Starting phenix.real_space_refine on Mon Sep 23 14:33:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/09_2024/7swp_25478_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/09_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_25478/09_2024/7swp_25478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/09_2024/7swp_25478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/09_2024/7swp_25478_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swp_25478/09_2024/7swp_25478_neut.cif" } 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. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 2.78, per 1000 atoms: 0.82 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 422.8 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: 0.43 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: 0.96 Time building geometry restraints manager: 0.99 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: 0.00 - 1.61: 4371 1.61 - 3.21: 276 3.21 - 4.82: 43 4.82 - 6.42: 12 6.42 - 8.03: 5 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 3.040 nonbonded pdb=" NE2 GLN H 13 " pdb=" O SER H 128 " model vdw 2.206 3.120 nonbonded pdb=" O TYR H 53 " pdb=" NH2 ARG H 72 " model vdw 2.214 3.120 nonbonded pdb=" OG1 THR A 415 " pdb=" OG SER L 58 " model vdw 2.216 3.040 nonbonded pdb=" O LYS A 444 " pdb=" NE2 GLN A 498 " model vdw 2.224 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.410 Find NCS groups from input model: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- 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 : 0.400 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: 0.1967 time to fit residues: 36.6518 Evaluate side-chains 98 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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: 8.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3461 Z= 0.259 Angle : 0.786 8.991 4707 Z= 0.403 Chirality : 0.050 0.140 495 Planarity : 0.006 0.040 617 Dihedral : 5.759 25.006 487 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.02 % Allowed : 13.46 % Favored : 83.52 % 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: -1.78 (0.38), residues: 430 helix: -3.53 (0.68), residues: 22 sheet: -0.73 (0.44), residues: 132 loop : -1.23 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP L 37 HIS 0.006 0.002 HIS A 519 PHE 0.018 0.002 PHE H 27 TYR 0.022 0.002 TYR A 365 ARG 0.008 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 146 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 356 LYS cc_start: 0.8316 (tppt) cc_final: 0.7735 (tptt) REVERT: A 365 TYR cc_start: 0.8360 (m-80) cc_final: 0.8031 (m-80) REVERT: A 387 LEU cc_start: 0.8864 (mp) cc_final: 0.8638 (mp) REVERT: A 388 ASN cc_start: 0.8705 (t0) cc_final: 0.8314 (m110) REVERT: A 398 ASP cc_start: 0.8286 (m-30) cc_final: 0.7829 (m-30) REVERT: A 403 ARG cc_start: 0.7267 (ptt90) cc_final: 0.6449 (ptt90) REVERT: A 406 GLU cc_start: 0.8697 (pm20) cc_final: 0.7854 (pm20) REVERT: A 467 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7027 (p0) REVERT: A 493 GLN cc_start: 0.7962 (tp40) cc_final: 0.7722 (tp40) REVERT: A 501 ASN cc_start: 0.7776 (t0) cc_final: 0.7489 (t0) REVERT: H 34 MET cc_start: 0.8188 (mmp) cc_final: 0.7811 (mmm) REVERT: H 35 GLN cc_start: 0.8382 (mp10) cc_final: 0.7761 (mp10) REVERT: H 95 TYR cc_start: 0.7573 (m-80) cc_final: 0.7187 (m-80) REVERT: H 105 ASP cc_start: 0.8629 (t70) cc_final: 0.7842 (t70) REVERT: H 111 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7748 (mp10) REVERT: L 34 ASP cc_start: 0.7654 (p0) cc_final: 0.7307 (p0) REVERT: L 38 TYR cc_start: 0.7557 (m-80) cc_final: 0.7117 (m-80) REVERT: L 89 TYR cc_start: 0.7909 (m-80) cc_final: 0.7576 (m-10) REVERT: L 101 VAL cc_start: 0.8377 (t) cc_final: 0.8057 (p) outliers start: 11 outliers final: 7 residues processed: 139 average time/residue: 0.1681 time to fit residues: 27.8586 Evaluate side-chains 112 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 467 ASP 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 65 SER 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: 3.9990 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3461 Z= 0.288 Angle : 