Starting phenix.real_space_refine on Tue Feb 13 05:04:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3s_35155/02_2024/8i3s_35155.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3s_35155/02_2024/8i3s_35155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3s_35155/02_2024/8i3s_35155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3s_35155/02_2024/8i3s_35155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3s_35155/02_2024/8i3s_35155.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3s_35155/02_2024/8i3s_35155.pdb" } resolution = 3.9 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= -0.003 sd= 0.032 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 16 5.16 5 C 2074 2.51 5 N 554 2.21 5 O 628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3272 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 897 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 809 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "A" 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: 2.34, per 1000 atoms: 0.72 Number of scatterers: 3272 At special positions: 0 Unit cell: (67.45, 68.4, 96.9, 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 16 16.00 O 628 8.00 N 554 7.00 C 2074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=1.56 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 A1301 " - " ASN A 343 " Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 573.1 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 10.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.873A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.658A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.542A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.000A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.725A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.189A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 7 removed outlier: 3.679A pdb=" N VAL H 18 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 12 through 13 removed outlier: 7.060A pdb=" N LYS H 12 " --> pdb=" O SER H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.670A pdb=" N ARG H 56 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE H 52 " --> pdb=" O ARG H 56 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AA9, first strand: chain 'L' and resid 45 through 46 82 hydrogen bonds defined for protein. 207 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: 0.75 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 863 1.33 - 1.45: 679 1.45 - 1.57: 1787 1.57 - 1.69: 0 1.69 - 1.82: 20 Bond restraints: 3349 Sorted by residual: bond pdb=" N PRO L 59 " pdb=" CA PRO L 59 " ideal model delta sigma weight residual 1.468 1.440 0.027 7.90e-03 1.60e+04 1.21e+01 bond pdb=" N ASN H 32 " pdb=" CA ASN H 32 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N PHE L 62 " pdb=" CA PHE L 62 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.49e+00 bond pdb=" N ILE L 58 " pdb=" CA ILE L 58 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" CA SER L 63 " pdb=" CB SER L 63 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.54e-02 4.22e+03 3.78e+00 ... (remaining 3344 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.61: 73 105.61 - 112.81: 1726 112.81 - 120.01: 1113 120.01 - 127.21: 1605 127.21 - 134.41: 30 Bond angle restraints: 4547 Sorted by residual: angle pdb=" CA ALA L 60 " pdb=" C ALA L 60 " pdb=" O ALA L 60 " ideal model delta sigma weight residual 120.81 116.22 4.59 1.15e+00 7.56e-01 1.60e+01 angle pdb=" N PRO L 59 " pdb=" CA PRO L 59 " pdb=" C PRO L 59 " ideal model delta sigma weight residual 113.12 107.27 5.85 1.65e+00 3.67e-01 1.26e+01 angle pdb=" CA PRO L 59 " pdb=" C PRO L 59 " pdb=" O PRO L 59 " ideal model delta sigma weight residual 121.38 118.69 2.69 7.70e-01 1.69e+00 1.22e+01 angle pdb=" C ILE H 31 " pdb=" N ASN H 32 " pdb=" CA ASN H 32 " ideal model delta sigma weight residual 122.87 117.62 5.25 1.61e+00 3.86e-01 1.06e+01 angle pdb=" N PRO L 59 " pdb=" CD PRO L 59 " pdb=" CG PRO L 59 " ideal model delta sigma weight residual 103.20 98.41 4.79 1.50e+00 4.44e-01 1.02e+01 ... (remaining 4542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.35: 1779 12.35 - 24.70: 150 24.70 - 37.05: 50 37.05 - 49.40: 12 49.40 - 61.75: 9 Dihedral angle restraints: 2000 sinusoidal: 789 harmonic: 1211 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -114.61 28.61 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ARG L 61 " pdb=" CB ARG L 61 " pdb=" CG ARG L 61 " pdb=" CD ARG L 61 " ideal model delta sinusoidal sigma