Starting phenix.real_space_refine on Tue Feb 13 05:42:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yh6_33820/02_2024/7yh6_33820.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yh6_33820/02_2024/7yh6_33820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yh6_33820/02_2024/7yh6_33820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yh6_33820/02_2024/7yh6_33820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yh6_33820/02_2024/7yh6_33820.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yh6_33820/02_2024/7yh6_33820.pdb" } resolution = 3.4 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2121 2.51 5 N 563 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3343 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 823 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "A" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1550 Unusual residues: {'NAG': 1} Classifications: {'peptide': 194, 'undetermined': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183, None: 1} Not linked: pdbres="GLY A 526 " pdbres="NAG A 601 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.35, per 1000 atoms: 0.70 Number of scatterers: 3343 At special positions: 0 Unit cell: (58.29, 75.04, 97.82, 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 14 16.00 O 645 8.00 N 563 7.00 C 2121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 726.3 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 776 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 8 sheets defined 11.9% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.081A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU L 85 " --> pdb=" O THR L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.281A pdb=" N THR H 91 " --> pdb=" O PRO H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.657A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.504A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.213A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.569A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.805A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.688A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 10 removed outlier: 4.052A pdb=" N ALA L 86 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 9 through 10 removed outlier: 4.052A pdb=" N ALA L 86 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU L 99 " --> pdb=" O ASP L 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.656A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU H 79 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.739A pdb=" N GLN H 39 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.517A pdb=" N PHE H 114 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.624A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 102 hydrogen bonds defined for protein. 252 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: 1.04 Time building geometry restraints manager: 1.23 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: 1082 1.34 - 1.46: 917 1.46 - 1.58: 1416 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3431 Sorted by residual: bond pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " ideal model delta sigma weight residual 1.534 1.515 0.019 1.77e-02 3.19e+03 1.18e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.427 -0.021 2.00e-02 2.50e+03 1.13e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.10e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.95e-01 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.469 0.029 3.10e-02 1.04e+03 8.84e-01 ... (remaining 3426 not shown) Histogram of bond angle deviations from ideal: 100.70 - 107.36: 115 107.36 - 114.02: 1817 114.02 - 120.68: 1358 120.68 - 127.33: 1341 127.33 - 133.99: 36 Bond angle restraints: 4667 Sorted by residual: angle pdb=" N VAL A 524 " pdb=" CA VAL A 524 " pdb=" C VAL A 524 " ideal model delta sigma weight residual 106.42 113.30 -6.88 1.51e+00 4.39e-01 2.07e+01 angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 124.22 -9.82 2.30e+00 1.89e-01 1.82e+01 angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.14 114.72 -5.58 1.49e+00 4.50e-01 1.40e+01 angle pdb=" C THR A 523 " pdb=" N VAL A 524 " pdb=" CA VAL A 524 " ideal model delta sigma weight residual 122.96 120.03 2.93 9.50e-01 1.11e+00 9.50e+00 angle pdb=" N VAL A 524 " pdb=" CA VAL A 524 " pdb=" CB VAL A 524 " ideal model delta sigma weight residual 112.65 109.98 2.67 1.00e+00 1.00e+00 7.12e+00 ... (remaining 4662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 1809 17.61 - 35.22: 175 35.22 - 52.83: 25 52.83 - 70.44: 5 70.44 - 88.05: 3 Dihedral angle restraints: 2017 sinusoidal: 785 harmonic: 1232 Sorted by residual: dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 2.05 -88.05 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -121.23 35.23 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 2014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 352 0.046 - 0.092: 103 