0.736 8.695 4707 Z= 0.382 Chirality : 0.047 0.160 495 Planarity : 0.005 0.047 617 Dihedral : 5.541 25.611 487 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 7.14 % Allowed : 15.11 % Favored : 77.75 % 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: -1.78 (0.37), residues: 430 helix: -2.88 (0.69), residues: 28 sheet: -0.68 (0.43), residues: 123 loop : -1.25 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP L 37 HIS 0.006 0.003 HIS A 519 PHE 0.022 0.002 PHE A 392 TYR 0.029 0.002 TYR A 351 ARG 0.006 0.001 ARG L 63 *********************** 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 142 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 356 LYS cc_start: 0.8383 (tppt) cc_final: 0.7835 (tttt) REVERT: A 365 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: A 388 ASN cc_start: 0.8709 (t0) cc_final: 0.8303 (m110) REVERT: A 389 ASP cc_start: 0.9124 (t0) cc_final: 0.8820 (t0) REVERT: A 398 ASP cc_start: 0.8472 (m-30) cc_final: 0.7853 (m-30) REVERT: A 401 VAL cc_start: 0.9100 (t) cc_final: 0.8894 (t) REVERT: A 406 GLU cc_start: 0.9005 (pm20) cc_final: 0.8337 (pm20) REVERT: A 487 ASN cc_start: 0.7041 (t0) cc_final: 0.6808 (t0) REVERT: A 493 GLN cc_start: 0.7984 (tp40) cc_final: 0.7752 (tp40) REVERT: H 2 VAL cc_start: 0.7803 (m) cc_final: 0.7546 (p) REVERT: H 35 GLN cc_start: 0.8435 (mp10) cc_final: 0.7934 (mp10) REVERT: H 95 TYR cc_start: 0.7661 (m-80) cc_final: 0.7246 (m-80) REVERT: H 105 ASP cc_start: 0.8925 (t70) cc_final: 0.8316 (t70) REVERT: H 111 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7523 (mp10) REVERT: H 114 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8429 (mp0) REVERT: L 34 ASP cc_start: 0.7585 (p0) cc_final: 0.7088 (p0) REVERT: L 36 HIS cc_start: 0.8860 (OUTLIER) cc_final: 0.7728 (m-70) REVERT: L 51 TYR cc_start: 0.8159 (p90) cc_final: 0.7805 (p90) REVERT: L 101 VAL cc_start: 0.8464 (t) cc_final: 0.8124 (p) outliers start: 26 outliers final: 18 residues processed: 130 average time/residue: 0.1238 time to fit residues: 20.0241 Evaluate side-chains 125 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 387 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 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 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 36 HIS Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 0.0770 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN L 6 GLN ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 0.044 3461 Z= 0.274 Angle : 0.724 7.938 4707 Z= 0.372 Chirality : 0.047 0.154 495 Planarity : 0.005 0.045 617 Dihedral : 5.404 24.254 487 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 7.42 % Allowed : 18.13 % Favored : 74.45 % 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: -1.40 (0.39), residues: 430 helix: -2.56 (0.76), residues: 28 sheet: -0.34 (0.44), residues: 131 loop : -1.05 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP L 37 HIS 0.004 0.002 HIS L 36 PHE 0.021 0.002 PHE A 392 TYR 0.025 0.002 TYR A 351 ARG 0.007 0.001 ARG A 466 *********************** 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 141 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 356 LYS cc_start: 0.8457 (tppt) cc_final: 0.7884 (tptt) REVERT: A 387 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8457 (mp) REVERT: A 389 ASP cc_start: 0.9214 (t0) cc_final: 0.8936 (t0) REVERT: A 398 ASP cc_start: 0.8351 (m-30) cc_final: 0.7800 (m-30) REVERT: A 401 VAL cc_start: 0.9146 (t) cc_final: 0.8928 (t) REVERT: A 493 GLN cc_start: 0.7925 (tp40) cc_final: 0.7709 (tp40) REVERT: H 2 VAL cc_start: 0.7841 (m) cc_final: 0.7587 (p) REVERT: H 35 GLN cc_start: 0.8268 (mp10) cc_final: 0.7779 (mp10) REVERT: H 95 TYR cc_start: 0.7645 (m-80) cc_final: 0.7226 (m-80) REVERT: H 105 ASP cc_start: 0.9009 (t70) cc_final: 0.8553 (t70) REVERT: H 111 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7483 (mp10) REVERT: H 112 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8941 (t) REVERT: L 34 ASP cc_start: 0.7391 (p0) cc_final: 0.6903 (p0) REVERT: L 36 HIS cc_start: 0.8885 (OUTLIER) cc_final: 0.7699 (m-70) REVERT: L 51 TYR cc_start: 0.8238 (p90) cc_final: 0.7861 (p90) REVERT: L 81 GLN cc_start: 0.7533 (tm-30) cc_final: 0.6337 (tt0) REVERT: L 97 LEU cc_start: 0.8084 (mp) cc_final: 0.7870 (tt) REVERT: L 101 VAL cc_start: 0.8419 (t) cc_final: 0.8064 (p) REVERT: L 107 LYS cc_start: 0.8683 (tppp) cc_final: 0.7933 (tmtt) outliers start: 27 outliers final: 18 residues processed: 130 average time/residue: 0.1305 time to fit residues: 21.1860 Evaluate side-chains 130 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 387 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 A residue 488 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 74 ASN 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 36 HIS Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 74 SER 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: 5.9990 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.0970 overall best weight: 1.1180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN ** L 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.5710 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= 0.186 Angle : 0.679 8.059 4707 Z= 0.347 Chirality : 0.046 0.164 495 Planarity : 0.005 0.042 617 Dihedral : 5.122 22.254 487 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 5.77 % Allowed : 21.43 % Favored : 72.80 % 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: -2.26 (0.80), residues: 28 sheet: -0.22 (0.42), residues: 142 loop : -0.96 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP L 37 HIS 0.004 0.002 HIS L 36 PHE 0.017 0.002 PHE A 392 TYR 0.031 0.002 TYR A 365 ARG 0.004 0.001 ARG A 466 *********************** 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 140 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8449 (tppt) cc_final: 0.7914 (tptt) REVERT: A 387 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8425 (mp) REVERT: A 388 ASN cc_start: 0.8636 (t0) cc_final: 0.8326 (m110) REVERT: A 389 ASP cc_start: 0.9229 (t0) cc_final: 0.8936 (t0) REVERT: A 398 ASP cc_start: 0.8282 (m-30) cc_final: 0.7764 (m-30) REVERT: A 401 VAL cc_start: 0.9098 (t) cc_final: 0.8897 (t) REVERT: A 414 GLN cc_start: 0.8577 (mp-120) cc_final: 0.7871 (mp10) REVERT: A 417 LYS cc_start: 0.8921 (tppt) cc_final: 0.8687 (tppt) REVERT: A 493 GLN cc_start: 0.8018 (tp40) cc_final: 0.7802 (tp40) REVERT: H 2 VAL cc_start: 0.7793 (m) cc_final: 0.7545 (p) REVERT: H 95 TYR cc_start: 0.7563 (m-80) cc_final: 0.7139 (m-80) REVERT: H 105 ASP cc_start: 0.8991 (t70) cc_final: 0.8560 (t70) REVERT: H 110 TYR cc_start: 0.8158 (t80) cc_final: 0.7865 (t80) REVERT: H 111 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7421 (mp10) REVERT: H 117 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7290 (mt0) REVERT: L 34 ASP cc_start: 0.7261 (p0) cc_final: 0.6782 (p0) REVERT: L 51 TYR cc_start: 0.8047 (p90) cc_final: 0.7693 (p90) REVERT: L 81 GLN cc_start: 0.7781 (tm-30) cc_final: 0.6836 (tt0) REVERT: L 97 LEU cc_start: 0.8126 (mp) cc_final: 0.7902 (tt) REVERT: L 101 VAL cc_start: 0.8223 (t) cc_final: 0.7913 (p) outliers start: 21 outliers final: 17 residues processed: 130 average time/residue: 0.1308 time to fit residues: 21.1409 Evaluate side-chains 128 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 387 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 A residue 494 SER Chi-restraints excluded: chain A residue 512 VAL 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 3 VAL 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 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 493 GLN H 13 GLN L 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3461 Z= 0.373 Angle : 0.752 9.904 4707 Z= 0.394 Chirality : 0.048 0.166 495 Planarity : 0.006 0.055 617 Dihedral : 5.568 21.657 487 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 7.97 % Allowed : 20.88 % Favored : 71.15 % 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: -1.35 (0.40), residues: 430 helix: -2.12 (0.81), residues: 34 sheet: -0.07 (0.45), residues: 129 loop : -1.17 (0.39), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP L 37 HIS 0.004 0.002 HIS H 118 PHE 0.023 0.002 PHE A 392 TYR 0.029 0.003 TYR A 365 ARG 0.005 0.001 ARG A 355 *********************** 