Starting phenix.real_space_refine on Sun Mar 10 17:04:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/03_2024/7swp_25478_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/03_2024/7swp_25478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/03_2024/7swp_25478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/03_2024/7swp_25478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/03_2024/7swp_25478_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/03_2024/7swp_25478_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 2137 2.51 5 N 573 2.21 5 O 648 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 PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 34": "OD1" <-> "OD2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3372 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1545 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1017 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 810 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 2.40, per 1000 atoms: 0.71 Number of scatterers: 3372 At special positions: 0 Unit cell: (84.15, 59.4, 89.1, 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 648 8.00 N 573 7.00 C 2137 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=2.03 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=2.04 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 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 628.5 milliseconds 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 15.1% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.584A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.236A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.828A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.876A pdb=" N TYR H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.782A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.547A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.687A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.623A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 17 through 23 119 hydrogen bonds defined for protein. 273 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: 0.94 Time building geometry restraints manager: 1.38 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: 1087 1.34 - 1.46: 924 1.46 - 1.58: 1434 1.58 - 1.71: 0 1.71 - 1.83: 16 Bond restraints: 3461 Sorted by residual: bond pdb=" C TYR A 421 " pdb=" N ASN A 422 " ideal model delta sigma weight residual 1.332 1.282 0.050 1.40e-02 5.10e+03 1.27e+01 bond pdb=" C LYS A 424 " pdb=" N LEU A 425 " ideal model delta sigma weight residual 1.331 1.233 0.098 2.83e-02 1.25e+03 1.19e+01 bond pdb=" N VAL L 100 " pdb=" CA VAL L 100 " ideal model delta sigma weight residual 1.458 1.495 -0.036 1.21e-02 6.83e+03 8.88e+00 bond pdb=" N VAL L 101 " pdb=" CA VAL L 101 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.24e-02 6.50e+03 8.21e+00 bond pdb=" N THR L 106 " pdb=" CA THR L 106 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.21e-02 6.83e+03 6.96e+00 ... (remaining 3456 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.86: 113 106.86 - 113.65: 1798 113.65 - 120.43: 1310 120.43 - 127.21: 1450 127.21 - 133.99: 36 Bond angle restraints: 4707 Sorted by residual: angle pdb=" C HIS L 36 " pdb=" N TRP L 37 " pdb=" CA TRP L 37 " ideal model delta sigma weight residual 122.94 115.73 7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" C TYR A 421 " pdb=" N ASN A 422 " pdb=" CA ASN A 422 " ideal model delta sigma weight residual 121.54 113.51 8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C PRO A 527 " pdb=" N LYS A 528 " pdb=" CA LYS A 528 " ideal model delta sigma weight residual 121.70 127.24 -5.54 1.80e+00 