weight residual 180.00 123.29 56.71 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CA ILE A 434 " pdb=" CB ILE A 434 " pdb=" CG1 ILE A 434 " pdb=" CD1 ILE A 434 " ideal model delta sinusoidal sigma weight residual 60.00 115.51 -55.51 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 1997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 387 0.046 - 0.092: 74 0.092 - 0.138: 31 0.138 - 0.184: 4 0.184 - 0.230: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" CA PHE L 62 " pdb=" N PHE L 62 " pdb=" C PHE L 62 " pdb=" CB PHE L 62 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ALA L 60 " pdb=" N ALA L 60 " pdb=" C ALA L 60 " pdb=" CB ALA L 60 " both_signs ideal model delta sigma weight residual False 2.48 2.67 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.51e-01 ... (remaining 494 not shown) Planarity restraints: 590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR L 56 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C THR L 56 " 0.034 2.00e-02 2.50e+03 pdb=" O THR L 56 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY L 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 31 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.69e+00 pdb=" C ILE H 31 " -0.033 2.00e-02 2.50e+03 pdb=" O ILE H 31 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN H 32 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 101 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO H 102 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 102 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 102 " 0.023 5.00e-02 4.00e+02 ... (remaining 587 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 560 2.77 - 3.30: 3130 3.30 - 3.83: 5250 3.83 - 4.37: 6115 4.37 - 4.90: 10669 Nonbonded interactions: 25724 Sorted by model distance: nonbonded pdb=" O VAL A 367 " pdb=" OG SER A 371 " model vdw 2.235 2.440 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.242 2.440 nonbonded pdb=" NH2 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 2.301 2.520 nonbonded pdb=" O ASP L 82 " pdb=" OH TYR L 86 " model vdw 2.340 2.440 nonbonded pdb=" OH TYR A 453 " pdb=" OE1 GLN A 493 " model vdw 2.369 2.440 ... (remaining 25719 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 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.590 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.670 Find NCS groups from input model: 0.090 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 0.038 3349 Z= 0.224 Angle : 0.587 5.846 4547 Z= 0.350 Chirality : 0.045 0.230 497 Planarity : 0.004 0.046 589 Dihedral : 11.402 61.753 1214 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.54 % Allowed : 11.02 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.18 (0.41), residues: 414 helix: -2.41 (0.71), residues: 38 sheet: -0.53 (0.53), residues: 110 loop : -0.60 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.009 0.001 PHE A 515 TYR 0.010 0.001 TYR L 49 ARG 0.002 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8021 (t80) cc_final: 0.7522 (t80) REVERT: A 368 LEU cc_start: 0.5658 (mm) cc_final: 0.5449 (mm) REVERT: A 403 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.8158 (ttp-110) REVERT: A 458 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8652 (mmtm) REVERT: A 507 PRO cc_start: 0.8330 (Cg_exo) cc_final: 0.8077 (Cg_endo) REVERT: H 10 GLU cc_start: 0.3299 (tt0) cc_final: 0.3026 (mt-10) REVERT: H 29 PHE cc_start: 0.7177 (m-80) cc_final: 0.6948 (m-10) REVERT: H 46 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7202 (mt-10) REVERT: H 79 TYR cc_start: 0.7709 (m-80) cc_final: 0.6961 (m-80) REVERT: L 4 MET cc_start: 0.7409 (mmm) cc_final: 0.6709 (mmm) REVERT: L 18 ARG cc_start: 0.7787 (ttp-170) cc_final: 0.6999 (tpp-160) REVERT: L 36 TYR cc_start: 0.8654 (m-10) cc_final: 0.8420 (m-10) REVERT: L 49 TYR cc_start: 0.8499 (p90) cc_final: 0.8092 (p90) REVERT: L 87 TYR cc_start: 0.8368 (m-80) cc_final: 0.8127 (m-10) outliers start: 9 outliers final: 3 residues processed: 139 average time/residue: 0.2008 time to fit residues: 32.1743 Evaluate side-chains 105 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain L residue 3 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN H 61 GLN L 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3349 Z= 0.319 Angle : 0.620 5.505 4547 Z= 0.333 Chirality : 0.047 0.178 497 Planarity : 0.006 0.061 589 Dihedral : 5.282 40.261 490 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.78 % Allowed : 18.08 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.17 (0.39), residues: 414 helix: -0.94 (0.98), residues: 25 sheet: -0.23 (0.53), residues: 94 loop : -0.98 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.014 0.002 PHE A 464 TYR 0.015 0.002 TYR A 489 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.368 Fit side-chains REVERT: A 354 ASN cc_start: 0.7893 (m-40) cc_final: 0.7684 (m110) REVERT: A 355 ARG cc_start: 0.7716 (ttt90) cc_final: 0.6182 (ttm170) REVERT: A 398 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7243 (m-30) REVERT: A 464 PHE cc_start: 0.7001 (OUTLIER) cc_final: 0.6266 (t80) REVERT: A 474 GLN cc_start: 0.6391 (mt0) cc_final: 0.5744 (mm-40) REVERT: A 505 TYR cc_start: 0.6652 (m-80) cc_final: 0.6437 (m-80) REVERT: A 507 PRO cc_start: 0.8169 (Cg_exo) cc_final: 0.7899 (Cg_endo) REVERT: H 29 PHE cc_start: 0.7275 (m-80) cc_final: 0.6950 (m-10) REVERT: H 79 TYR cc_start: 0.7559 (m-80) cc_final: 0.6940 (m-80) REVERT: H 97 VAL cc_start: 0.8831 (p) cc_final: 0.8628 (m) REVERT: L 4 MET cc_start: 0.7539 (mmm) cc_final: 0.7324 (mmm) REVERT: L 11 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7146 (tm) REVERT: L 18 ARG cc_start: 0.7847 (ttp-170) cc_final: 0.7035 (tpp-160) outliers start: 24 outliers final: 12 residues processed: 117 average time/residue: 0.1897 time to fit residues: 26.0223 Evaluate side-chains 109 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0570 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 35 optimal weight: 0.0020 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.3506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3349 Z= 0.185 Angle : 0.574 6.879 4547 Z= 0.292 Chirality : 0.045 0.167 497 Planarity : 0.005 0.045 589 Dihedral : 4.786 40.286 490 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.08 % Allowed : 20.34 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.01 (0.39), residues: 414 helix: -0.59 (1.13), residues: 25 sheet: -0.24 (0.53), residues: 90 loop : -0.84 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.001 0.000 HIS A 519 PHE 0.015 0.001 PHE A 338 TYR 0.015 0.001 TYR H 47 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7861 (m-40) cc_final: 0.7562 (m110) REVERT: A 355 ARG cc_start: 0.7840 (ttt90) cc_final: 0.6979 (ttm170) REVERT: A 464 PHE cc_start: 0.6657 (OUTLIER) cc_final: 0.5912 (t80) REVERT: A 474 GLN cc_start: 0.6489 (mt0) cc_final: 0.5834 (mm-40) REVERT: H 29 PHE cc_start: 0.7118 (m-80) cc_final: 0.6849 (m-10) REVERT: H 79 TYR cc_start: 0.7311 (m-80) cc_final: 0.6683 (m-80) REVERT: L 4 MET cc_start: 0.7464 (mmm) cc_final: 0.6830 (mmm) REVERT: L 11 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7104 (tm) REVERT: L 18 ARG cc_start: 0.7619 (ttp-170) cc_final: 0.6822 (tpp-160) outliers start: 18 outliers final: 12 residues processed: 113 average time/residue: 0.1735 time to fit residues: 23.1543 Evaluate side-chains 110 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 ASN H 61 GLN L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3349 Z= 0.320 Angle : 0.621 6.477 4547 Z= 0.328 Chirality : 0.047 0.202 497 Planarity : 0.005 0.049 589 Dihedral : 5.249 41.062 488 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 7.63 % Allowed : 18.64 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.10 (0.39), residues: 414 helix: -1.21 (0.90), residues: 32 sheet: -0.38 (0.52), residues: 88 loop : -0.80 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.012 0.002 PHE A 338 TYR 0.019 0.002 TYR A 489 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 96 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8017 (t80) cc_final: 0.7135 (t80) REVERT: A 354 ASN cc_start: 0.7881 (m-40) cc_final: 0.7546 (m110) REVERT: A 474 GLN cc_start: 0.6485 (OUTLIER) cc_final: 0.5764 (mm-40) REVERT: H 29 PHE cc_start: 0.7225 (m-80) cc_final: 0.6815 (m-10) REVERT: H 79 TYR cc_start: 0.7475 (m-80) cc_final: 0.6810 (m-80) REVERT: H 100 TYR cc_start: 0.7477 (p90) cc_final: 0.7228 (p90) REVERT: L 11 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7098 (tm) REVERT: L 18 ARG cc_start: 0.7765 (ttp-170) cc_final: 0.6931 (tpp-160) outliers start: 27 outliers final: 21 residues processed: 111 average time/residue: 0.1486 time to fit residues: 20.1009 Evaluate side-chains 111 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 91 TYR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 61 GLN L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3349 Z= 0.300 Angle : 0.623 5.166 4547 Z= 0.324 Chirality : 0.047 0.204 497 Planarity : 0.005 0.052 589 Dihedral : 5.332 42.049 488 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.78 % Allowed : 21.19 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.10 (0.39), residues: 414 helix: -1.03 (1.01), residues: 27 sheet: -0.45 (0.51), residues: 88 loop : -0.81 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.026 0.002 PHE A 338 TYR 0.018 0.002 TYR A 489 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.376 Fit side-chains revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7834 (t80) cc_final: 0.7584 (t80) REVERT: A 342 PHE cc_start: 0.7532 (m-10) cc_final: 0.7300 (m-80) REVERT: A 354 ASN cc_start: 0.7781 (m-40) cc_final: 0.7440 (m110) REVERT: A 474 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.5924 (mm-40) REVERT: H 29 PHE cc_start: 0.7283 (m-80) cc_final: 0.6808 (m-10) REVERT: H 79 TYR cc_start: 0.7496 (m-80) cc_final: 0.6863 (m-80) REVERT: H 100 TYR cc_start: 0.7586 (p90) cc_final: 0.7374 (p90) REVERT: H 109 VAL cc_start: 0.8203 (t) cc_final: 0.7989 (t) REVERT: L 4 MET cc_start: 0.7296 (mmm) cc_final: 0.6507 (tpp) REVERT: L 11 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7134 (tm) REVERT: L 18 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.6915 (tpp-160) REVERT: L 23 CYS cc_start: 0.5044 (t) cc_final: 0.3927 (t) outliers start: 24 outliers final: 19 residues processed: 108 average time/residue: 0.1497 time to fit residues: 19.6543 Evaluate side-chains 113 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.0470 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 61 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3349 Z= 0.217 Angle : 0.584 5.073 4547 Z= 0.300 Chirality : 0.046 0.190 497 Planarity : 0.005 0.047 589 Dihedral : 5.021 41.719 488 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 6.21 % Allowed : 24.01 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.02 (0.39), residues: 414 helix: -0.22 (1.24), residues: 21 sheet: -0.42 (0.50), residues: 88 loop : -0.81 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.015 0.001 PHE A 338 TYR 0.018 0.002 TYR H 90 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 338 PHE cc_start: 0.7754 (t80) cc_final: 0.7427 (t80) REVERT: A 354 ASN cc_start: 0.7683 (m-40) cc_final: 0.7348 (m110) REVERT: A 394 ASN cc_start: 0.7232 (p0) cc_final: 0.6384 (t0) REVERT: A 457 ARG cc_start: 0.7748 (ttt-90) cc_final: 0.7522 (ttt-90) REVERT: A 474 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.5842 (mm-40) REVERT: H 29 PHE cc_start: 0.7233 (m-80) cc_final: 0.6789 (m-10) REVERT: H 79 TYR cc_start: 0.7237 (m-80) cc_final: 0.6621 (m-80) REVERT: L 4 MET cc_start: 0.7256 (mmm) cc_final: 0.6507 (tpp) REVERT: L 11 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7098 (tm) REVERT: L 18 ARG cc_start: 0.7707 (ttp-170) cc_final: 0.6880 (tpp-160) REVERT: L 23 CYS cc_start: 0.5042 (t) cc_final: 0.4220 (t) outliers start: 22 outliers final: 19 residues processed: 105 average time/residue: 0.1496 time to fit residues: 19.0707 Evaluate side-chains 109 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.0370 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3349 Z= 0.218 Angle : 0.589 7.640 4547 Z= 0.300 Chirality : 0.046 0.182 497 Planarity : 0.005 0.046 589 Dihedral : 4.930 42.135 488 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.78 % Allowed : 23.45 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.39), residues: 414 helix: -0.42 (1.28), residues: 20 sheet: -0.32 (0.51), residues: 88 loop : -0.87 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.019 0.001 PHE A 338 TYR 0.016 0.001 TYR H 47 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7603 (m-40) cc_final: 0.7330 (m110) REVERT: A 457 ARG cc_start: 0.7779 (ttt-90) cc_final: 0.7568 (ttt-90) REVERT: A 474 GLN cc_start: 0.6515 (OUTLIER) cc_final: 0.5818 (mm-40) REVERT: H 29 PHE cc_start: 0.7226 (m-80) cc_final: 0.6777 (m-10) REVERT: H 79 TYR cc_start: 0.7356 (m-80) cc_final: 0.6845 (m-80) REVERT: L 4 MET cc_start: 0.7286 (mmm) cc_final: 0.6573 (mmm) REVERT: L 11 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7125 (tm) REVERT: L 18 ARG cc_start: 0.7696 (ttp-170) cc_final: 0.6864 (tpp-160) outliers start: 24 outliers final: 19 residues processed: 102 average time/residue: 0.1549 time to fit residues: 19.1432 Evaluate side-chains 107 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3349 Z= 0.206 Angle : 0.592 9.145 4547 Z= 0.298 Chirality : 0.046 0.176 497 Planarity : 0.005 0.045 589 Dihedral : 4.768 38.066 488 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.93 % Allowed : 24.58 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.90 (0.40), residues: 414 helix: -0.45 (1.27), residues: 20 sheet: 0.05 (0.51), residues: 95 loop : -0.86 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.019 0.001 PHE A 338 TYR 0.015 0.001 TYR A 489 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7571 (m-40) cc_final: 0.7295 (m110) REVERT: A 457 ARG cc_start: 0.7790 (ttt-90) cc_final: 0.7457 (ttt90) REVERT: A 474 GLN cc_start: 0.6544 (OUTLIER) cc_final: 0.5847 (mm-40) REVERT: H 29 PHE cc_start: 0.7183 (m-80) cc_final: 0.6726 (m-10) REVERT: H 79 TYR cc_start: 0.7286 (m-80) cc_final: 0.6689 (m-80) REVERT: L 4 MET cc_start: 0.7323 (mmm) cc_final: 0.6739 (tpp) REVERT: L 11 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7138 (tm) REVERT: L 18 ARG cc_start: 0.7652 (ttp-170) cc_final: 0.6843 (tpp-160) outliers start: 21 outliers final: 17 residues processed: 102 average time/residue: 0.1561 time to fit residues: 19.3024 Evaluate side-chains 106 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3349 Z= 0.221 Angle : 0.611 9.442 4547 Z= 0.307 Chirality : 0.047 0.213 497 Planarity : 0.005 0.046 589 Dihedral : 4.714 33.454 488 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.93 % Allowed : 24.01 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.39), residues: 414 helix: -0.71 (1.24), residues: 20 sheet: 0.07 (0.51), residues: 95 loop : -0.87 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.025 0.002 PHE A 338 TYR 0.015 0.001 TYR A 489 ARG 0.002 0.000 ARG H 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 342 PHE cc_start: 0.7339 (m-80) cc_final: 0.6916 (m-80) REVERT: A 354 ASN cc_start: 0.7571 (m-40) cc_final: 0.7280 (m110) REVERT: A 474 GLN cc_start: 0.6574 (OUTLIER) cc_final: 0.5886 (mm-40) REVERT: H 29 PHE cc_start: 0.7205 (m-80) cc_final: 0.6697 (m-10) REVERT: H 79 TYR cc_start: 0.7350 (m-80) cc_final: 0.6764 (m-80) REVERT: L 4 MET cc_start: 0.7420 (mmm) cc_final: 0.6813 (tpp) REVERT: L 11 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7241 (tm) REVERT: L 18 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.6921 (tpp-160) outliers start: 21 outliers final: 18 residues processed: 101 average time/residue: 0.1586 time to fit residues: 19.5840 Evaluate side-chains 105 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.0670 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3349 Z= 0.241 Angle : 0.631 9.780 4547 Z= 0.321 Chirality : 0.047 0.206 497 Planarity : 0.005 0.046 589 Dihedral : 4.697 24.267 488 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.93 % Allowed : 24.01 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.95 (0.39), residues: 414 helix: -1.41 (0.97), residues: 27 sheet: 0.10 (0.51), residues: 95 loop : -0.83 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.022 0.001 PHE A 338 TYR 0.016 0.001 TYR A 489 ARG 0.002 0.000 ARG H 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7614 (m-40) cc_final: 0.7275 (m110) REVERT: A 474 GLN cc_start: 0.6568 (OUTLIER) cc_final: 0.5886 (mm-40) REVERT: H 29 PHE cc_start: 0.7195 (m-80) cc_final: 0.6662 (m-10) REVERT: H 79 TYR cc_start: 0.7373 (m-80) cc_final: 0.6774 (m-80) REVERT: L 4 MET cc_start: 0.7445 (mmm) cc_final: 0.6804 (tpp) REVERT: L 11 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7242 (tm) REVERT: L 18 ARG cc_start: 0.7685 (ttp-170) cc_final: 0.6919 (tpp-160) outliers start: 21 outliers final: 18 residues processed: 100 average time/residue: 0.1527 time to fit residues: 18.4657 Evaluate side-chains 104 residues out of total 354 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.139119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.122168 restraints weight = 6992.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125438 restraints weight = 4261.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127794 restraints weight = 2988.868| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3349 Z= 0.249 Angle : 0.642 9.842 4547 Z= 0.327 Chirality : 0.047 0.194 497 Planarity : 0.005 0.046 589 Dihedral : 4.712 17.339 487 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 6.21 % Allowed : 24.01 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.01 (0.39), residues: 414 helix: -1.50 (0.97), residues: 27 sheet: 0.04 (0.51), residues: 94 loop : -0.86 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 353 HIS 0.000 0.000 HIS A 519 PHE 0.013 0.001 PHE A 342 TYR 0.016 0.001 TYR A 489 ARG 0.008 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1399.48 seconds wall clock time: 25 minutes 48.72 seconds (1548.72 seconds total)