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 137 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8518 (tppt) cc_final: 0.7965 (tptt) REVERT: A 389 ASP cc_start: 0.9337 (t0) cc_final: 0.9054 (t0) REVERT: A 398 ASP cc_start: 0.8458 (m-30) cc_final: 0.7819 (m-30) REVERT: A 484 GLU cc_start: 0.6521 (mm-30) cc_final: 0.3531 (pp20) REVERT: H 2 VAL cc_start: 0.8019 (m) cc_final: 0.7738 (p) REVERT: H 95 TYR cc_start: 0.7756 (m-80) cc_final: 0.7360 (m-80) REVERT: H 105 ASP cc_start: 0.9113 (t70) cc_final: 0.8822 (t70) REVERT: H 110 TYR cc_start: 0.8321 (t80) cc_final: 0.8020 (t80) REVERT: H 111 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7643 (mp10) REVERT: H 117 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: L 34 ASP cc_start: 0.7403 (p0) cc_final: 0.6808 (p0) REVERT: L 36 HIS cc_start: 0.8995 (OUTLIER) cc_final: 0.7881 (m-70) REVERT: L 51 TYR cc_start: 0.8324 (p90) cc_final: 0.7982 (p90) REVERT: L 81 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7402 (tt0) REVERT: L 97 LEU cc_start: 0.8251 (mp) cc_final: 0.8038 (tt) REVERT: L 101 VAL cc_start: 0.8280 (t) cc_final: 0.7947 (p) outliers start: 29 outliers final: 24 residues processed: 128 average time/residue: 0.1267 time to fit residues: 20.4550 Evaluate side-chains 131 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 488 CYS 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 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 36 HIS 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 74 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 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 117 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: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3461 Z= 0.253 Angle : 0.716 9.324 4707 Z= 0.367 Chirality : 0.047 0.175 495 Planarity : 0.005 0.046 617 Dihedral : 5.242 20.266 487 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 8.52 % Allowed : 21.15 % 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: -1.32 (0.39), residues: 430 helix: -2.46 (0.89), residues: 28 sheet: -0.08 (0.46), residues: 121 loop : -1.09 (0.36), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 47 HIS 0.004 0.002 HIS H 118 PHE 0.021 0.002 PHE L 102 TYR 0.023 0.002 TYR A 365 ARG 0.003 0.001 ARG H 31 *********************** 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 138 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 107 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8525 (tppt) cc_final: 0.7956 (tptt) REVERT: A 388 ASN cc_start: 0.8796 (t0) cc_final: 0.8472 (m110) REVERT: A 389 ASP cc_start: 0.9386 (t0) cc_final: 0.9065 (t0) REVERT: A 398 ASP cc_start: 0.8374 (m-30) cc_final: 0.7738 (m-30) REVERT: A 401 VAL cc_start: 0.9128 (t) cc_final: 0.8924 (t) REVERT: A 484 GLU cc_start: 0.6408 (mm-30) cc_final: 0.3475 (pp20) REVERT: H 2 VAL cc_start: 0.8002 (m) cc_final: 0.7741 (p) REVERT: H 95 TYR cc_start: 0.7661 (m-80) cc_final: 0.7243 (m-80) REVERT: H 105 ASP cc_start: 0.9103 (t70) cc_final: 0.8733 (t70) REVERT: H 110 TYR cc_start: 0.8223 (t80) cc_final: 0.7988 (t80) REVERT: H 111 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7549 (mp10) REVERT: H 117 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: L 34 ASP cc_start: 0.7457 (p0) cc_final: 0.6947 (p0) REVERT: L 36 HIS cc_start: 0.9056 (OUTLIER) cc_final: 0.8627 (m-70) REVERT: L 51 TYR cc_start: 0.8225 (p90) cc_final: 0.7849 (p90) REVERT: L 81 GLN cc_start: 0.7971 (tm-30) cc_final: 0.7641 (tt0) REVERT: L 101 VAL cc_start: 0.8100 (t) cc_final: 0.7819 (p) outliers start: 31 outliers final: 26 residues processed: 126 average time/residue: 0.1426 time to fit residues: 22.3343 Evaluate side-chains 133 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 470 THR Chi-restraints excluded: chain A residue 488 CYS 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 3 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 36 HIS 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 74 SER Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.6707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3461 Z= 0.225 Angle : 0.811 17.672 4707 Z= 0.389 Chirality : 0.047 0.173 495 Planarity : 