3.09e-01 9.48e+00 angle pdb=" N GLY A 526 " pdb=" CA GLY A 526 " pdb=" C GLY A 526 " ideal model delta sigma weight residual 112.34 118.59 -6.25 2.04e+00 2.40e-01 9.38e+00 angle pdb=" CA GLY L 103 " pdb=" C GLY L 103 " pdb=" O GLY L 103 " ideal model delta sigma weight residual 122.24 118.32 3.92 1.30e+00 5.92e-01 9.10e+00 ... (remaining 4702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1840 17.57 - 35.15: 163 35.15 - 52.72: 15 52.72 - 70.29: 4 70.29 - 87.87: 2 Dihedral angle restraints: 2024 sinusoidal: 776 harmonic: 1248 Sorted by residual: 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 -151.49 -28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 46.90 46.10 1 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CA SER A 477 " pdb=" C SER A 477 " pdb=" N THR A 478 " pdb=" CA THR A 478 " ideal model delta harmonic sigma weight residual -180.00 -157.35 -22.65 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 2021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 354 0.048 - 0.096: 103 0.096 - 0.145: 33 0.145 - 0.193: 3 0.193 - 0.241: 2 Chirality restraints: 495 Sorted by residual: chirality pdb=" CB ILE L 50 " pdb=" CA ILE L 50 " pdb=" CG1 ILE L 50 " pdb=" CG2 ILE L 50 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU H 81 " pdb=" CB LEU H 81 " pdb=" CD1 LEU H 81 " pdb=" CD2 LEU H 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL L 101 " pdb=" N VAL L 101 " pdb=" C VAL L 101 " pdb=" CB VAL L 101 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.86e-01 ... (remaining 492 not shown) Planarity restraints: 617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 37 " -0.035 2.00e-02 2.50e+03 4.40e-02 4.85e+01 pdb=" CG TRP L 37 " 0.109 2.00e-02 2.50e+03 pdb=" CD1 TRP L 37 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP L 37 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP L 37 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP L 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP L 37 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 37 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 37 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP L 37 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO A 527 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 453 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C TYR A 453 " -0.025 2.00e-02 2.50e+03 pdb=" O TYR A 453 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG A 454 " 0.009 2.00e-02 2.50e+03 ... (remaining 614 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 569 2.74 - 3.28: 3775 3.28 - 3.82: 6048 3.82 - 4.36: 7001 4.36 - 4.90: 11348 Nonbonded interactions: 28741 Sorted by model distance: nonbonded pdb=" OD2 ASP L 94 " pdb=" OG SER L 96 " model vdw 2.202 2.440 nonbonded pdb=" NE2 GLN H 13 " pdb=" O SER H 128 " model vdw 2.206 2.520 nonbonded pdb=" O TYR H 53 " pdb=" NH2 ARG H 72 " model vdw 2.214 2.520 nonbonded pdb=" OG1 THR A 415 " pdb=" OG SER L 58 " model vdw 2.216 2.440 nonbonded pdb=" O LYS A 444 " pdb=" NE2 GLN A 498 " model vdw 2.224 2.520 ... (remaining 28736 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.070 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.370 Find NCS groups from input model: 0.100 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 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 : 0.008 0.098 3461 Z= 0.534 Angle : 0.925 8.029 4707 Z= 0.525 Chirality : 0.051 0.241 495 Planarity : 0.006 0.056 617 Dihedral : 12.869 87.868 1224 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 40.