0.092 - 0.138: 40 0.138 - 0.184: 0 0.184 - 0.230: 2 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA CYS A 391 " pdb=" N CYS A 391 " pdb=" C CYS A 391 " pdb=" CB CYS A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB THR A 430 " pdb=" CA THR A 430 " pdb=" OG1 THR A 430 " pdb=" CG2 THR A 430 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 494 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 60 " 0.023 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO L 61 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.012 2.00e-02 2.50e+03 1.11e-02 1.54e+00 pdb=" CG ASN A 343 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.011 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 347 " 0.010 2.00e-02 2.50e+03 8.56e-03 1.28e+00 pdb=" CG PHE A 347 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 347 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 347 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 347 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 347 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 347 " 0.001 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 128 2.71 - 3.26: 3160 3.26 - 3.80: 4834 3.80 - 4.35: 5934 4.35 - 4.90: 10656 Nonbonded interactions: 24712 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OE2 GLU A 516 " model vdw 2.161 2.440 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.237 2.520 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.257 2.440 nonbonded pdb=" OG SER H 17 " pdb=" O MET H 83 " model vdw 2.272 2.440 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.280 2.440 ... (remaining 24707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.820 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: 26.460 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 0.029 3431 Z= 0.298 Angle : 0.635 11.365 4667 Z= 0.324 Chirality : 0.048 0.230 497 Planarity : 0.004 0.036 611 Dihedral : 13.192 80.334 1223 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.08 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.87 (0.42), residues: 424 helix: -3.28 (0.65), residues: 33 sheet: 0.96 (0.47), residues: 141 loop : -1.15 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.004 0.002 HIS H 35 PHE 0.019 0.001 PHE A 347 TYR 0.010 0.001 TYR H 106 ARG 0.006 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: H 56 ASN cc_start: 0.9234 (m110) cc_final: 0.8833 (m110) REVERT: H 62 ASP cc_start: 0.8516 (t70) cc_final: 0.8302 (t0) REVERT: H 73 ASP cc_start: 0.8079 (t0) cc_final: 0.7637 (t0) REVERT: H 99 ASP cc_start: 0.8765 (t70) cc_final: 0.8530 (t0) REVERT: A 420 ASP cc_start: 0.8704 (m-30) cc_final: 0.8300 (m-30) REVERT: A 489 TYR cc_start: 0.8761 (m-10) cc_final: 0.8525 (m-10) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1627 time to fit residues: 13.4109 Evaluate side-chains 60 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3431 Z= 0.174 Angle : 0.596 10.865 4667 Z= 0.299 Chirality : 0.046 0.145 497 Planarity : 0.004 0.038 611 Dihedral : 4.815 34.562 496 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.95 % Favored : 94.81 % Rotamer: Outliers : 0.83 % Allowed : 9.17 % Favored : 90.00 % 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: -0.84 (0.41), residues: 424 helix: -3.31 (0.63), residues: 33 sheet: 0.89 (0.45), residues: 144 loop : -1.09 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.003 0.001 HIS A 519 PHE 0.010 0.001 PHE A 392 TYR 0.019 0.001 TYR H 53 ARG 0.002 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.388 Fit side-chains REVERT: L 85 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7297 (pm20) REVERT: H 43 LYS cc_start: 0.8336 (mmmt) cc_final: 0.8102 (mmmt) REVERT: H 56 ASN cc_start: 0.9226 (m110) cc_final: 0.8845 (m110) REVERT: H 62 ASP cc_start: 0.8458 (t70) cc_final: 0.8256 (t0) REVERT: H 73 ASP cc_start: 0.8027 (t0) cc_final: 0.7583 (t0) REVERT: A 420 ASP cc_start: 0.8715 (m-30) cc_final: 0.8236 (m-30) REVERT: A 525 CYS cc_start: 0.5595 (p) cc_final: 0.5390 (p) outliers start: 3 outliers final: 3 residues processed: 64 average time/residue: 0.1496 time to fit residues: 11.8787 Evaluate side-chains 65 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 0.0000 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3431 Z= 0.144 Angle : 0.536 9.283 4667 Z= 0.271 Chirality : 0.044 0.131 497 Planarity : 0.003 0.043 611 Dihedral : 4.241 29.878 496 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.11 % Allowed : 12.22 % Favored : 86.67 % 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: -0.78 (0.41), residues: 424 helix: -3.14 (0.69), residues: 33 sheet: 0.81 (0.44), residues: 154 loop : -1.05 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.008 0.001 PHE L 51 TYR 0.019 0.001 TYR H 53 ARG 0.002 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.344 Fit side-chains REVERT: L 85 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7326 (pm20) REVERT: H 43 