0.005 0.045 617 Dihedral : 5.050 19.454 487 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 8.52 % Allowed : 22.80 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.39), residues: 430 helix: -3.05 (0.79), residues: 28 sheet: -0.10 (0.46), residues: 123 loop : -1.03 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 47 HIS 0.003 0.002 HIS L 36 PHE 0.020 0.002 PHE A 392 TYR 0.018 0.002 TYR A 351 ARG 0.003 0.001 ARG H 31 *********************** 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 145 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7958 (m-40) cc_final: 0.7395 (m-40) REVERT: A 356 LYS cc_start: 0.8525 (tppt) cc_final: 0.8017 (tptt) REVERT: A 398 ASP cc_start: 0.8333 (m-30) cc_final: 0.7675 (m-30) REVERT: A 406 GLU cc_start: 0.9015 (pm20) cc_final: 0.8489 (pm20) REVERT: A 484 GLU cc_start: 0.6313 (mm-30) cc_final: 0.3284 (pp20) REVERT: A 517 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8288 (tp) REVERT: H 2 VAL cc_start: 0.8112 (m) cc_final: 0.7901 (p) REVERT: H 95 TYR cc_start: 0.7645 (m-80) cc_final: 0.7260 (m-80) REVERT: H 105 ASP cc_start: 0.9094 (t70) cc_final: 0.8725 (t70) REVERT: H 110 TYR cc_start: 0.8227 (t80) cc_final: 0.8017 (t80) REVERT: H 111 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7537 (mp10) REVERT: H 117 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8075 (mt0) REVERT: H 121 GLN cc_start: 0.8193 (tp40) cc_final: 0.7823 (mp10) REVERT: L 34 ASP cc_start: 0.7393 (p0) cc_final: 0.6901 (p0) REVERT: L 36 HIS cc_start: 0.9038 (OUTLIER) cc_final: 0.8508 (m-70) REVERT: L 51 TYR cc_start: 0.8162 (p90) cc_final: 0.7744 (p90) REVERT: L 81 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7735 (tt0) REVERT: L 101 VAL cc_start: 0.8015 (t) cc_final: 0.7644 (p) outliers start: 31 outliers final: 27 residues processed: 132 average time/residue: 0.1286 time to fit residues: 21.0485 Evaluate side-chains 139 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 470 THR Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU 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 29 ILE Chi-restraints excluded: chain L residue 36 HIS 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 74 SER Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 0.0070 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- 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: 0.7305 moved from start: 0.6966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3461 Z= 0.214 Angle : 0.780 13.294 4707 Z= 0.380 Chirality : 0.047 0.172 495 Planarity : 0.005 0.047 617 Dihedral : 4.842 18.340 487 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 8.24 % Allowed : 22.53 % 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: -1.23 (0.40), residues: 430 helix: -3.00 (0.78), residues: 28 sheet: -0.02 (0.46), residues: 124 loop : -0.97 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.004 0.002 HIS L 36 PHE 0.022 0.002 PHE A 392 TYR 0.022 0.002 TYR A 351 ARG 0.003 0.000 ARG H 98 *********************** 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 145 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7910 (m-40) cc_final: 0.7360 (m-40) REVERT: A 356 LYS cc_start: 0.8518 (tppt) cc_final: 0.8038 (tptt) REVERT: A 388 ASN cc_start: 0.8809 (t0) cc_final: 0.8605 (m110) REVERT: A 398 ASP cc_start: 0.8316 (m-30) cc_final: 0.7664 (m-30) REVERT: A 417 LYS cc_start: 0.9046 (tppt) cc_final: 0.8705 (tptt) REVERT: A 484 GLU cc_start: 0.6301 (mm-30) cc_final: 0.3308 (pp20) REVERT: A 517 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8309 (tp) REVERT: H 2 VAL cc_start: 0.8064 (m) cc_final: 0.7805 (p) REVERT: H 5 VAL cc_start: 0.7542 (m) cc_final: 0.6609 (t) REVERT: H 95 TYR cc_start: 0.7536 (m-80) cc_final: 0.7130 (m-80) REVERT: H 105 ASP cc_start: 0.9083 (t70) cc_final: 0.8717 (t70) REVERT: H 111 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7586 (mp10) REVERT: H 117 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: H 121 GLN cc_start: 0.8101 (tp40) cc_final: 0.7807 (mp10) REVERT: L 36 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8458 (m-70) REVERT: L 101 VAL cc_start: 0.8052 (t) cc_final: 0.7659 (p) outliers