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -2.17 (0.38), residues: 430 helix: -3.11 (0.87), residues: 21 sheet: -1.11 (0.44), residues: 122 loop : -1.50 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.006 TRP L 37 HIS 0.007 0.003 HIS L 36 PHE 0.023 0.002 PHE A 490 TYR 0.021 0.003 TYR L 51 ARG 0.011 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8298 (tm-30) REVERT: A 356 LYS cc_start: 0.8283 (tppt) cc_final: 0.7661 (tptt) REVERT: A 398 ASP cc_start: 0.7717 (m-30) cc_final: 0.7370 (m-30) REVERT: A 403 ARG cc_start: 0.6932 (ptt90) cc_final: 0.6642 (ptt90) REVERT: A 501 ASN cc_start: 0.7847 (t0) cc_final: 0.7428 (t0) REVERT: A 517 LEU cc_start: 0.8767 (mt) cc_final: 0.8271 (tt) REVERT: H 2 VAL cc_start: 0.7845 (m) cc_final: 0.7345 (m) REVERT: H 16 ARG cc_start: 0.5405 (ptt-90) cc_final: 0.5174 (ptp-110) REVERT: H 34 MET cc_start: 0.8260 (mmp) cc_final: 0.8041 (mmm) REVERT: H 35 GLN cc_start: 0.8219 (mp10) cc_final: 0.7931 (mp10) REVERT: H 95 TYR cc_start: 0.7581 (m-80) cc_final: 0.7352 (m-80) REVERT: H 105 ASP cc_start: 0.8435 (t70) cc_final: 0.7971 (t70) REVERT: H 111 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7824 (mp10) REVERT: H 112 THR cc_start: 0.8451 (p) cc_final: 0.8147 (m) REVERT: L 34 ASP cc_start: 0.7296 (p0) cc_final: 0.6964 (p0) REVERT: L 87 ASP cc_start: 0.7942 (p0) cc_final: 0.7573 (t70) REVERT: L 101 VAL cc_start: 0.8380 (t) cc_final: 0.8081 (t) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.1931 time to fit residues: 35.9328 Evaluate side-chains 98 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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: 7.9990 chunk 31 optimal weight: 0.0770 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 0.0370 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3461 Z= 0.224 Angle : 0.758 8.229 4707 Z= 0.389 Chirality : 0.048 0.140 495 Planarity : 0.005 0.036 617 Dihedral : 5.651 24.791 487 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.47 % Allowed : 13.19 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.38), residues: 430 helix: -3.32 (0.75), residues: 22 sheet: -0.74 (0.44), residues: 127 loop : -1.19 (0.35), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP L 37 HIS 0.006 0.002 HIS A 519 PHE 0.015 0.002 PHE H 27 TYR 0.020 0.002 TYR A 365 ARG 0.006 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8253 (tm-30) REVERT: A 356 LYS cc_start: 0.8322 (tppt) cc_final: 0.7749 (tptt) REVERT: A 365 TYR cc_start: 0.8312 (m-80) cc_final: 0.7892 (m-10) REVERT: A 387 LEU cc_start: 0.8828 (mp) cc_final: 0.8602 (mp) REVERT: A 388 ASN cc_start: 0.8711 (t0) cc_final: 0.8343 (m110) REVERT: A 398 ASP cc_start: 0.8026 (m-30) cc_final: 0.7521 (m-30) REVERT: A 403 ARG cc_start: 0.6982 (ptt90) cc_final: 0.6013 (ptt90) REVERT: A 406 GLU cc_start: 0.8487 (pm20) cc_final: 0.7604 (pm20) REVERT: A 493 GLN cc_start: 0.7887 (tp40) cc_final: 0.7630 (tp40) REVERT: H 34 MET cc_start: 0.8169 (mmp) cc_final: 0.7778 (mmm) REVERT: H 35 GLN cc_start: 0.8240 (mp10) cc_final: 0.7642 (mp10) REVERT: H 95 TYR cc_start: 0.7538 (m-80) cc_final: 0.7236 (m-80) REVERT: H 105 ASP cc_start: 0.8523 (t70) cc_final: 0.8160 (t70) REVERT: L 34 ASP cc_start: 0.7596 (p0) cc_final: 0.7252 (p0) REVERT: L 89 TYR cc_start: 0.7779 (m-80) cc_final: 0.7212 (m-10) REVERT: L 101 VAL cc_start: 0.8321 (t) cc_final: 0.8057 (p) REVERT: L 102 PHE cc_start: 0.7582 (m-80) cc_final: 0.7373 (m-10) outliers start: 9 outliers final: 6 residues processed: 129 average time/residue: 0.1635 time to fit residues: 25.1429 Evaluate side-chains 109 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 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 0.038 3461 Z= 0.190 Angle : 0.668 7.455 4707 Z= 0.340 Chirality : 0.046 0.142 495 Planarity : 0.005 0.038 617 Dihedral : 5.130 22.424 487 