLN B 608 " model vdw 2.362 3.120 nonbonded pdb=" NH2 ARG F 400 " pdb=" O TYR F 405 " model vdw 2.378 3.120 ... (remaining 26837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 6.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 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 : 0.003 0.026 3588 Z= 0.173 Angle : 0.599 7.021 4885 Z= 0.335 Chirality : 0.043 0.154 572 Planarity : 0.004 0.035 615 Dihedral : 9.873 79.577 1340 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.46 % Allowed : 3.93 % Favored : 95.61 % Rotamer: Outliers : 2.94 % Allowed : 6.13 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: 0.29 (0.38), residues: 433 helix: 0.92 (0.47), residues: 97 sheet: 0.83 (0.39), residues: 134 loop : -0.57 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 367 HIS 0.003 0.001 HIS B 465 PHE 0.010 0.001 PHE B 493 TYR 0.009 0.001 TYR F 424 ARG 0.002 0.000 ARG B 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 45 ILE cc_start: 0.7042 (mt) cc_final: 0.6621 (mm) REVERT: A 63 ILE cc_start: 0.8987 (mt) cc_final: 0.8664 (tt) REVERT: A 93 ASN cc_start: 0.7569 (m-40) cc_final: 0.7287 (m-40) REVERT: B 436 THR cc_start: 0.9047 (m) cc_final: 0.8331 (m) REVERT: B 540 ASN cc_start: 0.8477 (t0) cc_final: 0.8226 (t0) REVERT: B 565 ASN cc_start: 0.8276 (m-40) cc_final: 0.7795 (p0) REVERT: B 572 TYR cc_start: 0.8019 (p90) cc_final: 0.7631 (p90) REVERT: B 585 GLU cc_start: 0.8506 (mp0) cc_final: 0.8236 (pm20) REVERT: B 609 VAL cc_start: 0.9427 (t) cc_final: 0.9200 (m) REVERT: B 612 ARG cc_start: 0.8665 (ttt180) cc_final: 0.7832 (ttt-90) REVERT: F 365 VAL cc_start: 0.8987 (m) cc_final: 0.8090 (p) REVERT: F 388 LYS cc_start: 0.8796 (tttt) cc_final: 0.8555 (tttp) REVERT: F 393 ASN cc_start: 0.7524 (t0) cc_final: 0.7077 (t0) outliers start: 12 outliers final: 2 residues processed: 155 average time/residue: 0.1639 time to fit residues: 30.4442 Evaluate side-chains 97 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3588 Z= 0.217 Angle : 0.631 10.846 4885 Z= 0.322 Chirality : 0.046 0.266 572 Planarity : 0.004 0.042 615 Dihedral : 4.335 16.588 496 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.49 % Allowed : 1.72 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 (0.40), residues: 433 helix: 2.30 (0.50), residues: 103 sheet: 0.55 (0.38), residues: 135 loop : 0.16 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 620 HIS 0.003 0.001 HIS F 418 PHE 0.012 0.002 PHE A 113 TYR 0.020 0.002 TYR A 82 ARG 0.004 0.000 ARG F 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8167 (ttpt) REVERT: A 93 ASN cc_start: 0.7424 (m-40) cc_final: 0.7222 (m-40) REVERT: B 572 TYR cc_start: 0.8182 (p90) cc_final: 0.7817 (p90) REVERT: B 609 VAL cc_start: 0.9509 (t) cc_final: 0.9307 (m) REVERT: B 612 ARG cc_start: 0.8831 (ttt180) cc_final: 0.8281 (ttt-90) REVERT: F 381 ILE cc_start: 0.8663 (pt) cc_final: 0.8422 (mm) REVERT: F 393 ASN cc_start: 0.7706 (t0) cc_final: 0.7076 (t0) outliers start: 2 outliers final: 0 residues processed: 112 average time/residue: 0.1434 time to fit residues: 19.8666 Evaluate side-chains 89 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 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 103 ASN B 453 GLN B 461 GLN B 499 GLN F 354 ASN F 369 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3588 Z= 0.232 Angle : 0.625 14.193 4885 Z= 0.321 Chirality : 0.046 0.229 572 Planarity : 0.004 0.031 615 Dihedral : 4.478 26.141 496 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.25 % Allowed : 2.70 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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 (0.41), residues: 433 helix: 2.65 (0.50), residues: 102 sheet: 0.67 (0.42), residues: 123 loop : 0.24 (0.46), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 447 HIS 0.003 0.001 HIS B 465 PHE 0.011 0.001 PHE F 348 TYR 0.017 0.002 TYR F 352 ARG 0.002 0.000 ARG F 368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.321 Fit side-chains REVERT: A 56 ARG cc_start: 0.8604 (ptm-80) cc_final: 0.8399 (ttp80) REVERT: A 74 LYS cc_start: 0.8642 (ttpt) cc_final: 0.8384 (ttpt) REVERT: B 429 ASN cc_start: 0.8837 (t0) cc_final: 0.8528 (t0) REVERT: B 609 VAL cc_start: 0.9477 (t) cc_final: 0.9239 (m) REVERT: B 612 ARG cc_start: 0.8829 (ttt180) cc_final: 0.8377 (ttt-90) REVERT: F 381 ILE cc_start: 0.8652 (pt) cc_final: 0.8308 (mm) REVERT: F 393 ASN cc_start: 0.7663 (t0) cc_final: 0.7145 (t0) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1429 time to fit residues: 18.3406 Evaluate side-chains 85 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN F 369 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3588 Z= 0.193 Angle : 0.588 11.765 4885 Z= 0.299 Chirality : 0.045 0.193 572 Planarity : 0.004 0.031 615 Dihedral : 4.341 24.807 496 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.25 % Allowed : 1.96 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % 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: 1.43 (0.41), residues: 433 helix: 2.78 (0.50), residues: 102 sheet: 0.71 (0.42), residues: 130 loop : 0.23 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 447 HIS 0.003 0.001 HIS B 465 PHE 0.009 0.001 PHE F 348 TYR 0.019 0.002 TYR B 572 ARG 0.002 0.000 ARG F 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 0.427 Fit side-chains REVERT: A 69 ILE cc_start: 0.7193 (tp) cc_final: 0.6990 (tp) REVERT: A 74 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8332 (ttpt) REVERT: B 429 ASN cc_start: 0.8827 (t0) cc_final: 0.8506 (t0) REVERT: B 572 TYR cc_start: 0.8098 (p90) cc_final: 0.7755 (p90) REVERT: B 609 VAL cc_start: 0.9486 (t) cc_final: 0.9238 (m) REVERT: B 612 ARG cc_start: 0.8823 (ttt180) cc_final: 0.8380 (ttt-90) REVERT: F 381 ILE cc_start: 0.8633 (pt) cc_final: 0.8210 (mm) REVERT: F 393 ASN cc_start: 0.7660 (t0) cc_final: 0.7055 (t0) outliers start: 1 outliers final: 0 residues processed: 102 average time/residue: 0.1449 time to fit residues: 18.3728 Evaluate side-chains 82 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN B 461 GLN F 369 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3588 Z= 0.221 Angle : 0.608 11.666 4885 Z= 0.310 Chirality : 0.045 0.193 572 Planarity : 0.004 0.027 615 Dihedral : 4.583 32.411 496 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 1.45 (0.41), residues: 433 helix: 3.26 (0.51), residues: 96 sheet: 0.74 (0.42), residues: 128 loop : 0.06 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 447 HIS 0.003 0.001 HIS B 465 PHE 0.009 0.001 PHE F 334 TYR 0.014 0.001 TYR B 572 ARG 0.003 0.000 ARG F 398 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.463 Fit side-chains REVERT: A 56 ARG cc_start: 0.8570 (ptm-80) cc_final: 0.8231 (ttp-110) REVERT: A 69 ILE cc_start: 0.7131 (tp) cc_final: 0.6911 (tp) REVERT: A 74 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8396 (ttpt) REVERT: B 429 ASN cc_start: 0.8788 (t0) cc_final: 0.8492 (t0) REVERT: B 453 GLN cc_start: 0.8805 (pt0) cc_final: 0.8261 (pm20) REVERT: B 542 LYS cc_start: 0.8633 (mmmm) cc_final: 0.8311 (mmtm) REVERT: B 612 ARG cc_start: 0.8843 (ttt180) cc_final: 0.8343 (ttt-90) REVERT: F 393 ASN cc_start: 0.7693 (t0) cc_final: 0.6902 (t0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.1404 time to fit residues: 16.7732 Evaluate side-chains 80 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 23 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3588 Z= 0.256 Angle : 0.617 10.660 4885 Z= 0.317 Chirality : 0.046 0.195 572 Planarity : 0.004 0.031 615 Dihedral : 4.685 33.323 496 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.41), residues: 433 helix: 2.63 (0.51), residues: 102 sheet: 0.77 (0.42), residues: 128 loop : -0.08 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 447 HIS 0.004 0.001 HIS B 465 PHE 0.013 0.001 PHE F 334 TYR 0.020 0.002 TYR A 82 ARG 0.006 0.000 ARG F 398 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.422 Fit side-chains REVERT: A 69 ILE cc_start: 0.7168 (tp) cc_final: 0.6857 (tp) REVERT: A 74 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8373 (ttpt) REVERT: B 429 ASN cc_start: 0.8754 (t0) cc_final: 0.8472 (t0) REVERT: B 453 GLN cc_start: 0.8832 (pt0) cc_final: 0.8133 (pm20) REVERT: B 542 LYS cc_start: 0.8647 (mmmm) cc_final: 0.8309 (mmtm) REVERT: B 572 TYR cc_start: 0.8079 (p90) cc_final: 0.7641 (p90) REVERT: B 612 ARG cc_start: 0.8888 (ttt180) cc_final: 0.8424 (ttt-90) REVERT: F 393 ASN cc_start: 0.7673 (t0) cc_final: 0.6815 (t0) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1492 time to fit residues: 18.3135 Evaluate side-chains 79 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN B 453 GLN B 461 GLN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3588 Z= 0.209 Angle : 0.601 9.731 4885 Z= 0.307 Chirality : 0.045 0.174 572 Planarity : 0.003 0.026 615 Dihedral : 4.538 30.466 496 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 1.20 (0.41), residues: 433 helix: 2.37 (0.51), residues: 108 sheet: 0.87 (0.43), residues: 128 loop : -0.10 (0.46), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 447 HIS 0.003 0.001 HIS B 465 PHE 0.009 0.001 PHE F 334 TYR 0.010 0.001 TYR F 424 ARG 0.001 0.000 ARG B 613 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.367 Fit side-chains REVERT: A 69 ILE cc_start: 0.7215 (tp) cc_final: 0.6820 (tp) REVERT: A 74 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8318 (ttpt) REVERT: B 429 ASN cc_start: 0.8749 (t0) cc_final: 0.8460 (t0) REVERT: B 453 GLN cc_start: 0.8775 (pt0) cc_final: 0.8094 (pm20) REVERT: B 542 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8320 (mmtm) REVERT: B 572 TYR cc_start: 0.8093 (p90) cc_final: 0.7639 (p90) REVERT: B 612 ARG cc_start: 0.8881 (ttt180) cc_final: 0.8518 (ttt-90) REVERT: F 393 ASN cc_start: 0.7609 (t0) cc_final: 0.6764 (t0) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1494 time to fit residues: 18.3345 Evaluate side-chains 83 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 34 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 103 ASN ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3588 Z= 0.232 Angle : 0.616 9.428 4885 Z= 0.315 Chirality : 0.046 0.189 572 Planarity : 0.004 0.030 615 Dihedral : 4.645 33.835 496 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.41), residues: 433 helix: 2.52 (0.51), residues: 102 sheet: 0.81 (0.43), residues: 128 loop : -0.21 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 447 HIS 0.004 0.001 HIS B 465 PHE 0.013 0.001 PHE F 334 TYR 0.012 0.001 TYR F 424 ARG 0.002 0.000 ARG F 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.433 Fit side-chains REVERT: A 56 ARG cc_start: 0.8563 (ptm160) cc_final: 0.8344 (ttp-110) REVERT: A 69 ILE cc_start: 0.7013 (tp) cc_final: 0.6794 (tp) REVERT: A 74 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8383 (ttpt) REVERT: B 429 ASN cc_start: 0.8739 (t0) cc_final: 0.8268 (t0) REVERT: B 542 LYS cc_start: 0.8681 (mmmm) cc_final: 0.8320 (mmtm) REVERT: B 553 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7808 (ptpp) REVERT: B 612 ARG cc_start: 0.8888 (ttt180) cc_final: 0.8488 (ttt-90) REVERT: F 393 ASN cc_start: 0.7623 (t0) cc_final: 0.6748 (t0) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1493 