start: 30 outliers final: 27 residues processed: 132 average time/residue: 0.1284 time to fit residues: 21.0878 Evaluate side-chains 141 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 111 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 470 THR Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU 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 116 PHE Chi-restraints excluded: chain H residue 117 GLN Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain L residue 36 HIS 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 74 SER Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.7128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3461 Z= 0.216 Angle : 0.780 13.723 4707 Z= 0.379 Chirality : 0.047 0.171 495 Planarity : 0.005 0.047 617 Dihedral : 4.744 18.232 487 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 7.97 % Allowed : 23.63 % Favored : 68.41 % 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: -1.10 (0.40), residues: 430 helix: -2.85 (0.81), residues: 28 sheet: 0.12 (0.47), residues: 123 loop : -0.91 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 HIS 0.002 0.001 HIS L 36 PHE 0.020 0.002 PHE A 392 TYR 0.028 0.002 TYR L 51 ARG 0.003 0.001 ARG A 457 ********************** 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 143 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.7907 (m-40) cc_final: 0.7356 (m-40) REVERT: A 356 LYS cc_start: 0.8521 (tppt) cc_final: 0.8058 (tptt) REVERT: A 398 ASP cc_start: 0.8366 (m-30) cc_final: 0.7659 (m-30) REVERT: A 414 GLN cc_start: 0.8733 (mp-120) cc_final: 0.8157 (mm-40) REVERT: A 484 GLU cc_start: 0.6340 (mm-30) cc_final: 0.3202 (pp20) REVERT: A 517 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8314 (tp) REVERT: H 2 VAL cc_start: 0.8052 (m) cc_final: 0.7767 (p) REVERT: H 5 VAL cc_start: 0.7516 (m) cc_final: 0.6546 (t) REVERT: H 28 THR cc_start: 0.8701 (m) cc_final: 0.8296 (p) REVERT: H 95 TYR cc_start: 0.7505 (m-80) cc_final: 0.7087 (m-80) REVERT: H 105 ASP cc_start: 0.9113 (t70) cc_final: 0.8733 (t70) REVERT: H 110 TYR cc_start: 0.8174 (t80) cc_final: 0.7943 (t80) REVERT: H 111 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7600 (mp10) REVERT: H 117 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7830 (mt0) REVERT: H 121 GLN cc_start: 0.8095 (tp40) cc_final: 0.7798 (mp10) REVERT: L 34 ASP cc_start: 0.7203 (p0) cc_final: 0.6806 (p0) REVERT: L 36 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.7650 (m-70) REVERT: L 51 TYR cc_start: 0.8400 (p90) cc_final: 0.7922 (p90) REVERT: L 101 VAL cc_start: 0.7981 (t) cc_final: 0.7598 (p) outliers start: 29 outliers final: 25 residues processed: 130 average time/residue: 0.1427 time to fit residues: 22.8979 Evaluate side-chains 142 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 470 THR Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 517 LEU 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 36 HIS Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 74 SER Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 117 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 = 0.3860 r_free = 0.3860 target = 0.122007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104382 restraints weight = 9078.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.107789 restraints weight = 5049.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.110066 restraints weight = 3345.898| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.7266 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= 0.215 Angle : 0.785 13.359 4707 Z= 0.381 Chirality : 0.047 0.172 495 Planarity : 0.005 0.048 617 Dihedral : 4.649 18.002 487 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 7.69 % Allowed : 23.63 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.40), residues: 430 helix: -2.92 (0.81), residues: 27 sheet: 0.10 (0.46), residues: 123 loop : -0.89 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS A 519 PHE 0.020 0.002 PHE A 392 TYR 0.026 0.002 TYR L 51 ARG 0.002 0.001 ARG H 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1165.46 seconds wall clock time: 21 minutes 46.24 seconds (1306.24 seconds total)