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 5.22 % Allowed : 16.48 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.38), residues: 430 helix: -2.72 (0.68), residues: 28 sheet: -0.44 (0.43), residues: 132 loop : -1.05 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP L 37 HIS 0.005 0.002 HIS A 519 PHE 0.021 0.002 PHE A 400 TYR 0.031 0.002 TYR A 351 ARG 0.003 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8362 (tppt) cc_final: 0.7826 (tttt) REVERT: A 385 THR cc_start: 0.9556 (OUTLIER) cc_final: 0.9333 (t) REVERT: A 398 ASP cc_start: 0.8166 (m-30) cc_final: 0.7308 (m-30) REVERT: A 403 ARG cc_start: 0.6953 (ptt90) cc_final: 0.6118 (ptt90) REVERT: A 406 GLU cc_start: 0.8666 (pm20) cc_final: 0.7861 (pm20) REVERT: A 493 GLN cc_start: 0.8096 (tp40) cc_final: 0.7802 (tp40) REVERT: H 2 VAL cc_start: 0.7770 (m) cc_final: 0.7478 (p) REVERT: H 35 GLN cc_start: 0.8194 (mp10) cc_final: 0.7787 (mp10) REVERT: H 105 ASP cc_start: 0.8808 (t70) cc_final: 0.8251 (t70) REVERT: H 110 TYR cc_start: 0.7897 (t80) cc_final: 0.7682 (t80) REVERT: H 111 GLN cc_start: 0.7972 (mp10) cc_final: 0.7261 (mp10) REVERT: L 34 ASP cc_start: 0.7583 (p0) cc_final: 0.7187 (p0) REVERT: L 87 ASP cc_start: 0.7728 (p0) cc_final: 0.7436 (p0) REVERT: L 89 TYR cc_start: 0.7788 (m-80) cc_final: 0.7026 (m-80) REVERT: L 101 VAL cc_start: 0.8443 (t) cc_final: 0.8162 (p) outliers start: 19 outliers final: 12 residues processed: 124 average time/residue: 0.1388 time to fit residues: 21.1425 Evaluate side-chains 121 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 117 GLN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 0.3980 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3461 Z= 0.179 Angle : 0.689 9.919 4707 Z= 0.345 Chirality : 0.045 0.161 495 Planarity : 0.004 0.034 617 Dihedral : 4.829 23.658 487 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.40 % Allowed : 20.60 % Favored : 75.00 % 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: -1.17 (0.39), residues: 430 helix: -2.34 (0.85), residues: 28 sheet: -0.31 (0.43), residues: 129 loop : -0.82 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 37 HIS 0.004 0.002 HIS A 519 PHE 0.016 0.002 PHE A 392 TYR 0.018 0.001 TYR A 369 ARG 0.003 0.000 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8353 (tppt) cc_final: 0.7866 (tptt) REVERT: A 396 TYR cc_start: 0.8019 (m-80) cc_final: 0.7373 (m-80) REVERT: A 398 ASP cc_start: 0.8031 (m-30) cc_final: 0.7815 (m-30) REVERT: A 401 VAL cc_start: 0.8979 (t) cc_final: 0.8760 (t) REVERT: A 406 GLU cc_start: 0.8715 (pm20) cc_final: 0.8185 (pm20) REVERT: A 462 LYS cc_start: 0.9370 (mtmt) cc_final: 0.9048 (mtmm) REVERT: A 465 GLU cc_start: 0.7997 (pm20) cc_final: 0.7507 (pm20) REVERT: A 493 GLN cc_start: 0.8138 (tp40) cc_final: 0.7872 (tp40) REVERT: H 2 VAL cc_start: 0.7721 (m) cc_final: 0.7424 (p) REVERT: H 64 VAL cc_start: 0.6585 (m) cc_final: 0.6383 (m) REVERT: H 95 TYR cc_start: 0.7510 (m-80) cc_final: 0.7197 (m-80) REVERT: H 105 ASP cc_start: 0.8765 (t70) cc_final: 0.8347 (t70) REVERT: H 111 GLN cc_start: 0.7897 (mp10) cc_final: 0.7314 (mp10) REVERT: L 34 ASP cc_start: 0.7363 (p0) cc_final: 0.7109 (p0) REVERT: L 101 VAL cc_start: 0.8400 (t) cc_final: 0.8078 (p) outliers start: 16 outliers final: 13 residues processed: 126 average time/residue: 0.1516 time to fit residues: 23.2341 Evaluate side-chains 119 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 91 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.0370 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.5262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3461 Z= 0.279 Angle : 0.692 7.353 4707 Z= 0.357 Chirality : 0.046 0.163 495 Planarity : 0.005 0.043 