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7931 (mmmt) REVERT: H 56 ASN cc_start: 0.9230 (m110) cc_final: 0.8854 (m110) REVERT: H 73 ASP cc_start: 0.7920 (t0) cc_final: 0.7541 (t0) REVERT: A 420 ASP cc_start: 0.8720 (m-30) cc_final: 0.8220 (m-30) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.1522 time to fit residues: 12.4504 Evaluate side-chains 63 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3431 Z= 0.311 Angle : 0.614 9.166 4667 Z= 0.311 Chirality : 0.046 0.140 497 Planarity : 0.004 0.040 611 Dihedral : 4.431 26.214 496 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.78 % Allowed : 14.17 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.41), residues: 424 helix: -2.91 (0.73), residues: 33 sheet: 0.73 (0.44), residues: 152 loop : -1.14 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.002 HIS A 519 PHE 0.010 0.001 PHE A 347 TYR 0.019 0.001 TYR H 53 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.382 Fit side-chains REVERT: L 85 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7464 (pm20) REVERT: H 43 LYS cc_start: 0.8246 (mmmt) cc_final: 0.8009 (mmmt) REVERT: H 56 ASN cc_start: 0.9239 (m110) cc_final: 0.8829 (m110) REVERT: H 73 ASP cc_start: 0.7939 (t0) cc_final: 0.7555 (t0) REVERT: A 369 TYR cc_start: 0.8874 (t80) cc_final: 0.8657 (t80) REVERT: A 420 ASP cc_start: 0.8727 (m-30) cc_final: 0.8176 (m-30) REVERT: A 489 TYR cc_start: 0.8818 (m-10) cc_final: 0.8552 (m-10) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.1528 time to fit residues: 12.1741 Evaluate side-chains 66 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 471 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3431 Z= 0.415 Angle : 0.664 9.713 4667 Z= 0.337 Chirality : 0.047 0.137 497 Planarity : 0.004 0.041 611 Dihedral : 4.663 23.858 496 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.84 % Favored : 92.92 % Rotamer: Outliers : 3.61 % Allowed : 13.89 % Favored : 82.50 % 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: -1.05 (0.41), residues: 424 helix: -2.91 (0.73), residues: 33 sheet: 0.53 (0.44), residues: 154 loop : -1.23 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 353 HIS 0.005 0.002 HIS A 519 PHE 0.010 0.001 PHE A 347 TYR 0.019 0.002 TYR H 53 ARG 0.003 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.343 Fit side-chains REVERT: L 85 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7585 (pm20) REVERT: H 56 ASN cc_start: 0.9254 (m110) cc_final: 0.8792 (m110) REVERT: A 398 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8699 (p0) REVERT: A 420 ASP cc_start: 0.8747 (m-30) cc_final: 0.8157 (m-30) outliers start: 13 outliers final: 8 residues processed: 64 average time/residue: 0.1483 time to fit residues: 11.7063 Evaluate side-chains 65 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3431 Z= 0.180 Angle : 0.591 9.168 4667 Z= 0.295 Chirality : 0.045 0.157 497 Planarity : 0.004 0.042 611 Dihedral : 4.331 23.913 496 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.94 % Allowed : 17.22 % Favored : 80.83 % 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: -0.91 (0.41), residues: 424 helix: -2.91 (0.75), residues: 33 sheet: 0.62 (0.44), residues: 153 loop : -1.11 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS A 519 PHE 0.011 0.001 PHE L 51 TYR 0.019 0.001 TYR H 53 ARG 0.001 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: L 85 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7617 (pm20) REVERT: H 43 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7785 (mmmt) REVERT: H 56 ASN cc_start: 0.9250 (m110) cc_final: 0.8836 (m110) REVERT: A 420 ASP cc_start: 0.8700 (m-30) cc_final: 0.8113 (m-30) outliers start: 7 outliers final: 6 residues processed: 64 average time/residue: 0.1616 time to fit residues: 12.9347 Evaluate side-chains 61 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3431 Z= 0.280 Angle : 0.615 9.172 4667 Z= 0.308 Chirality : 0.046 0.135 497 Planarity : 0.004 0.040 611 Dihedral : 4.410 23.129 496 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.06 % Allowed : 16.94 % Favored : 80.00 % 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: -0.92 (0.41), residues: 424 helix: -2.90 (0.76), residues: 33 sheet: 0.61 (0.45), residues: 152 loop : -1.10 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS A 519 PHE 0.010 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.438 Fit side-chains REVERT: L 85 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7649 (pm20) REVERT: H 43 LYS cc_start: 0.8049 (mmmt) cc_final: 0.7810 (mmmt) REVERT: H 56 ASN cc_start: 0.9256 (m110) cc_final: 0.8790 (m110) REVERT: A 398 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8522 (p0) REVERT: A 420 ASP cc_start: 0.8730 (m-30) cc_final: 0.8287 (m-30) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.1525 time to fit residues: 11.5902 Evaluate side-chains 64 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 55 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain L residue 84 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.0050 chunk 38 optimal weight: 0.0370 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.5072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3431 Z= 0.148 Angle : 0.584 9.484 4667 Z= 0.287 Chirality : 0.044 0.132 497 Planarity : 0.003 0.040 611 Dihedral : 4.138 22.798 496 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.06 % Allowed : 16.67 % Favored : 80.28 % 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: -0.82 (0.41), residues: 424 helix: -2.92 (0.75), residues: 33 sheet: 0.67 (0.44), residues: 153 loop : -1.02 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS A 519 PHE 0.010 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.412 Fit side-chains REVERT: L 85 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7645 (pm20) REVERT: H 43 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7672 (mmmt) REVERT: H 56 ASN cc_start: 0.9253 (m110) cc_final: 0.8836 (m110) REVERT: H 73 ASP cc_start: 0.7880 (t0) cc_final: 0.7492 (t0) REVERT: A 420 ASP cc_start: 0.8682 (m-30) cc_final: 0.8088 (m-30) outliers start: 11 outliers final: 6 residues processed: 67 average time/residue: 0.1579 time to fit residues: 12.9766 Evaluate side-chains 65 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.0170 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.0050 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.7836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3431 Z= 0.179 Angle : 0.600 9.630 4667 Z= 0.295 Chirality : 0.045 0.163 497 Planarity : 0.003 0.040 611 Dihedral : 4.079 21.815 496 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.94 % Allowed : 17.50 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.41), residues: 424 helix: -2.96 (0.74), residues: 33 sheet: 0.68 (0.44), residues: 153 loop : -1.01 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS A 519 PHE 0.010 0.001 PHE L 51 TYR 0.017 0.001 TYR H 53 ARG 0.001 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.357 Fit side-chains REVERT: L 85 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7646 (pm20) REVERT: H 43 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7702 (mmmt) REVERT: H 56 ASN cc_start: 0.9249 (m110) cc_final: 0.8807 (m110) REVERT: H 73 ASP cc_start: 0.7887 (t0) cc_final: 0.7497 (t0) REVERT: A 420 ASP cc_start: 0.8695 (m-30) cc_final: 0.8110 (m-30) outliers start: 7 outliers final: 7 residues processed: 64 average time/residue: 0.1773 time to fit residues: 13.6789 Evaluate side-chains 67 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3431 Z= 0.196 Angle : 0.620 11.954 4667 Z= 0.301 Chirality : 0.045 0.130 497 Planarity : 0.003 0.040 611 Dihedral : 4.082 20.769 496 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.67 % Allowed : 18.06 % Favored : 80.28 % 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 (0.41), residues: 424 helix: -2.95 (0.74), residues: 33 sheet: 0.70 (0.44), residues: 153 loop : -1.02 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS A 519 PHE 0.010 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG H 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.389 Fit side-chains REVERT: L 81 GLN cc_start: 0.7900 (mp10) cc_final: 0.7567 (mp10) REVERT: L 85 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7661 (pm20) REVERT: H 43 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7724 (mmmt) REVERT: H 56 ASN cc_start: 0.9253 (m110) cc_final: 0.8801 (m110) REVERT: H 73 ASP cc_start: 0.7896 (t0) cc_final: 0.7504 (t0) REVERT: A 420 ASP cc_start: 0.8700 (m-30) cc_final: 0.8112 (m-30) outliers start: 6 outliers final: 6 residues processed: 64 average time/residue: 0.1677 time to fit residues: 13.2019 Evaluate side-chains 66 residues out of total 360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 34 ASP Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 41 optimal weight: 0.8980 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** 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 = 0.3153 r_free = 0.3153 target = 0.078089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.057876 restraints weight = 8196.051| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.71 r_work: 0.2605 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3431 Z= 0.205 Angle : 0.622 11.587 4667 Z= 0.303 Chirality : 0.045 0.128 497 Planarity : 0.003 0.040 611 Dihedral : 4.088 20.221 496 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 1.67 % Allowed : 18.61 % Favored : 79.72 % 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: -0.80 (0.41), residues: 424 helix: -2.95 (0.74), residues: 33 sheet: 0.71 (0.43), residues: 153 loop : -1.03 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.001 HIS A 519 PHE 0.010 0.001 PHE L 51 TYR 0.018 0.001 TYR H 53 ARG 0.002 0.000 ARG H 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.73 seconds wall clock time: 27 minutes 31.94 seconds (1651.94 seconds total)