time to fit residues: 18.1476 Evaluate side-chains 81 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN B 453 GLN B 499 GLN F 369 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3588 Z= 0.226 Angle : 0.623 8.831 4885 Z= 0.321 Chirality : 0.046 0.165 572 Planarity : 0.004 0.030 615 Dihedral : 4.762 37.719 496 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.41), residues: 433 helix: 2.61 (0.51), residues: 102 sheet: 0.87 (0.44), residues: 128 loop : -0.17 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 367 HIS 0.004 0.001 HIS B 465 PHE 0.013 0.001 PHE F 348 TYR 0.015 0.001 TYR A 82 ARG 0.005 0.000 ARG F 368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.397 Fit side-chains REVERT: A 56 ARG cc_start: 0.8543 (ptm160) cc_final: 0.8327 (ttp-110) REVERT: A 69 ILE cc_start: 0.7009 (tp) cc_final: 0.6429 (tp) REVERT: A 74 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8251 (ttpt) REVERT: A 167 CYS cc_start: 0.7540 (m) cc_final: 0.7194 (m) REVERT: B 429 ASN cc_start: 0.8723 (t0) cc_final: 0.8269 (t0) REVERT: B 453 GLN cc_start: 0.8870 (pt0) cc_final: 0.8251 (pm20) REVERT: B 542 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8362 (mmtm) REVERT: B 572 TYR cc_start: 0.8088 (p90) cc_final: 0.7631 (p90) REVERT: B 612 ARG cc_start: 0.8903 (ttt180) cc_final: 0.8528 (ttt-90) REVERT: F 393 ASN cc_start: 0.7617 (t0) cc_final: 0.6748 (t0) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1481 time to fit residues: 18.4856 Evaluate side-chains 83 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.0060 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN F 369 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3588 Z= 0.189 Angle : 0.604 7.691 4885 Z= 0.309 Chirality : 0.045 0.180 572 Planarity : 0.004 0.031 615 Dihedral : 4.689 36.272 496 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 1.15 (0.41), residues: 433 helix: 2.41 (0.51), residues: 108 sheet: 0.78 (0.44), residues: 130 loop : -0.15 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 367 HIS 0.003 0.001 HIS B 465 PHE 0.012 0.001 PHE F 348 TYR 0.009 0.001 TYR F 424 ARG 0.005 0.000 ARG F 368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8543 (ptm160) cc_final: 0.8328 (ttp-110) REVERT: A 69 ILE cc_start: 0.7005 (tp) cc_final: 0.6683 (tp) REVERT: A 74 LYS cc_start: 0.8619 (ttpt) cc_final: 0.8324 (ttpt) REVERT: B 429 ASN cc_start: 0.8705 (t0) cc_final: 0.8480 (t0) REVERT: B 542 LYS cc_start: 0.8658 (mmmm) cc_final: 0.8334 (mmtm) REVERT: B 612 ARG cc_start: 0.8925 (ttt180) cc_final: 0.8575 (ttt-90) REVERT: F 393 ASN cc_start: 0.7654 (t0) cc_final: 0.6737 (t0) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1543 time to fit residues: 19.8288 Evaluate side-chains 85 residues out of total 408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** F 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090616 restraints weight = 8145.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093096 restraints weight = 5043.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.094876 restraints weight = 3595.248| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3588 Z= 0.225 Angle : 0.622 7.388 4885 Z= 0.319 Chirality : 0.045 0.183 572 Planarity : 0.004 0.031 615 Dihedral : 4.712 34.838 496 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 1.08 (0.41), residues: 433 helix: 2.30 (0.51), residues: 108 sheet: 0.74 (0.44), residues: 130 loop : -0.15 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 447 HIS 0.004 0.001 HIS B 465 PHE 0.013 0.001 PHE F 348 TYR 0.011 0.001 TYR F 424 ARG 0.005 0.000 ARG F 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.84 seconds wall clock time: 26 minutes 57.96 seconds (1617.96 seconds total)