617 Dihedral : 5.069 21.268 487 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 6.32 % Allowed : 21.43 % Favored : 72.25 % 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: -1.12 (0.40), residues: 430 helix: -2.01 (0.93), residues: 28 sheet: -0.22 (0.43), residues: 132 loop : -0.85 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 37 HIS 0.003 0.002 HIS H 118 PHE 0.014 0.002 PHE A 400 TYR 0.019 0.002 TYR A 369 ARG 0.005 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8233 (m-80) cc_final: 0.8011 (m-80) REVERT: A 356 LYS cc_start: 0.8430 (tppt) cc_final: 0.7901 (tptt) REVERT: A 389 ASP cc_start: 0.9171 (t0) cc_final: 0.8893 (t0) REVERT: A 394 ASN cc_start: 0.6963 (t0) cc_final: 0.6453 (t0) REVERT: A 398 ASP cc_start: 0.8375 (m-30) cc_final: 0.7982 (m-30) REVERT: A 406 GLU cc_start: 0.9053 (pm20) cc_final: 0.8573 (pm20) REVERT: A 461 LEU cc_start: 0.9024 (tp) cc_final: 0.8810 (tp) REVERT: A 462 LYS cc_start: 0.9352 (mtmt) cc_final: 0.8875 (mtmm) REVERT: A 493 GLN cc_start: 0.8103 (tp40) cc_final: 0.7780 (tp40) REVERT: H 2 VAL cc_start: 0.7757 (m) cc_final: 0.7484 (p) REVERT: H 34 MET cc_start: 0.8273 (mmt) cc_final: 0.8057 (mmm) REVERT: H 35 GLN cc_start: 0.8319 (mp10) cc_final: 0.7910 (mp10) REVERT: H 47 TRP cc_start: 0.7716 (t60) cc_final: 0.7514 (t60) REVERT: H 95 TYR cc_start: 0.7623 (m-80) cc_final: 0.7381 (m-80) REVERT: H 114 GLU cc_start: 0.8496 (mp0) cc_final: 0.8058 (mp0) REVERT: L 34 ASP cc_start: 0.7244 (p0) cc_final: 0.7002 (p0) REVERT: L 101 VAL cc_start: 0.8401 (t) cc_final: 0.8007 (p) outliers start: 23 outliers final: 20 residues processed: 120 average time/residue: 0.1376 time to fit residues: 20.1170 Evaluate side-chains 123 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 117 GLN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 91 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3461 Z= 0.248 Angle : 0.692 8.440 4707 Z= 0.352 Chirality : 0.046 0.151 495 Planarity : 0.005 0.040 617 Dihedral : 4.994 19.814 487 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 6.32 % Allowed : 22.25 % Favored : 71.43 % 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: -1.19 (0.39), residues: 430 helix: -1.99 (0.87), residues: 28 sheet: -0.11 (0.44), residues: 132 loop : -1.01 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 37 HIS 0.003 0.002 HIS L 36 PHE 0.019 0.002 PHE A 392 TYR 0.018 0.002 TYR A 369 ARG 0.003 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8180 (m-80) cc_final: 0.7957 (m-80) REVERT: A 356 LYS cc_start: 0.8494 (tppt) cc_final: 0.7966 (tptt) REVERT: A 389 ASP cc_start: 0.9283 (t0) cc_final: 0.9000 (t0) REVERT: A 398 ASP cc_start: 0.8425 (m-30) cc_final: 0.7893 (m-30) REVERT: A 406 GLU cc_start: 0.9091 (pm20) cc_final: 0.8635 (pm20) REVERT: A 493 GLN cc_start: 0.8035 (tp40) cc_final: 0.7802 (tp40) REVERT: H 2 VAL cc_start: 0.7873 (m) cc_final: 0.7565 (p) REVERT: H 47 TRP cc_start: 0.7670 (t60) cc_final: 0.7415 (t60) REVERT: H 114 GLU cc_start: 0.8521 (mp0) cc_final: 0.8129 (mp0) REVERT: L 34 ASP cc_start: 0.7209 (p0) cc_final: 0.6896 (p0) REVERT: L 81 GLN cc_start: 0.7798 (tm-30) cc_final: 0.6870 (tt0) REVERT: L 87 ASP cc_start: 0.7943 (p0) cc_final: 0.7616 (p0) REVERT: L 89 TYR cc_start: 0.7966 (m-80) cc_final: 0.7668 (m-80) REVERT: L 101 VAL cc_start: 0.8357 (t) cc_final: 0.7952 (p) outliers start: 23 outliers final: 18 residues processed: 123 average time/residue: 0.1343 time to fit residues: 20.4178 Evaluate side-chains 122 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3461 Z= 0.347 Angle : 0.760 10.538 4707 Z= 0.393 Chirality : 0.048 0.169 495 Planarity : 0.006 0.052 617 Dihedral : 5.491 19.340 487 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 26.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 8.79 % Allowed : 20.88 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.39), residues: 430 helix: -2.05 (0.82), residues: 34 sheet: -0.52 (0.44), residues: 127 loop : -0.98 (0.37), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 37 HIS 0.003 0.002 HIS H 118 PHE 0.026 0.002 PHE A 392 TYR 0.020 0.002 TYR A 369 ARG 0.004 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8277 (m-80) cc_final: 0.8068 (m-80) REVERT: A 356 LYS cc_start: 0.8500 (tppt) cc_final: 0.7944 (tptt) REVERT: A 398 ASP cc_start: 0.8443 (m-30) cc_final: 0.7845 (m-30) REVERT: H 2 VAL cc_start: 0.8025 (m) cc_final: 0.7718 (p) REVERT: H 114 GLU cc_start: 0.8566 (mp0) cc_final: 0.8139 (mp0) REVERT: L 34 ASP cc_start: 0.7137 (p0) cc_final: 0.6800 (p0) REVERT: L 81 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7559 (tt0) REVERT: L 87 ASP cc_start: 0.7844 (p0) cc_final: 0.7484 (p0) REVERT: L 101 VAL cc_start: 0.8347 (t) cc_final: 0.8006 (p) REVERT: L 107 LYS cc_start: 0.8694 (tppp) cc_final: 0.8079 (tmtt) outliers start: 32 outliers final: 26 residues processed: 127 average time/residue: 0.1385 time to fit residues: 21.6261 Evaluate side-chains 130 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 108 LEU Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 0.0980 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3461 Z= 0.206 Angle : 0.782 15.499 4707 Z= 0.378 Chirality : 0.046 0.165 495 Planarity : 0.005 0.047 617 Dihedral : 5.038 18.685 487 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 6.32 % Allowed : 24.45 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.39), residues: 430 helix: -2.41 (0.76), residues: 33 sheet: -0.14 (0.46), residues: 124 loop : -0.90 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.005 0.002 HIS L 36 PHE 0.022 0.002 PHE A 392 TYR 0.014 0.001 TYR A 369 ARG 0.002 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8501 (tppt) cc_final: 0.7961 (tptt) REVERT: A 386 LYS cc_start: 0.9279 (mmtt) cc_final: 0.9004 (ptmm) REVERT: A 398 ASP cc_start: 0.8338 (m-30) cc_final: 0.7689 (m-30) REVERT: A 484 GLU cc_start: 0.6600 (mm-30) cc_final: 0.3601 (pp20) REVERT: A 493 GLN cc_start: 0.8180 (tp-100) cc_final: 0.7958 (tp-100) REVERT: H 2 VAL cc_start: 0.8012 (m) cc_final: 0.7707 (p) REVERT: H 95 TYR cc_start: 0.7621 (m-80) cc_final: 0.7379 (m-80) REVERT: H 114 GLU cc_start: 0.8365 (mp0) cc_final: 0.7902 (mp0) REVERT: H 117 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: L 34 ASP cc_start: 0.7156 (p0) cc_final: 0.6854 (p0) REVERT: L 81 GLN cc_start: 0.7947 (tm-30) cc_final: 0.7565 (tt0) REVERT: L 87 ASP cc_start: 0.7833 (p0) cc_final: 0.7561 (p0) REVERT: L 101 VAL cc_start: 0.8228 (t) cc_final: 0.7857 (p) outliers start: 23 outliers final: 20 residues processed: 118 average time/residue: 0.1471 time to fit residues: 21.2125 Evaluate side-chains 119 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 117 GLN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3461 Z= 0.218 Angle : 0.752 12.071 4707 Z= 0.369 Chirality : 0.047 0.190 495 Planarity : 0.005 0.048 617 Dihedral : 4.873 17.430 487 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 6.04 % Allowed : 23.90 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.40), residues: 430 helix: -2.62 (0.71), residues: 34 sheet: -0.21 (0.46), residues: 131 loop : -0.76 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.004 0.002 HIS L 36 PHE 0.023 0.002 PHE A 392 TYR 0.016 0.001 TYR A 369 ARG 0.002 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8474 (tppt) cc_final: 0.7995 (tptt) REVERT: A 386 LYS cc_start: 0.9286 (mmtt) cc_final: 0.9009 (ptmm) REVERT: A 398 ASP cc_start: 0.8340 (m-30) cc_final: 0.7659 (m-30) REVERT: A 420 ASP cc_start: 0.7967 (t0) cc_final: 0.7541 (m-30) REVERT: A 493 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7861 (tp-100) REVERT: H 2 VAL cc_start: 0.7822 (m) cc_final: 0.7532 (p) REVERT: H 47 TRP cc_start: 0.7962 (t60) cc_final: 0.7398 (t60) REVERT: H 95 TYR cc_start: 0.7630 (m-80) cc_final: 0.7352 (m-80) REVERT: H 114 GLU cc_start: 0.8464 (mp0) cc_final: 0.8026 (mp0) REVERT: L 34 ASP cc_start: 0.7169 (p0) cc_final: 0.6857 (p0) REVERT: L 81 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7688 (tt0) REVERT: L 101 VAL cc_start: 0.8294 (t) cc_final: 0.7929 (p) outliers start: 22 outliers final: 21 residues processed: 112 average time/residue: 0.1430 time to fit residues: 19.6606 Evaluate side-chains 125 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3461 Z= 0.241 Angle : 0.792 18.232 4707 Z= 0.384 Chirality : 0.046 0.195 495 Planarity : 0.005 0.048 617 Dihedral : 4.888 17.960 487 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 5.77 % Allowed : 25.27 % Favored : 68.96 % 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: -1.02 (0.41), residues: 430 helix: -2.57 (0.71), residues: 34 sheet: 0.05 (0.45), residues: 140 loop : -0.80 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.002 HIS L 36 PHE 0.023 0.002 PHE A 392 TYR 0.018 0.001 TYR A 369 ARG 0.003 0.000 ARG A 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 860 Ramachandran restraints generated. 430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8509 (tppt) cc_final: 0.8017 (tptt) REVERT: A 386 LYS cc_start: 0.9309 (mmtt) cc_final: 0.9012 (ptmm) REVERT: A 398 ASP cc_start: 0.8303 (m-30) cc_final: 0.7657 (m-30) REVERT: A 417 LYS cc_start: 0.8974 (tppt) cc_final: 0.8700 (tptt) REVERT: A 420 ASP cc_start: 0.7935 (t0) cc_final: 0.7662 (m-30) REVERT: A 493 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7780 (tp-100) REVERT: H 2 VAL cc_start: 0.7965 (m) cc_final: 0.7651 (p) REVERT: H 95 TYR cc_start: 0.7628 (m-80) cc_final: 0.7363 (m-80) REVERT: H 114 GLU cc_start: 0.8500 (mp0) cc_final: 0.8054 (mp0) REVERT: H 117 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7511 (mt0) REVERT: L 34 ASP cc_start: 0.7210 (p0) cc_final: 0.6918 (p0) REVERT: L 101 VAL cc_start: 0.8325 (t) cc_final: 0.7993 (p) outliers start: 21 outliers final: 20 residues processed: 115 average time/residue: 0.1423 time to fit residues: 20.1243 Evaluate side-chains 126 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 117 GLN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 13 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 = 0.3817 r_free = 0.3817 target = 0.118573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.100717 restraints weight = 9048.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.105415 restraints weight = 6035.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.107665 restraints weight = 3310.691| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3461 Z= 0.253 Angle : 0.763 12.364 4707 Z= 0.377 Chirality : 0.047 0.200 495 Planarity : 0.005 0.048 617 Dihedral : 5.005 17.163 487 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 6.59 % Allowed : 23.90 % Favored : 69.51 % 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: -1.18 (0.40), residues: 430 helix: -2.87 (0.63), residues: 40 sheet: -0.12 (0.44), residues: 146 loop : -0.77 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.002 HIS L 36 PHE 0.022 0.002 PHE A 392 TYR 0.019 0.002 TYR A 369 ARG 0.003 0.001 ARG A 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1237.27 seconds wall clock time: 22 minutes 52.38 seconds (1372.38 seconds total)